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Sample records for integrative biology spider

  1. Biological control of fruit-tree red spider mite

    NARCIS (Netherlands)

    Rabbinge, R.

    1976-01-01

    During the last decade, integrated pest control systems have been developed for several crops. One of the main fields of research in integrated control has been the control of orchard pests. Experience with modified spraying programmes in apple orchards, the increasing resistance of spider

  2. Recent advances in the understanding of brown spider venoms: From the biology of spiders to the molecular mechanisms of toxins.

    Science.gov (United States)

    Gremski, Luiza Helena; Trevisan-Silva, Dilza; Ferrer, Valéria Pereira; Matsubara, Fernando Hitomi; Meissner, Gabriel Otto; Wille, Ana Carolina Martins; Vuitika, Larissa; Dias-Lopes, Camila; Ullah, Anwar; de Moraes, Fábio Rogério; Chávez-Olórtegui, Carlos; Barbaro, Katia Cristina; Murakami, Mario Tyago; Arni, Raghuvir Krishnaswamy; Senff-Ribeiro, Andrea; Chaim, Olga Meiri; Veiga, Silvio Sanches

    2014-06-01

    The Loxosceles genus spiders (the brown spiders) are encountered in all the continents, and the clinical manifestations following spider bites include skin necrosis with gravitational lesion spreading and occasional systemic manifestations, such as intravascular hemolysis, thrombocytopenia and acute renal failure. Brown spider venoms are complex mixtures of toxins especially enriched in three molecular families: the phospholipases D, astacin-like metalloproteases and Inhibitor Cystine Knot (ICK) peptides. Other toxins with low level of expression also present in the venom include the serine proteases, serine protease inhibitors, hyaluronidases, allergen factors and translationally controlled tumor protein (TCTP). The mechanisms by which the Loxosceles venoms act and exert their noxious effects are not fully understood. Except for the brown spider venom phospholipase D, which causes dermonecrosis, hemolysis, thrombocytopenia and renal failure, the pathological activities of the other venom toxins remain unclear. The objective of the present review is to provide insights into the brown spider venoms and loxoscelism based on recent results. These insights include the biology of brown spiders, the clinical features of loxoscelism and the diagnosis and therapy of brown spider bites. Regarding the brown spider venom, this review includes a description of the novel toxins revealed by molecular biology and proteomics techniques, the data regarding three-dimensional toxin structures, and the mechanism of action of these molecules. Finally, the biotechnological applications of the venom components, especially for those toxins reported as recombinant molecules, and the challenges for future study are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Brown Spider (Loxosceles genus Venom Toxins: Tools for Biological Purposes

    Directory of Open Access Journals (Sweden)

    Andrea Senff-Ribeiro

    2011-03-01

    Full Text Available Venomous animals use their venoms as tools for defense or predation. These venoms are complex mixtures, mainly enriched of proteic toxins or peptides with several, and different, biological activities. In general, spider venom is rich in biologically active molecules that are useful in experimental protocols for pharmacology, biochemistry, cell biology and immunology, as well as putative tools for biotechnology and industries. Spider venoms have recently garnered much attention from several research groups worldwide. Brown spider (Loxosceles genus venom is enriched in low molecular mass proteins (5–40 kDa. Although their venom is produced in minute volumes (a few microliters, and contain only tens of micrograms of protein, the use of techniques based on molecular biology and proteomic analysis has afforded rational projects in the area and permitted the discovery and identification of a great number of novel toxins. The brown spider phospholipase-D family is undoubtedly the most investigated and characterized, although other important toxins, such as low molecular mass insecticidal peptides, metalloproteases and hyaluronidases have also been identified and featured in literature. The molecular pathways of the action of these toxins have been reported and brought new insights in the field of biotechnology. Herein, we shall see how recent reports describing discoveries in the area of brown spider venom have expanded biotechnological uses of molecules identified in these venoms, with special emphasis on the construction of a cDNA library for venom glands, transcriptome analysis, proteomic projects, recombinant expression of different proteic toxins, and finally structural descriptions based on crystallography of toxins.

  4. Spider-Ant Associations: An Updated Review of Myrmecomorphy, Myrmecophily, and Myrmecophagy in Spiders

    Directory of Open Access Journals (Sweden)

    Paula E. Cushing

    2012-01-01

    Full Text Available This paper provides a summary of the extensive theoretical and empirical work that has been carried out in recent years testing the adaptational significance of various spider-ant associations. Hundreds of species of spiders have evolved close relationships with ants and can be classified as myrmecomorphs, myrmecophiles, or myrmecophages. Myrmecomorphs are Batesian mimics. Their close morphological and behavioral resemblance to ants confers strong survival advantages against visually hunting predators. Some species of spiders have become integrated into the ant society as myrmecophiles or symbionts. These spider myrmecophiles gain protection against their own predators, live in an environment with a stable climate, and are typically surrounded by abundant food resources. The adaptations by which this integration is made possible are poorly known, although it is hypothesized that most spider myrmecophiles are chemical mimics and some are even phoretic on their hosts. The third type of spider-ant association discussed is myrmecophagy—or predatory specialization on ants. A table of known spider myrmecophages is provided as is information on their biology and hunting strategies. Myrmecophagy provides these predators with an essentially unlimited food supply and may even confer other protections to the spiders.

  5. Solid-phase synthesis and biological evaluation of Joro spider toxin-4 from Nephila clavata

    DEFF Research Database (Denmark)

    Barslund, Anne Fuglsang; Poulsen, Mette Homann; Bach, Tinna Brøbech

    2011-01-01

    Polyamine toxins from orb weaver spiders are attractive pharmacological tools particularly for studies of ionotropic glutamate (iGlu) receptors in the brain. These polyamine toxins are biosynthesized in a combinatorial manner, providing a plethora of related, but structurally complex toxins...... to be exploited in biological studies. Here, we have used solid-phase synthetic methodology for the efficient synthesis of Joro spider toxin-4 (JSTX-4) (1) from Nephila clavata, providing sufficient amounts of the toxin for biological evaluation at iGlu receptor subtypes using electrophysiology. Biological...

  6. Brown spider (Loxosceles genus) venom toxins: Evaluation of biological conservation by immune cross-reactivity.

    Science.gov (United States)

    Buch, Daniela Regina; Souza, Fernanda Nunes; Meissner, Gabriel Otto; Morgon, Adriano Marcelo; Gremski, Luiza Helena; Ferrer, Valéria Pereira; Trevisan-Silva, Dilza; Matsubara, Fernando Hitomi; Boia-Ferreira, Mariana; Sade, Youssef Bacila; Chaves-Moreira, Daniele; Gremski, Waldemiro; Veiga, Silvio Sanches; Chaim, Olga Meiri; Senff-Ribeiro, Andrea

    2015-12-15

    Loxosceles spiders are responsible for serious human envenomations worldwide. The collection of symptoms found in victims after accidents is called loxoscelism and is characterized by two clinical conditions: cutaneous loxoscelism and systemic loxocelism. The only specific treatment is serum therapy, in which an antiserum produced with Loxosceles venom is administered to the victims after spider accidents. Our aim was to improve our knowledge, regarding the immunological relationship among toxins from the most epidemiologic important species in Brazil (Loxosceles intermedia, Loxosceles gaucho and Loxosceles laeta). Immunoassays using spider venoms and L. intermedia recombinant toxins were performed and their cross-reactivity assessed. The biological conservation of the main Loxosceles toxins (Phospholipases-D, Astacin-like metalloproteases, Hyaluronidase, ICK-insecticide peptide and TCTP-histamine releasing factor) were investigated. An in silico analysis of the putative epitopes was performed and is discussed on the basis of the experimental results. Our data is an immunological investigation in light of biological conservation throughout the Loxosceles genus. The results bring out new insights on brown spider venom toxins for study, diagnosis and treatment of loxoscelism and putative biotechnological applications concerning immune conserved features in the toxins. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Evaluation of the efficacy of vacuum cleaners for the integrated control of brown spider Loxosceles intermedia

    Directory of Open Access Journals (Sweden)

    E. N. Ramires

    2007-01-01

    Full Text Available Some venomous spiders of the genus Loxosceles can reach high population densities inside and around houses. In Brazil, most spider accidents are related to Loxosceles intermedia. Control of loxoscelism should utilize integrated pest management tools, such as vacuum cleaners, to eliminate egg sacs, webs and spiders. The present study tested the efficacy of one type of vacuum cleaner (for professional and domestic use in the control of L. intermedia populations. Cockroaches (Pycnoscelus surinamensis were used in some tests for comparison. Vacuuming using standard accessories or a paper tube resulted in the death of all female (n=60, male (n=60, young (n=60 and just-hatched (n=60 L. intermedia, and all egg sacs (n=5 were destroyed. The removal of the plastic plate present at the bottom of the vacuuming tube inside the machine allowed some spiders to survive the vacuuming process. When kept inside a vacuum bag full of dust and debris, adult females (n=10 survived for 10 days; however, significant mortality was observed among male (n=10 and young individuals (n=10. Addition of cornstarch to the vacuum bag did not affect the spiders (n=20. Vacuum cleaners, such as the one used in the present investigation, are promising tools for integrated management of L. intermedia and other spiders in domestic environments.

  8. Integrated Assessment Plan Template and Operational Demonstration for SPIDERS Phase 2: Fort Carson

    Energy Technology Data Exchange (ETDEWEB)

    Barr, Jonathan L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tuffner, Francis K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hadley, Mark D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kreyling, Sean J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Schneider, Kevin P. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-09-01

    This document contains the Integrated Assessment Plan (IAP) for the Phase 2 Operational Demonstration (OD) of the Smart Power Infrastructure Demonstration for Energy Reliability (SPIDERS) Joint Capability Technology Demonstration (JCTD) project. SPIDERS will be conducted over a three year period with Phase 2 being conducted at Fort Carson, Colorado. This document includes the Operational Demonstration Execution Plan (ODEP) and the Operational Assessment Execution Plan (OAEP), as approved by the Operational Manager (OM) and the Integrated Management Team (IMT). The ODEP describes the process by which the OD is conducted and the OAEP describes the process by which the data collected from the OD is processed. The execution of the OD, in accordance with the ODEP and the subsequent execution of the OAEP, will generate the necessary data for the Quick Look Report (QLR) and the Utility Assessment Report (UAR). These reports will assess the ability of the SPIDERS JCTD to meet the four critical requirements listed in the Implementation Directive (ID).

  9. Mites and spiders act as biological control agent to sand flies

    Directory of Open Access Journals (Sweden)

    Diwakar Singh Dinesh

    2014-02-01

    Full Text Available Objective: To find out natural biological control agents of sand flies vector of kala azar in Bihar, India. Methods: Sand flies collected from the field using CDC light trap installing overnight to the collection site scrutitinized for Phlebotomus argentipes, the established vector of visceral leishmaniasis. Blood fed adult females were confined in the insectary for its development of life cycle. During developmental stages 2nd to 4th instars larvae were examined closely by using compound microscope for mite infestation. Adult spider residing along with sand flies collected in trap were kept in cage along with sand flies and their activities were watched closely and recorded by video and picture. Results: Mites were found predating 2nd to 4th instars larvae only under the laboratory conditions and lowering down the population of sand flies up to basal level within 15 d after infestation. One specific spider was found eating blood fed female sand flies kept inside the cage (n=50 attacking on lower part of thoracic region to kill the sand fly and ate desired soft part. Conclusions: Both predators, mites and spiders are acting as biological control agents to larvae and adults of sand flies respectively resulting variable density of vectors due to variable association with these predators and also cause lowering the transmission of the disease as hidden natural controlling agent of sand flies. The extensive study will be of immense help in controlling sand flies without use of environmental pollutant i.e. chemical insecticide.

  10. SPIDER SILK

    Directory of Open Access Journals (Sweden)

    PORAV Viorica

    2014-05-01

    Full Text Available The strengthness and toughness of spider fiber and its multifunctional nature is only surpassed in some cases by synthetic high performance fibers. In the world of natural fibers, spider silk has been long time recognized as a wonder fiber for its unique combination of high strength and rupture elongation. Scientists in civil military engineering reveal that the power of biological material (spider silk lies in the geometric configuration of structural protein, and the small cluster of week hydrogen bonds that works together to resist force and dissipate energy. Each spider and each type of silk has a set of mechanical properties optimized for their biological function. Most silks, in particular deagline silk, have exceptional mechanical properties. They exhibit a unique combination of high tensile strength and extensibility (ductility. This enables a silk fiber to absorb a lot of energy before breaking (toughness, the area under a stress- strain curve. A frequent mistake made in the mainstream media is to confuse strength and toughness when comparing silk to other materials. As shown below in detail, weight for weight, silk is stronger than steel, but not as strong as Kevlar. Silk is,however, tougher than both.This paper inform about overview on the today trend in the world of spider silk.

  11. Phenotypic integration in a series of trophic traits: tracing the evolution of myrmecophagy in spiders (Araneae).

    Science.gov (United States)

    Pekár, Stano; Michalko, Radek; Korenko, Stanislav; Sedo, Ondřej; Líznarová, Eva; Sentenská, Lenka; Zdráhal, Zbyněk

    2013-02-01

    Several hypotheses have been put forward to explain the evolution of prey specificity (stenophagy). Yet little light has so far been shed on the process of evolution of stenophagy in carnivorous predators. We performed a detailed analysis of a variety of trophic adaptations in one species. Our aim was to determine whether a specific form of stenophagy, myrmecophagy, has evolved from euryphagy via parallel changes in several traits from pre-existing characters. For that purpose, we studied the trophic niche and morphological, behavioural, venomic and physiological adaptations in a euryphagous spider, Selamia reticulata. It is a species that is branching off earlier in phylogeny than stenophagous ant-eating spiders of the genus Zodarion (both Zodariidae). The natural diet was wide and included ants. Laboratory feeding trials revealed versatile prey capture strategies that are effective on ants and other prey types. The performance of spiders on two different diets - ants only and mixed insects - failed to reveal differences in most fitness components (survival and developmental rate). However, the weight increase was significantly higher in spiders on the mixed diet. As a result, females on a mixed diet had higher fecundity and oviposited earlier. No differences were found in incubation period, hatching success or spiderling size. S. reticulata possesses a more diverse venom composition than Zodarion. Its venom is more effective for the immobilisation of beetle larvae than of ants. Comparative analysis of morphological traits related to myrmecophagy in the family Zodariidae revealed that their apomorphic states appeared gradually along the phylogeny to derived prey-specialised genera. Our results suggest that myrmecophagy has evolved gradually from the ancestral euryphagous strategy by integrating a series of trophic traits. Copyright © 2012 Elsevier GmbH. All rights reserved.

  12. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  13. Integrative Radiation Biology

    Energy Technology Data Exchange (ETDEWEB)

    Barcellos-Hoff, Mary Helen [New York University School of Medicine, NY (United States)

    2015-02-27

    We plan to study tissue-level mechanisms important to human breast radiation carcinogenesis. We propose that the cell biology of irradiated tissues reveals a coordinated multicellular damage response program in which individual cell contributions are primarily directed towards suppression of carcinogenesis and reestablishment of homeostasis. We identified transforming growth factor β1 (TGFβ) as a pivotal signal. Notably, we have discovered that TGFβ suppresses genomic instability by controlling the intrinsic DNA damage response and centrosome integrity. However, TGFβ also mediates disruption of microenvironment interactions, which drive epithelial to mesenchymal transition in irradiated human mammary epithelial cells. This apparent paradox of positive and negative controls by TGFβ is the topic of the present proposal. First, we postulate that these phenotypes manifest differentially following fractionated or chronic exposures; second, that the interactions of multiple cell types in tissues modify the responses evident in this single cell type culture models. The goals are to: 1) study the effect of low dose rate and fractionated radiation exposure in combination with TGFβ on the irradiated phenotype and genomic instability of non-malignant human epithelial cells; and 2) determine whether stromal-epithelial interactions suppress the irradiated phenotype in cell culture and the humanized mammary mouse model. These data will be used to 3) develop a systems biology model that integrates radiation effects across multiple levels of tissue organization and time. Modeling multicellular radiation responses coordinated via extracellular signaling could have a significant impact on the extrapolation of human health risks from high dose to low dose/rate radiation exposure.

  14. Spiders in caves.

    Science.gov (United States)

    Mammola, Stefano; Isaia, Marco

    2017-04-26

    World experts of different disciplines, from molecular biology to macro-ecology, recognize the value of cave ecosystems as ideal ecological and evolutionary laboratories. Among other subterranean taxa, spiders stand out as intriguing model organisms for their ecological role of top predators, their unique adaptations to the hypogean medium and their sensitivity to anthropogenic disturbance. As the description of the first eyeless spider ( Stalita taenaria ), an array of papers on subterranean spider biology, ecology and evolution has been published, but a comprehensive review on these topics is still lacking. We provide a general overview of the spider families recorded in hypogean habitats worldwide, we review the different adaptations of hypogean spiders to subterranean life, and we summarize the information gathered so far about their origin, population structure, ecology and conservation status. Finally, we point out the limits of the knowledge we currently have regarding hypogean spiders, aiming to stimulate future research. © 2017 The Author(s).

  15. Plant integration of MITICA and SPIDER experiments with auxiliary plants and buildings on PRIMA site

    Energy Technology Data Exchange (ETDEWEB)

    Fellin, Francesco, E-mail: francesco.fellin@igi.cnr.it; Boldrin, Marco; Zaccaria, Pierluigi; Agostinetti, Piero; Battistella, Manuela; Bigi, Marco; Palma, Samuele Dal Bello Mauro Dalla; Fiorentin, Aldo; Luchetta, Adriano; Maistrello, Alberto; Marcuzzi, Diego; Ocello, Edoardo; Pasqualotto, Roberto; Pavei, Mauro; Pomaro, Nicola; Rizzolo, Andrea; Toigo, Vanni; Valente, Matteo; Zanotto, Loris; Calore, Luca; and others

    2015-10-15

    Highlights: • Focus on plant integration work supporting the realization of SPIDER and MITICA fusion experiments hosted in PRIMA buildings complex in Padova, Italy. • Huge effort of coordination and integration among many stakeholders, taking into account several constrains coming from experiments requirements (on-going) and precise time schedule and budget on buildings construction. • The paper also deals of interfaces management, coordination and integration of many competences, problems solving to find best solution also considering other aspects like safety and maintenance. - Abstract: This paper presents a description of the PRIMA (Padova Research on ITER Megavolt Accelerator) Plant Integration work, aimed at the construction of PRIMA Buildings, which will host two nuclear fusion test facilities named SPIDER and MITICA, finalized to test and optimize the neutral beam injectors for ITER experiment. These activities are very complex: inputs coming from the experiments design are changing time to time, while the buildings construction shall fulfill precise time schedule and budget. Moreover the decision process is often very long due to the high number of stakeholders (RFX, IO, third parties, suppliers, domestic agencies from different countries). The huge effort includes: forecasting what will be necessary for the integration of many experimental plants; collecting requirements and translating into inputs; interfaces management; coordination meetings with hundreds of people with various and different competences in construction and operation of fusion facilities, thermomechanics, electrical and control, buildings design and construction (civil plants plus architectural and structural aspects), safety, maintenance and management. The paper describes these activities and also the tools created to check and to validate the building design, to manage the interfaces and the organization put in place to achieve the required targets.

  16. Plant integration of MITICA and SPIDER experiments with auxiliary plants and buildings on PRIMA site

    International Nuclear Information System (INIS)

    Fellin, Francesco; Boldrin, Marco; Zaccaria, Pierluigi; Agostinetti, Piero; Battistella, Manuela; Bigi, Marco; Palma, Samuele Dal Bello Mauro Dalla; Fiorentin, Aldo; Luchetta, Adriano; Maistrello, Alberto; Marcuzzi, Diego; Ocello, Edoardo; Pasqualotto, Roberto; Pavei, Mauro; Pomaro, Nicola; Rizzolo, Andrea; Toigo, Vanni; Valente, Matteo; Zanotto, Loris; Calore, Luca

    2015-01-01

    Highlights: • Focus on plant integration work supporting the realization of SPIDER and MITICA fusion experiments hosted in PRIMA buildings complex in Padova, Italy. • Huge effort of coordination and integration among many stakeholders, taking into account several constrains coming from experiments requirements (on-going) and precise time schedule and budget on buildings construction. • The paper also deals of interfaces management, coordination and integration of many competences, problems solving to find best solution also considering other aspects like safety and maintenance. - Abstract: This paper presents a description of the PRIMA (Padova Research on ITER Megavolt Accelerator) Plant Integration work, aimed at the construction of PRIMA Buildings, which will host two nuclear fusion test facilities named SPIDER and MITICA, finalized to test and optimize the neutral beam injectors for ITER experiment. These activities are very complex: inputs coming from the experiments design are changing time to time, while the buildings construction shall fulfill precise time schedule and budget. Moreover the decision process is often very long due to the high number of stakeholders (RFX, IO, third parties, suppliers, domestic agencies from different countries). The huge effort includes: forecasting what will be necessary for the integration of many experimental plants; collecting requirements and translating into inputs; interfaces management; coordination meetings with hundreds of people with various and different competences in construction and operation of fusion facilities, thermomechanics, electrical and control, buildings design and construction (civil plants plus architectural and structural aspects), safety, maintenance and management. The paper describes these activities and also the tools created to check and to validate the building design, to manage the interfaces and the organization put in place to achieve the required targets.

  17. Integrated Biological Control

    International Nuclear Information System (INIS)

    JOHNSON, A.R.

    2002-01-01

    Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

  18. Bioprospecting finds the toughest biological material: extraordinary silk from a giant riverine orb spider.

    Directory of Open Access Journals (Sweden)

    Ingi Agnarsson

    Full Text Available BACKGROUND: Combining high strength and elasticity, spider silks are exceptionally tough, i.e., able to absorb massive kinetic energy before breaking. Spider silk is therefore a model polymer for development of high performance biomimetic fibers. There are over 41,000 described species of spiders, most spinning multiple types of silk. Thus we have available some 200,000+ unique silks that may cover an amazing breadth of material properties. To date, however, silks from only a few tens of species have been characterized, most chosen haphazardly as model organisms (Nephila or simply from researchers' backyards. Are we limited to 'blindly fishing' in efforts to discover extraordinary silks? Or, could scientists use ecology to predict which species are likely to spin silks exhibiting exceptional performance properties? METHODOLOGY: We examined the biomechanical properties of silk produced by the remarkable Malagasy 'Darwin's bark spider' (Caerostris darwini, which we predicted would produce exceptional silk based upon its amazing web. The spider constructs its giant orb web (up to 2.8 m(2 suspended above streams, rivers, and lakes. It attaches the web to substrates on each riverbank by anchor threads as long as 25 meters. Dragline silk from both Caerostris webs and forcibly pulled silk, exhibits an extraordinary combination of high tensile strength and elasticity previously unknown for spider silk. The toughness of forcibly silked fibers averages 350 MJ/m(3, with some samples reaching 520 MJ/m(3. Thus, C. darwini silk is more than twice tougher than any previously described silk, and over 10 times better than Kevlar®. Caerostris capture spiral silk is similarly exceptionally tough. CONCLUSIONS: Caerostris darwini produces the toughest known biomaterial. We hypothesize that this extraordinary toughness coevolved with the unusual ecology and web architecture of these spiders, decreasing the likelihood of bridgelines breaking and collapsing the web

  19. Spider (Araneae) predations on white-backed planthopper Sogatella furcifera in subtropical rice ecosystems, China.

    Science.gov (United States)

    Wang, Xue-Qin; Wang, Guang-Hua; Zhu, Zeng-Rong; Tang, Qi-Yi; Hu, Yang; Qiao, Fei; Heong, Kong Luen; Cheng, Jia-An

    2017-06-01

    Spiders are effective biological control agents in rice ecosystems, but the comparative study of predations among main spider species under field conditions has not been fully explored owing to a lack of practical methodology. In this study, more than 6000 spiders of dominant species were collected from subtropical rice ecosystems to compare their predations on Sogatella furcifera (Horváth) (white-backed planthopper, WBPH) using DNA-based gut content analysis. The positive rates for all spider taxa were closely related to prey densities, as well as their behaviors and niches. The relationships of positive rates to prey planthopper densities for Pardosa pseudoannulata (Böes. et Str.), Coleosoma octomaculata (Böes. et Str.), Tetragnatha maxillosa Thorell and Ummeliata insecticeps (Böes. et Str.) under field conditions could be described using saturated response curves. Quantitative comparisons of predations among the four spider species confirmed that P. pseudoannulata and C. octomaculata were more rapacious than U. insecticeps and T. maxillosa under field conditions. A comparison of ratio of spiders to WBPH and positive rates between fields revealed that biological control by spiders could be effectively integrated with variety resistance. Generalist spiders could follow up WBPH population timely, and assemblages of spiders coupled with variety resistance could effectively suppress WBPH population. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  20. An Integrated Approach to Biology

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 8. An Integrated Approach to Biology. Aniket Bhattacharya. General Article Volume 16 Issue 8 August 2011 pp 742-753. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/016/08/0742-0753 ...

  1. A self-assembling peptide RADA16-I integrated with spider fibroin uncrystalline motifs

    Directory of Open Access Journals (Sweden)

    Sun L

    2012-02-01

    Full Text Available Lijuan Sun1,2, Xiaojun Zhao1,31West China Hospital Laboratory of Nanomedicine and Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, Chengdu 610041, Sichuan, China; 2Dept of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China; 3Center for Biomedical Engineering NE47-378, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USAAbstract: Mechanical strength of nanofiber scaffolds formed by the self-assembling peptide RADA16-I or its derivatives is not very good and limits their application. To address this problem, we inserted spidroin uncrystalline motifs, which confer incomparable elasticity and hydrophobicity to spider silk GGAGGS or GPGGY, into the C-terminus of RADA16-I to newly design two peptides: R3 (n-RADARADARADARADA-GGAGGS-c and R4 (n-RADARADARADARADA-GPGGY-c, and then observed the effect of these motifs on biophysical properties of the peptide. Atomic force microscopy, transmitting electron microscopy, and circular dichroism spectroscopy confirm that R3 and R4 display ß-sheet structure and self-assemble into long nanofibers. Compared with R3, the ß-sheet structure and nanofibers formed by R4 are more stable; they change to random coil and unordered aggregation at higher temperature. Rheology measurements indicate that novel peptides form hydrogel when induced by DMEM, and the storage modulus of R3 and R4 hydrogel is 0.5 times and 3 times higher than that of RADA16-I, respectively. Furthermore, R4 hydrogel remarkably promotes growth of liver cell L02 and liver cancer cell SMCC7721 compared with 2D culture, determined by MTT assay. Novel peptides still have potential as hydrophobic drug carriers; they can stabilize pyrene microcrystals in aqueous solution and deliver this into a lipophilic environment, identified by fluorescence emission spectra. Altogether, the spider fibroin motif GPGGY most effectively enhances mechanical

  2. Evaluation of airborne methyl salicylate for improved conservation biological control of two-spotted spider mites and hop aphid in Oregon hop yards

    Science.gov (United States)

    The use of synthetic herbivore-induced plant volatiles (HIPV) to attract natural enemies has received interest as a tool to enhance conservation biological control (CBC). Methyl salicylate (MeSA) is a HIPV that is attractive to several key predators of two-spotted spider mite, Tetranychus urticae K...

  3. Tarantula spider

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/002855.htm Tarantula spider bite To use the sharing features on this ... This article describes the effects of a tarantula spider bite. The class of insects to which the ...

  4. Reproductive biology of the Suez Canal spider crab Schizophrys aspera (H. Milne Edwards, 1834: Crustacea: Brachyura: Majidae).

    Science.gov (United States)

    El-Serehy, Hamed A; Al-Rasheid, Khaled A; Ibrahim, Nesreen K; Al-Misned, Fahad A

    2015-11-01

    A reproductive biology study of the spider crab Schizophrys aspera (H. Milne Edwards, 1834) was conducted in the Suez Canal from July 2012 to June 2013. The annual sex ratio (Male:Female) of S. aspera was female biased with values of 1:1.25. Out of the four ovarian development stages of this crab, two stages were observed in the Suez Canal throughout the whole year. The ovigerous crab's carapace width varied from 28 to 52 mm. This crab species can spawn during most of the year in the canal water, with a peak during late spring and early winter. The fecundity of ovigerous females ranged between 2349 and 13600 eggs with a mean of 5494 ± 1486 eggs. Female crabs that reached sexual maturity exhibited a minimum carapace width varying between 22 and 46 mm, and fifty percentage of all ovigerous females showed a carapace width of 36 mm.

  5. Integrative biological analysis for neuropsychopharmacology.

    Science.gov (United States)

    Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

    2014-01-01

    Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

  6. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  7. Taxonomy, systematics and biology of the Australian halotolerant wolf spider genus Tetralycosa (Araneae: Lycosidae: Artoriinae

    Directory of Open Access Journals (Sweden)

    Volker W. Framenau

    2017-07-01

    Full Text Available The Australian wolf spider genus Tftralycosa Roewer, 1960, with Lycosa meracula Simon, 1909 (junior synonym of Lycosa oraria L. Koch, 1877 as type species, is revised to include 13 species, eight of which are described as new here: Tetralycosa adarca sp. nov., T. alteripa (McKay, 1976, T. arabanae Framenau, Gotch & Austin, 2006, T. baudinettei sp. nov., T. caudex sp. nov., T. eyrei (Hickman, 1944, T. floundersi sp. nov., T. halophila sp. nov., T. oraria (L. Koch, 1876, T. orariola sp. nov., T. williamsi sp. nov., T. wundurra (McKay, 1979 comb. nov. and T. rebecca sp. nov. Members of Tetralycosa are halotolerant, exclusively inhabiting saline environments such as coastal beaches, and mound springs, clay pans and salt lakes in the Australian interior. A phylogenetic analysis of the genus identified a monophyletic clade of eight species that live permanently on the barren surface of salt lakes suggesting a single radiation into this extremely inhospitable habitat. Some of these Tetralycosa species are currently known from single salt lakes only and with increasing disturbances of these systems by mining, agriculture and recreational use, research effort should be increased to study their ecology and conservation status.

  8. Biology as an Integrating Natural Science Domain

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 3. Biology as an Integrating Natural Science Domain: A Proposal for BSc (Hons) in Integrated Biology. Kambadur Muralidhar. Classroom Volume 13 Issue 3 March 2008 pp 272-276 ...

  9. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  10. Evaluation of airborne methyl salicylate for improved conservation biological control of two-spotted spider mite and hop aphid in Oregon hop yards.

    Science.gov (United States)

    Woods, J L; James, D G; Lee, J C; Gent, D H

    2011-12-01

    The use of synthetic herbivore-induced plant volatiles (HIPV) to attract natural enemies has received interest as a tool to enhance conservation biological control (CBC). Methyl salicylate (MeSA) is a HIPV that is attractive to several key predators of two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and hop aphid, Phorodon humuli (Schrank) (Homoptera: Aphididae). A 2-year study was conducted to evaluate the recommended commercial use of MeSA in hop yards in Oregon. Slow-release MeSA dispensers were stapled to supporting poles in 0.5 ha plots and these plots were compared to a paired non-treated plot on each of three farms in 2008 and 2009. Across both years, there was a trend for reduced (range 40-91%) mean seasonal numbers of T. urticae in five of the six MeSA-baited plots. Stethorus spp., key spider mite predators, tended to be more numerous in MeSA-baited plots compared to control plots on a given farm. Mean seasonal densities of hop aphid and other natural enemies (e.g., Orius spp. and Anystis spp.) were similar between MeSA-treated and control plots. Variability among farms in suppression of two-spotted spider mites and attraction of Stethorus spp. suggests that the use of MeSA to enhance CBC of spider mites in commercial hop yards may be influenced by site-specific factors related to the agroecology of individual farms or seasonal effects that require further investigation. The current study also suggests that CBC of hop aphid with MeSA in this environment may be unsatisfactory.

  11. Data integration in biological research: an overview.

    Science.gov (United States)

    Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

    2015-12-01

    Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

  12. Integrating immunomarking with ecological and behavioural approaches to assess predation of Helicoverpa spp. larvae by wolf spiders in cotton

    Science.gov (United States)

    Wolf spiders (Araneae: Lycosidae) are abundant soil-dwelling predators found in cotton fields and can contribute important pest management services. These spiders can kill and consume larvae of the cotton bollworm Helicoverpa spp. (Lepidoptera: Noctuidae) that survive foraging on Bt cotton and desce...

  13. Inoculate Release of Stethorus gilvifrons Mulsan (Coleoptera: Coccinellidae for Biological Control of Date Palm Spider Mite, Oligonychus afrasiaticusMcGregor (Prostigmata: Tetranychidae

    Directory of Open Access Journals (Sweden)

    M. Latifian

    2017-12-01

    Full Text Available Introduction: The spider mite, Oligonychus afrasiaticus feeds by sucking the sap from the immature fruits tissue. The natural color of fruits changes to pale yellow or gray by mite's feeding. Damaged fruit are cracked and its damage can dry out the fruits. Because of resistance to pesticides, resurgence of date palm spider mite causes to disrupt the natural balance of their population. Tiny black ladybird beetle, Stethorous gilvifrons is the most important and active lady beetle species in Khuzestan province and is very effective on biological control of the spider mite. Determination of the amount and release time of the lady beetles are the most important factors in the implementation of biological control programs of date palm spider mite. So, careful monitoring, time of the release and the ability of deployment of predatory ladybird are essential steps to success in the programs of biological control. Materials and Methods: This research was conducted in Shadegan region of Khuzestan province. The nested design was used to compare the efficiency of different inoculate release methods of the predator, S. gilvifrons. The main niches include three release times which were at the time of emergence, three days and one week after emergence of date palm spider mite in date palm plantation. Sub nesting including three different levels of predator release including minimum, moderate and maximum release with 0.5, 1 and 3 predator /m2 per day and were continued for two weeks. The two or three-days ladybirds were used to release. First, the infected clusters were covered by mesh fabric and ladybirds were released under them. After a week, mantles were opened up to the establishment of ladybird run on the normal condition of date palm plantations. This experiment was repeated three times, and each replication consists of a quarter- hectare plantation with dominant cultivar Sayer.Three date Palm trees from each release and control were randomly selected

  14. Integrating rehabilitation engineering technology with biologics.

    Science.gov (United States)

    Collinger, Jennifer L; Dicianno, Brad E; Weber, Douglas J; Cui, Xinyan Tracy; Wang, Wei; Brienza, David M; Boninger, Michael L

    2011-06-01

    Rehabilitation engineers apply engineering principles to improve function or to solve challenges faced by persons with disabilities. It is critical to integrate the knowledge of biologics into the process of rehabilitation engineering to advance the field and maximize potential benefits to patients. Some applications in particular demonstrate the value of a symbiotic relationship between biologics and rehabilitation engineering. In this review we illustrate how researchers working with neural interfaces and integrated prosthetics, assistive technology, and biologics data collection are currently integrating these 2 fields. We also discuss the potential for further integration of biologics and rehabilitation engineering to deliver the best technologies and treatments to patients. Engineers and clinicians must work together to develop technologies that meet clinical needs and are accessible to the intended patient population. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  15. Semantic Web meets Integrative Biology: a survey.

    Science.gov (United States)

    Chen, Huajun; Yu, Tong; Chen, Jake Y

    2013-01-01

    Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

  16. Spider Vein Removal

    Science.gov (United States)

    Spider veins: How are they removed? I have spider veins on my legs. What options are available ... M.D. Several options are available to remove spider veins — thin red lines or weblike networks of ...

  17. Spider Bites (For Parents)

    Science.gov (United States)

    ... Videos for Educators Search English Español First Aid: Spider Bites KidsHealth / For Parents / First Aid: Spider Bites ... rare. Signs and Symptoms Of a brown recluse spider bite: red blister in the center with surrounding ...

  18. Calculation of integrated biological response in brachytherapy

    International Nuclear Information System (INIS)

    Dale, Roger G.; Coles, Ian P.; Deehan, Charles; O'Donoghue, Joseph A.

    1997-01-01

    Purpose: To present analytical methods for calculating or estimating the integrated biological response in brachytherapy applications, and which allow for the presence of dose gradients. Methods and Materials: The approach uses linear-quadratic (LQ) formulations to identify an equivalent biologically effective dose (BED eq ) which, if applied to a specified tissue volume, would produce the same biological effect as that achieved by a given brachytherapy application. For simple geometrical cases, BED multiplying factors have been derived which allow the equivalent BED for tumors to be estimated from a single BED value calculated at a dose reference point. For more complex brachytherapy applications a voxel-by-voxel determination of the equivalent BED will be more accurate. Equations are derived which when incorporated into brachytherapy software would facilitate such a process. Results: At both high and low dose rates, the BEDs calculated at the dose reference point are shown to be lower than the true values by an amount which depends primarily on the magnitude of the prescribed dose; the BED multiplying factors are higher for smaller prescribed doses. The multiplying factors are less dependent on the assumed radiobiological parameters. In most clinical applications involving multiple sources, particularly those in multiplanar arrays, the multiplying factors are likely to be smaller than those derived here for single sources. The overall suggestion is that the radiobiological consequences of dose gradients in well-designed brachytherapy treatments, although important, may be less significant than is sometimes supposed. The modeling exercise also demonstrates that the integrated biological effect associated with fractionated high-dose-rate (FHDR) brachytherapy will usually be different from that for an 'equivalent' continuous low-dose-rate (CLDR) regime. For practical FHDR regimes involving relatively small numbers of fractions, the integrated biological effect to

  19. Spider Bites: First Aid

    Science.gov (United States)

    ... care immediately if: You were bitten by a black widow or brown recluse spider You are unsure whether the bite ... in the South. Signs and symptoms of a black widow spider bite may include: At ... fever and nausea Brown recluse spider The brown recluse spider has a ...

  20. Environmental Engineering Approaches toward Sustainable Management of Spider Mites.

    Science.gov (United States)

    Suzuki, Takeshi

    2012-10-26

    Integrated pest management (IPM), which combines physical, biological, and chemical control measures to complementary effect, is one of the most important approaches to environmentally friendly sustainable agriculture. To expand IPM, we need to develop new pest control measures, reinforce existing measures, and investigate interactions between measures. Continued progress in the development of environmental control technologies and consequent price drops have facilitated their integration into plant production and pest control. Here I describe environmental control technologies for the IPM of spider mites through: (1) the disturbance of photoperiod-dependent diapause by artificial light, which may lead to death in seasonal environments; (2) the use of ultraviolet radiation to kill or repel mites; and (3) the use of water vapor control for the long-term cold storage of commercially available natural enemies. Such environmental control technologies have great potential for the efficient control of spider mites through direct physical effects and indirect effects via natural enemies.

  1. Extended spider cognition.

    Science.gov (United States)

    Japyassú, Hilton F; Laland, Kevin N

    2017-05-01

    There is a tension between the conception of cognition as a central nervous system (CNS) process and a view of cognition as extending towards the body or the contiguous environment. The centralised conception requires large or complex nervous systems to cope with complex environments. Conversely, the extended conception involves the outsourcing of information processing to the body or environment, thus making fewer demands on the processing power of the CNS. The evolution of extended cognition should be particularly favoured among small, generalist predators such as spiders, and here, we review the literature to evaluate the fit of empirical data with these contrasting models of cognition. Spiders do not seem to be cognitively limited, displaying a large diversity of learning processes, from habituation to contextual learning, including a sense of numerosity. To tease apart the central from the extended cognition, we apply the mutual manipulability criterion, testing the existence of reciprocal causal links between the putative elements of the system. We conclude that the web threads and configurations are integral parts of the cognitive systems. The extension of cognition to the web helps to explain some puzzling features of spider behaviour and seems to promote evolvability within the group, enhancing innovation through cognitive connectivity to variable habitat features. Graded changes in relative brain size could also be explained by outsourcing information processing to environmental features. More generally, niche-constructed structures emerge as prime candidates for extending animal cognition, generating the selective pressures that help to shape the evolving cognitive system.

  2. WISB: Warwick Integrative Synthetic Biology Centre.

    Science.gov (United States)

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

  3. Checklist of spider fauna of FR Peshawar, FATA, Pakistan

    Directory of Open Access Journals (Sweden)

    F. Perveen

    2012-03-01

    Full Text Available The spiders are known as poisonous arthropods, but they also act as the predator or biological pests control agent. Their 23 species belonging to 15 genera and 09 families were reported during 2009-2010 from FR Peshawar, FATA, Pakistan. The reported families Clubionidae, Scytodidae and Sprassidae covered each 4%, Araneidae, Gnaphosidae, Pholicidae and Salticidae each 9%, Thomisidae 13% and Lycosidae 43% biodiversity of spiders of FATA. However, the largest spider collected was huntsman, Isopoda tuhodnigra (Barrion with total body length 15.80+-0.83 mm. Moreover, the smallest spider was wolf spider, Pardosa birmanica (Simon with total body length 4.20+-1.30 mm. Further, the crab spiders, Thomisus pugilis (Stoliczka, T. spectabilis (Doleschall and Diaea evanida (Thorell were the most colorful species belonging to family Thomisidae. A detail study is required for further exploration of spider fauna of FATA.

  4. Cyber integrated MEMS microhand for biological applications

    Science.gov (United States)

    Weissman, Adam; Frazier, Athena; Pepen, Michael; Lu, Yen-Wen; Yang, Shanchieh Jay

    2009-05-01

    Anthropomorphous robotic hands at microscales have been developed to receive information and perform tasks for biological applications. To emulate a human hand's dexterity, the microhand requires a master-slave interface with a wearable controller, force sensors, and perception displays for tele-manipulation. Recognizing the constraints and complexity imposed in developing feedback interface during miniaturization, this project address the need by creating an integrated cyber environment incorporating sensors with a microhand, haptic/visual display, and object model, to emulates human hands' psychophysical perception at microscale.

  5. Data mining and data integration in biology

    DEFF Research Database (Denmark)

    Ólason, Páll Ísólfur

    2008-01-01

    . They also necessitate new ways of data preparation as established methods for sequence sets are often useless when dealing with sets of sequence pairs. Therefore careful analysis on the sequence level as well as the integrated network level is needed to benchmark these data prior to use. The networks, which...... between molecules, the essence of systems biology. Internet technologies are very important in this respect as bioinformatics labs around the world generate staggering amounts of novel annotations, increasing the importance of on-line processing and distributed systems. One of the most important new data...... types in proteomics is protein-protein interactions. Interactions between the functional elements in the cell are a natural place to start when integrating protein annotations with the aim of gaining a systems view of the cell. Interaction data, however, are notoriously biased, erroneous and incomplete...

  6. Brown Recluse Spider

    Science.gov (United States)

    ... to a group of spiders commonly known as violin spiders or fiddlebacks. The characteristic fiddle-shaped pattern ... 4-19.1mm) • Color: Golden brown • A dark violin/fiddle shape (see top photo) is located on ...

  7. Nature Study Tips. Spiders.

    Science.gov (United States)

    Mulaik, Stanley B.

    1990-01-01

    Different types of spiders, their ranges and habits are discussed. Activities associated with the study of spiders are suggested. Four references are listed which may be of interest to beginners. (CW)

  8. Black widow spider

    Science.gov (United States)

    ... medlineplus.gov/ency/article/002858.htm Black widow spider To use the sharing features on this page, please enable JavaScript. The black widow spider (Latrodectus) has a shiny black body with a ...

  9. The Virtual Institute for Integrative Biology (VIIB)

    International Nuclear Information System (INIS)

    Rivera, G.; Gonzalez-Nieto, F.; Perez-Acle, T.; Isea, R.; Holmes, D. S.

    2007-01-01

    The Virtual Institute for Integrative Biology (VII B) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, Metagenomic, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomic, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: inter operability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible work flows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions. (Author)

  10. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  11. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  12. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Maternal care and subsocial behaviour in spiders.

    Science.gov (United States)

    Yip, Eric C; Rayor, Linda S

    2014-05-01

    While most spiders are solitary and opportunistically cannibalistic, a variety of social organisations has evolved in a minority of spider species. One form of social organisation is subsociality, in which siblings remain together with their parent for some period of time but disperse prior to independent reproduction. We review the literature on subsocial and maternal behaviour in spiders to highlight areas in which subsocial spiders have informed our understanding of social evolution and to identify promising areas of future research. We show that subsocial behaviour has evolved independently at least 18 times in spiders, across a wide phylogenetic distribution. Subsocial behaviour is diverse in terms of the form of care provided by the mother, the duration of care and sibling association, the degree of interaction and cooperation among siblings, and the use of vibratory and chemical communication. Subsocial spiders are useful model organisms to study various topics in ecology, such as kin recognition and the evolution of cheating and its impact on societies. Further, why social behaviour evolved in some lineages and not others is currently a topic of debate in behavioural ecology, and we argue that spiders offer an opportunity to untangle the ecological causes of parental care, which forms the basis of many other animal societies. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

  14. Did You Say Spiders?

    Science.gov (United States)

    Campbell, Alene

    This spider unit focuses on students' development of cooperative learning and inquiry-based skills. Students read "The Very Busy Spider" by Eric Carle, and then work in cooperative groups using the Internet to research and synthesize important information about spiders. Technology is used for vocabulary instruction and to create a…

  15. Spiders in dermatology.

    Science.gov (United States)

    Kang, Jun K; Bhate, Chinmoy; Schwartz, Robert A

    2014-09-01

    Spider bites represent an unusual and potentially over-represented clinical diagnosis. Despite a common fear of spiders, known as arachnophobia, current knowledge suggests that only a small number of families within the order Araneae are medically relevant. Moreover, most cutaneous spider reactions, including both evenomations and physical trauma, produce mild, local symptoms which may be managed with supportive care alone. The differential diagnosis for spider bites may be broad, especially if the offending arachnid is not seen or found. We describe a series of spiders relevant to the dermatologist in the United States.

  16. Attending to detail by communal spider-eating spiders.

    Science.gov (United States)

    Jackson, Robert R; Nelson, Ximena J

    2012-07-01

    Communal predators may often need to make especially intricate foraging decisions, as a predator's success may depend on the actions of its neighbours. Here,we consider the decisions made by Portia africana, a jumping spider (Salticidae) that preys on other spiders, including Oecobius amboseli (Oecobiidae), a small prey spider that lives under small sheets of silk (nests) on the walls of buildings. P. africana juveniles settle near oecobiid nests and then ambush oecobiids as they leave or enter the nest. Two or more P. africana juveniles sometimes settle at the same nest and, when an oecobiid is captured, the P. africana juveniles may share the meal. We investigated the joining decisions made by naïve P. africana juveniles. Experiments were based on using lures (dead spiders positioned in lifelike posture) arranged in a series of 17 different scenes defined by the presence/absence of a nest, the lure types present and the configuration of the lures and the nest. Our findings imply that P. africana juveniles make remarkably precise predatory decisions, with the variables that matter including whether a nest is present, the identity of spiders inside and outside a nest and how spiders are positioned relative to each other and the nest.

  17. Biological condition gradient: Applying a framework for determining the biological integrity of coral reefs

    Science.gov (United States)

    The goals of the U.S. Clean Water Act (CWA) are to restore and maintain the chemical, physical and biological integrity of water resources. Although clean water is a goal, another is to safeguard biological communities by defining levels of biological integrity to protect aquatic...

  18. Funnel-web spider bite

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/002844.htm Funnel-web spider bite To use the sharing features on ... the effects of a bite from the funnel-web spider. Male funnel-web spiders are more poisonous ...

  19. Single versus multiple enemies and the impact on biological control of spider mites in cassava fields in West-Africa

    NARCIS (Netherlands)

    Onzo, A.; Sabelis, M.W.; Hanna, R.

    2014-01-01

    To determine whether to use single or multiple predator species for biological pest control requires manipulative field experiments. We performed such tests in Benin (West Africa) in cassava fields infested by the cassava green mite Mononychellus tanajoa, and the cotton red mite Oligonychus

  20. Reconstruction of biological networks based on life science data integration

    Directory of Open Access Journals (Sweden)

    Kormeier Benjamin

    2010-06-01

    Full Text Available For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

  1. Reconstruction of biological networks based on life science data integration.

    Science.gov (United States)

    Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

    2010-10-27

    For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH--an integration toolkit for building life science data warehouses, CardioVINEdb--a information system for biological data in cardiovascular-disease and VANESA--a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

  2. Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

    Science.gov (United States)

    Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

    2014-01-01

    Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students' apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning.

  3. Integrating Quantitative Thinking into an Introductory Biology Course Improves Students’ Mathematical Reasoning in Biological Contexts

    Science.gov (United States)

    Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

    2014-01-01

    Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students’ apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students’ understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students’ inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students’ biology learning. PMID:24591504

  4. Integrating interactive computational modeling in biology curricula.

    Directory of Open Access Journals (Sweden)

    Tomáš Helikar

    2015-03-01

    Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  5. Integrating interactive computational modeling in biology curricula.

    Science.gov (United States)

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  6. Comparing chemical and biological control strategies for twospotted spider mites (Acari: Tetranychidae) in commercial greenhouse production of bedding plants.

    Science.gov (United States)

    Opit, George P; Perret, Jamis; Holt, Kiffnie; Nechols, James R; Margolies, David C; Williams, Kimberly A

    2009-02-01

    Efficacy, costs, and impact on crop salability of various biological and chemical control strategies for Tetranychus urticae Koch (Acari: Tetranychidae) were evaluated on mixed plantings of impatiens, Impatiens wallerana Hook.f (Ericales: Balsaminaceae), and ivy geranium, Pelargonium peltatum (1.) L'Hér. Ex Aiton (Geraniales: Geraniaceae), cultivars in commercial greenhouses. Chemical control consisting of the miticide bifenazate (Floramite) was compared with two biological control strategies using the predatory mite Phytoseiulus persimilis Athias-Henriot (Acari: Phytoseiidae). Treatments were 1) a single, early application of bifenazate; 2) a single, early release of predatory mites at a 1:4 predator:pest ratio based on leaf samples to estimate pest density; 3) a weekly release of predatory mites at numbers based on the area covered by the crop; and 4) an untreated control. T. urticae populations were monitored for 3 wk after the earliest treatment. When plants were ready for market, their salability was estimated. Bifenazate and density-based P. persimilis treatments effectively reduced T. urticae numbers starting 1 wk after plants had been treated, whereas the scheduled, area-based P. persimilis treatment had little or no effect. The percentage of flats that could be sold at the highest market wholesale price ranged from 15 to 33%, 44 to 86%, 84 to 95%, and 92 to 100%, in the control, weekly area-based P. persimilis, bifenazate, and single density-based P. persimilis treatments, respectively. We have shown that in commercial greenhouse production of herbaceous ornamental bedding plants, estimating pest density to determine the appropriate number of predators to release is as effective and offers nearly the same economic benefit as prophylactic use of pesticides.

  7. Respiration in spiders (Araneae).

    Science.gov (United States)

    Schmitz, Anke

    2016-05-01

    Spiders (Araneae) are unique regarding their respiratory system: they are the only animal group that breathe simultaneously with lungs and tracheae. Looking at the physiology of respiration the existence of tracheae plays an important role in spiders with a well-developed tracheal system. Other factors as sex, life time, type of prey capture and the high ability to gain energy anaerobically influence the resting and the active metabolic rate intensely. Most spiders have metabolic rates that are much lower than expected from body mass; but especially those with two pairs of lungs. Males normally have higher resting rates than females; spiders that are less evolved and possess a cribellum have lower metabolic rates than higher evolved species. Freely hunting spiders show a higher energy turnover than spiders hunting with a web. Spiders that live longer than 1 year will have lower metabolic rates than those species that die after 1 year in which development and reproduction must be completed. Lower temperatures and starvation, which most spiders can cope with, will decrease the metabolic rate as well.

  8. Spider silk reinforced by graphene or carbon nanotubes

    Science.gov (United States)

    Lepore, Emiliano; Bosia, Federico; Bonaccorso, Francesco; Bruna, Matteo; Taioli, Simone; Garberoglio, Giovanni; Ferrari, Andrea C.; Pugno, Nicola Maria

    2017-09-01

    Spider silk has promising mechanical properties, since it conjugates high strength (~1.5 GPa) and toughness (~150 J g-1). Here, we report the production of silk incorporating graphene and carbon nanotubes by spider spinning, after feeding spiders with the corresponding aqueous dispersions. We observe an increment of the mechanical properties with respect to pristine silk, up to a fracture strength ~5.4 GPa and a toughness modulus ~1570 J g-1. This approach could be extended to other biological systems and lead to a new class of artificially modified biological, or ‘bionic’, materials.

  9. Biological and ecological characterization of two mites (Tetranychus Urticae and Phytoseiulus Persimilis) occurring in some agro-ecosystems; Caratterizzazione biologica ed ecologica di due acari (Tetranichus Urticae e Phytoseiulus Persimilis) interagenti in alcuni ecosistemi agrari

    Energy Technology Data Exchange (ETDEWEB)

    Calvitti, M [ENEA, Centro Ricerche Casaccia, Roma (Italy). Dip. Innovazione

    1995-12-01

    This work is a brief review of the actual knowledge about biological and ecological characteristics of two species of mites: Tetranychus urticae Koch (Acarina Tetranychidae) (two-spotted spider mite) and the predaceous mite Phytoseiulus persimilis Athias Henriot (Acarina Phytoseiidae). Success obtained in biological control of spider mite, by mass release of P. persimilis, has increased the interest in biological and ecological study of these mites. Particularly, the following biological and ecological aspects of both P. persimilis and T. urticae are hereby discussed: reproductive biology; population dynamics (spider mites outbreaks) and natural regulation of the trophic interaction; feeding behaviour; biological control of two-spotted spider mite by P. persimilis. In this report experimental data obtained in laboratory have been integrated with bibliographic information concerning studies produced in natural conditions.

  10. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  11. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  12. Bat Predation by Spiders

    Science.gov (United States)

    Nyffeler, Martin; Knörnschild, Mirjam

    2013-01-01

    In this paper more than 50 incidences of bats being captured by spiders are reviewed. Bat-catching spiders have been reported from virtually every continent with the exception of Antarctica (∼90% of the incidences occurring in the warmer areas of the globe between latitude 30° N and 30° S). Most reports refer to the Neotropics (42% of observed incidences), Asia (28.8%), and Australia-Papua New Guinea (13.5%). Bat-catching spiders belong to the mygalomorph family Theraphosidae and the araneomorph families Nephilidae, Araneidae, and Sparassidae. In addition to this, an attack attempt by a large araneomorph hunting spider of the family Pisauridae on an immature bat was witnessed. Eighty-eight percent of the reported incidences of bat catches were attributable to web-building spiders and 12% to hunting spiders. Large tropical orb-weavers of the genera Nephila and Eriophora in particular have been observed catching bats in their huge, strong orb-webs (of up to 1.5 m diameter). The majority of identifiable captured bats were small aerial insectivorous bats, belonging to the families Vespertilionidae (64%) and Emballonuridae (22%) and usually being among the most common bat species in their respective geographic area. While in some instances bats entangled in spider webs may have died of exhaustion, starvation, dehydration, and/or hyperthermia (i.e., non-predation death), there were numerous other instances where spiders were seen actively attacking, killing, and eating the captured bats (i.e., predation). This evidence suggests that spider predation on flying vertebrates is more widespread than previously assumed. PMID:23516436

  13. Bat predation by spiders.

    Science.gov (United States)

    Nyffeler, Martin; Knörnschild, Mirjam

    2013-01-01

    In this paper more than 50 incidences of bats being captured by spiders are reviewed. Bat-catching spiders have been reported from virtually every continent with the exception of Antarctica (≈ 90% of the incidences occurring in the warmer areas of the globe between latitude 30° N and 30° S). Most reports refer to the Neotropics (42% of observed incidences), Asia (28.8%), and Australia-Papua New Guinea (13.5%). Bat-catching spiders belong to the mygalomorph family Theraphosidae and the araneomorph families Nephilidae, Araneidae, and Sparassidae. In addition to this, an attack attempt by a large araneomorph hunting spider of the family Pisauridae on an immature bat was witnessed. Eighty-eight percent of the reported incidences of bat catches were attributable to web-building spiders and 12% to hunting spiders. Large tropical orb-weavers of the genera Nephila and Eriophora in particular have been observed catching bats in their huge, strong orb-webs (of up to 1.5 m diameter). The majority of identifiable captured bats were small aerial insectivorous bats, belonging to the families Vespertilionidae (64%) and Emballonuridae (22%) and usually being among the most common bat species in their respective geographic area. While in some instances bats entangled in spider webs may have died of exhaustion, starvation, dehydration, and/or hyperthermia (i.e., non-predation death), there were numerous other instances where spiders were seen actively attacking, killing, and eating the captured bats (i.e., predation). This evidence suggests that spider predation on flying vertebrates is more widespread than previously assumed.

  14. Integrated biological, chemical and physical processes kinetic ...

    African Journals Online (AJOL)

    ... for C and N removal, only gas and liquid phase processes were considered for this integrated model. ... kLA value for the aeration system, which affects the pH in the anoxic and aerobic reactors through CO2 gas exchange. ... Water SA Vol.

  15. Brain systems underlying encounter expectancy bias in spider phobia.

    Science.gov (United States)

    Aue, Tatjana; Hoeppli, Marie-Eve; Piguet, Camille; Hofstetter, Christoph; Rieger, Sebastian W; Vuilleumier, Patrik

    2015-06-01

    Spider-phobic individuals are characterized by exaggerated expectancies to be faced with spiders (so-called encounter expectancy bias). Whereas phobic responses have been linked to brain systems mediating fear, little is known about how the recruitment of these systems relates to exaggerated expectancies of threat. We used fMRI to examine spider-phobic and control participants while they imagined visiting different locations in a forest after having received background information about the likelihood of encountering different animals (spiders, snakes, and birds) at these locations. Critically, imagined encounter expectancies modulated brain responses differently in phobics as compared with controls. Phobics displayed stronger negative modulation of activity in the lateral prefrontal cortex, precuneus, and visual cortex by encounter expectancies for spiders, relative to snakes or birds (within-participants analysis); these effects were not seen in controls. Between-participants correlation analyses within the phobic group further corroborated the hypothesis that these phobia-specific modulations may underlie irrationality in encounter expectancies (deviations of encounter expectancies from objective background information) in spider phobia; the greater the negative modulation a phobic participant displayed in the lateral prefrontal cortex, precuneus, and visual cortex, the stronger was her bias in encounter expectancies for spiders. Interestingly, irrationality in expectancies reflected in frontal areas relied on right rather than left hemispheric deactivations. Our data accord with the idea that expectancy biases in spider phobia may reflect deficiencies in cognitive control and contextual integration that are mediated by right frontal and parietal areas.

  16. Biologics in dermatology: An integrated review

    Directory of Open Access Journals (Sweden)

    Virendra N Sehgal

    2014-01-01

    Full Text Available The advent of biologics in dermatologic treatment armentarium has added refreshing dimensions, for it is a major breakthrough. Several agents are now available for use. It is therefore imperative to succinctly comprehend their pharmacokinetics for their apt use. A concerted endeavor has been made to delve on this subject. The major groups of biologics have been covered and include: Drugs acting against TNF-α, Alefacept, Ustekinumab, Rituximab, IVIG and Omalizumab. The relevant pharmacokinetic characteristics have been detailed. Their respective label (approved and off-label (unapproved indications have been defined, highlighting their dosage protocol, availability and mode of administration. The evidence level of each indication has also been discussed to apprise the clinician of their current and prospective uses. Individual anti-TNF drugs are not identical in their actions and often one is superior to the other in a particular disease. Hence, the section on anti-TNF agents mentions the literature on each drug separately, and not as a group. The limitations for their use have also been clearly brought out.

  17. SPIDER: A Framework for Understanding Driver Distraction.

    Science.gov (United States)

    Strayer, David L; Fisher, Donald L

    2016-02-01

    The objective was to identify key cognitive processes that are impaired when drivers divert attention from driving. Driver distraction is increasingly recognized as a significant source of injuries and fatalities on the roadway. A "SPIDER" model is developed that identifies key cognitive processes that are impaired when drivers divert attention from driving. SPIDER is an acronym standing for scanning, predicting, identifying, decision making, and executing a response. When drivers engage in secondary activities unrelated to the task of driving, SPIDER-related processes are impaired, situation awareness is degraded, and the ability to safely operate a motor vehicle may be compromised. The pattern of interference helps to illuminate the sources of driver distraction and may help guide the integration of new technology into the automobile. © 2015, Human Factors and Ergonomics Society.

  18. Integrating cell biology and proteomic approaches in plants.

    Science.gov (United States)

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-10-03

    Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

  19. Integration of genomic information with biological networks using Cytoscape.

    Science.gov (United States)

    Bauer-Mehren, Anna

    2013-01-01

    Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein-protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.

  20. Spider fauna of semiarid eastern Colorado agroecosystems: diversity, abundance, and effects of crop intensification.

    Science.gov (United States)

    Kerzicnik, Lauren M; Peairs, Frank B; Cushing, Paula E; Draney, Michael L; Merrill, Scott C

    2013-02-01

    Spiders are critical predators in agroecosystems. Crop management practices can influence predator density and diversity, which, in turn, can influence pest management strategies. Crop intensification is a sustainable agricultural technique that can enhance crop production although optimizing soil moisture. To date, there is no information on how crop intensification affects natural enemy populations, particularly spiders. This study had two objectives: to characterize the abundance and diversity of spiders in eastern Colorado agroecosystems, and to test the hypothesis that spider diversity and density would be higher in wheat (Triticum aestivum L.) in crop-intensified rotations compared with wheat in conventional rotations. We collected spiders through pitfall, vacuum, and lookdown sampling from 2002 to 2007 to test these objectives. Over 11,000 spiders in 19 families from 119 species were captured from all sampling techniques. Interestingly, the hunting spider guild represented 89% of the spider fauna captured from all sites with the families Gnaphosidae and Lycosidae representing 75% of these spiders. Compared with European agroecosystems, these agroecosystems had greater diversity, which can be beneficial for the biological control of pests. Overall, spider densities were low in these semiarid cropping systems, and crop intensification effects on spider densities were not evident at this scale.

  1. Biomechanics of Spider Silks

    Science.gov (United States)

    2006-03-02

    water and deformation conditions. Such fibres [Nexia ’ biosteel ’ silk ] were spun from recombinant silk ’cloned’ from Spidroin II and indeed show 67...SUBTITLE 5. FUNDING NUMBERS Biomechanics of Spider Silks F49620-03-1-0111 6. AUTHOR(S) Fritz Vollrath 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES...Perform Pro, WHSIDIOR, Oct 94 COVER SHEET FINAL (3rd Year) Report to AFOSR on: BIOMECHANICS OF SPIDER SILKS Fritz Vollrath, Oxford University, England

  2. Attentional bias to moving spiders in spider fearful individuals.

    Science.gov (United States)

    Vrijsen, Janna N; Fleurkens, Pascal; Nieuwboer, Wieteke; Rinck, Mike

    2009-05-01

    We investigated if an attentional bias for spiders in spider fearful individuals (SFs) can also be found for moving spiders, rather than static images. In Study 1, 28 SFs and 33 non-anxious controls (NACs) participated in a modified version of the dot probe paradigm: they had to react to a probe that appeared either in the next, previous, or side position of a spider's or a wheel's path. 24 SFs and 29 NACs participated in Study 2, in which a fourth, highly predictable, probe position was added. We expected that moving spiders would capture the attention of SFs. In addition, we tested whether SFs try to predict the movement of the spider to make it less threatening. As expected, SFs showed an attentional bias towards moving spiders. However, both groups reacted fastest to unpredictable movements, indicating that SFs and NACs alike anticipate unpredictable spider movements.

  3. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  4. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  5. Biological data integration: wrapping data and tools.

    Science.gov (United States)

    Lacroix, Zoé

    2002-06-01

    Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

  6. BiologicalNetworks 2.0 - an integrative view of genome biology data

    Directory of Open Access Journals (Sweden)

    Ponomarenko Julia

    2010-12-01

    Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

  7. An integrative approach to inferring biologically meaningful gene modules

    Directory of Open Access Journals (Sweden)

    Wang Kai

    2011-07-01

    Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

  8. Physical integrity: the missing link in biological monitoring and TMDLs.

    Science.gov (United States)

    Asmus, Brenda; Magner, Joseph A; Vondracek, Bruce; Perry, Jim

    2009-12-01

    The Clean Water Act mandates that the chemical, physical, and biological integrity of our nation's waters be maintained and restored. Physical integrity has often been defined as physical habitat integrity, and as such, data collected during biological monitoring programs focus primarily on habitat quality. However, we argue that channel stability is a more appropriate measure of physical integrity and that channel stability is a foundational element of physical habitat integrity in low-gradient alluvial streams. We highlight assessment tools that could supplement stream assessments and the Total Maximum Daily Load stressor identification process: field surveys of bankfull cross-sections; longitudinal thalweg profiles; particle size distribution; and regionally calibrated, visual, stream stability assessments. Benefits of measuring channel stability include a more informed selection of reference or best attainable stream condition for an Index of Biotic Integrity, establishment of a baseline for monitoring changes in present and future condition, and indication of channel stability for investigations of chemical and biological impairments associated with sediment discontinuity and loss of habitat quality.

  9. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    Science.gov (United States)

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  10. Characteristics of the first recorded spider (Arthropoda: Arachnida fauna from Sheringal, Khyber Pakhtunkhwa, Pakistan

    Directory of Open Access Journals (Sweden)

    Farzana Khan Perveen

    2015-12-01

    Full Text Available The spiders (order: Aranae are an important environmental indicator and play a significant role as predators in biological control of the most of the key insect pests. The present study was conducted to establish the characteristics of the first recorded spider fauna from Sheringal, Dir Upper (DU, Khyber Pakhtunkhwa (KP, Pakistan during June 2013-July 2014. Their 10 species belong to 7 families, and 10 genera (nt=123: total; ni=77: identified; nui=46: unidentified were recorded in the 6 quadrates, i.e., Daramdala, Doki, Guryaal, Samang, Shahoor and Sia-Sheringal of Sheringal. The largest family was Lycosidae (wolf spiders with respect to size and numbers of specimens collected (n=20, which contained Arctosa littorali Simon, 1897; Hippasa partita Takidar, 1970; Pardosa distincta Backwall, 1867, while the smallest family was Gnphosidae (ground spiders (n=3 with Gnaphosa eucalyptus Ghafoor and Beg, 2002; while other families Sparassidae (huntsman spiders (n=19 Halconia insignis Thorell, 1836, and Isopeda tuhogniga Barrion and Litsinger, 1995, Opilionidae (harvestmen spiders (n=12 Hadrobunus grandis Sundevall, 1833; Pholcidae (cellar spider (n=10 have Crossopriza lyoni Blackwall, 1867; Hersiliidae (two-tailed spiders (n=6 is having Harsilia savignyi Lucas, 1836; (n=5 with Araneus diadematus Clerck, 1757 were recorded. It was concluded that 50% of the spiders collected from the study area were venomous. A detail study is required for further exploration of spider fauna of Sheringal, KP, Pakistan with special reference to their taxonomical, physiological and ecological characteristics.

  11. Integrated Network Analysis and Effective Tools in Plant Systems Biology

    Directory of Open Access Journals (Sweden)

    Atsushi eFukushima

    2014-11-01

    Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

  12. Optical surface profiling of orb-web spider capture silks

    Energy Technology Data Exchange (ETDEWEB)

    Kane, D M; Joyce, A M; Staib, G R [Department of Physics, Macquarie University, Sydney, NSW 2109 (Australia); Herberstein, M E, E-mail: deb.kane@mq.edu.a [Department of Biological Sciences, Macquarie University, Sydney, NSW 2109 (Australia)

    2010-09-15

    Much spider silk research to date has focused on its mechanical properties. However, the webs of many orb-web spiders have evolved for over 136 million years to evade visual detection by insect prey. It is therefore a photonic device in addition to being a mechanical device. Herein we use optical surface profiling of capture silks from the webs of adult female St Andrews cross spiders (Argiope keyserlingi) to successfully measure the geometry of adhesive silk droplets and to show a bowing in the aqueous layer on the spider capture silk between adhesive droplets. Optical surface profiling shows geometric features of the capture silk that have not been previously measured and contributes to understanding the links between the physical form and biological function. The research also demonstrates non-standard use of an optical surface profiler to measure the maximum width of a transparent micro-sized droplet (microlens).

  13. Optical surface profiling of orb-web spider capture silks

    International Nuclear Information System (INIS)

    Kane, D M; Joyce, A M; Staib, G R; Herberstein, M E

    2010-01-01

    Much spider silk research to date has focused on its mechanical properties. However, the webs of many orb-web spiders have evolved for over 136 million years to evade visual detection by insect prey. It is therefore a photonic device in addition to being a mechanical device. Herein we use optical surface profiling of capture silks from the webs of adult female St Andrews cross spiders (Argiope keyserlingi) to successfully measure the geometry of adhesive silk droplets and to show a bowing in the aqueous layer on the spider capture silk between adhesive droplets. Optical surface profiling shows geometric features of the capture silk that have not been previously measured and contributes to understanding the links between the physical form and biological function. The research also demonstrates non-standard use of an optical surface profiler to measure the maximum width of a transparent micro-sized droplet (microlens).

  14. Nutrient Deprivation Induces Property Variations in Spider Gluey Silk

    Science.gov (United States)

    Blamires, Sean J.; Sahni, Vasav; Dhinojwala, Ali; Blackledge, Todd A.; Tso, I-Min

    2014-01-01

    Understanding the mechanisms facilitating property variability in biological adhesives may promote biomimetic innovations. Spider gluey silks such as the spiral threads in orb webs and the gumfoot threads in cobwebs, both of which comprise of an axial thread coated by glue, are biological adhesives that have variable physical and chemical properties. Studies show that the physical and chemical properties of orb web gluey threads change when spiders are deprived of food. It is, however, unknown whether gumfoot threads undergo similar property variations when under nutritional stress. Here we tested whether protein deprivation induces similar variations in spiral and gumfoot thread morphology and stickiness. We manipulated protein intake for the orb web spider Nephila clavipes and the cobweb spider Latrodectus hesperus and measured the diameter, glue droplet volume, number of droplets per mm, axial thread width, thread stickiness and adhesive energy of their gluey silks. We found that the gluey silks of both species were stickier when the spiders were deprived of protein than when the spiders were fed protein. In N. clavipes a concomitant increase in glue droplet volume was found. Load-extension curves showed that protein deprivation induced glue property variations independent of the axial thread extensions in both species. We predicted that changes in salt composition of the glues were primarily responsible for the changes in stickiness of the silks, although changes in axial thread properties might also contribute. We, additionally, showed that N. clavipes' glue changes color under protein deprivation, probably as a consequence of changes to its biochemical composition. PMID:24523902

  15. Towards Integration of Biological and Physiological Functions at Multiple Levels

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

    Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

  16. Data Integration and Mining for Synthetic Biology Design.

    Science.gov (United States)

    Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

    2016-10-21

    One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

  17. Integrated pathway clusters with coherent biological themes for target prioritisation.

    Directory of Open Access Journals (Sweden)

    Yi-An Chen

    Full Text Available Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.

  18. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  19. The Spider Files

    Science.gov (United States)

    McDonald, James; Dominguez, Lynn

    2012-01-01

    As children develop misconceptions about animals they believe are dangerous, they also adopt attitudes that are difficult to change. Changing these attitudes is challenging for teachers. One animal that is easy to find but difficult for children to understand is a spider. As with most wild animals, they are difficult to teach about because…

  20. PATHWAYS TO SPIDER PHOBIA

    NARCIS (Netherlands)

    MERCKELBACH, H; ARNTZ, A; ARRINDELL, WA; DEJONG, PJ

    Using a revised version of the Phobic Origin Questionnaire (POQ; Ost, L. G. & Hugdahl, K. Behaviour Research and Therapy, 19,439-477; 1981), the present study examined whether conditioning experiences, modeling experiences, and/or informational learning experiences were more often reported by spider

  1. Spider Web Pattern

    Science.gov (United States)

    2006-01-01

    A delicate pattern, like that of a spider web, appears on top of the Mars residual polar cap, after the seasonal carbon-dioxide ice slab has disappeared. Next spring, these will likely mark the sites of vents when the carbon-dioxide ice cap returns. This Mars Global Surveyor, Mars Orbiter Camera image is about 3-kilometers wide (2-miles).

  2. Small Molecules from Spiders Used as Chemical Probes

    DEFF Research Database (Denmark)

    Olsen, Christian Adam; Kristensen, Anders S.; Strømgaard, Kristian

    2011-01-01

    Spiders are important species in ecological systems and as major predators of insects they are endowed with a plethora of low‐molecular‐weight natural products having intriguing biological activities. The isolation and biological characterization of these entities are well established, however......, only very recently have these compounds been used as templates for the design, synthesis, and biological evaluation of synthetic analogues. In contrast, the investigation of compounds responsible for chemical communication between spiders is far less developed, but recently new light has been shed onto...... the area of pheromones and allomones from spiders. Herein, we recapitulate these recent results, put them into perspective with previous findings, and provide an outlook for future studies of these chemotypes....

  3. West-Life, Tools for Integrative Structural Biology

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Structural biology is part of molecular biology focusing on determining structure of macromolecules inside living cells and cell membranes. As macromolecules determines most of the functions of cells the structural knowledge is very useful for further research in metabolism, physiology to application in pharmacology etc. As macromolecules are too small to be observed directly by light microscope, there are other methods used to determine the structure including nuclear magnetic resonance (NMR), X-Ray crystalography, cryo electron microscopy and others. Each method has it's advantages and disadvantages in the terms of availability, sample preparation, resolution. West-Life project has ambition to facilitate integrative approach using multiple techniques mentioned above. As there are already lot of software tools to process data produced by the techniques above, the challenge is to integrate them together in a way they can be used by experts in one technique but not experts in other techniques. One product ...

  4. Semiconductor Devices Inspired By and Integrated With Biology

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, John [University of Illinois

    2012-04-25

    Biology is curved, soft and elastic; silicon wafers are not. Semiconductor technologies that can bridge this gap in form and mechanics will create new opportunities in devices that adopt biologically inspired designs or require intimate integration with the human body. This talk describes the development of ideas for electronics that offer the performance of state-of-the-art, wafer- based systems but with the mechanical properties of a rubber band. We explain the underlying materials science and mechanics of these approaches, and illustrate their use in (1) bio- integrated, ‘tissue-like’ electronics with unique capabilities for mapping cardiac and neural electrophysiology, and (2) bio-inspired, ‘eyeball’ cameras with exceptional imaging properties enabled by curvilinear, Petzval designs.

  5. Early events in the evolution of spider silk genes.

    Directory of Open Access Journals (Sweden)

    James Starrett

    Full Text Available Silk spinning is essential to spider ecology and has had a key role in the expansive diversification of spiders. Silk is composed primarily of proteins called spidroins, which are encoded by a multi-gene family. Spidroins have been studied extensively in the derived clade, Orbiculariae (orb-weavers, from the suborder Araneomorphae ('true spiders'. Orbicularians produce a suite of different silks, and underlying this repertoire is a history of duplication and spidroin gene divergence. A second class of silk proteins, Egg Case Proteins (ECPs, is known only from the orbicularian species, Lactrodectus hesperus (Western black widow. In L. hesperus, ECPs bond with tubuliform spidroins to form egg case silk fibers. Because most of the phylogenetic diversity of spiders has not been sampled for their silk genes, there is limited understanding of spidroin gene family history and the prevalence of ECPs. Silk genes have not been reported from the suborder Mesothelae (segmented spiders, which diverged from all other spiders >380 million years ago, and sampling from Mygalomorphae (tarantulas, trapdoor spiders and basal araneomorph lineages is sparse. In comparison to orbicularians, mesotheles and mygalomorphs have a simpler silk biology and thus are hypothesized to have less diversity of silk genes. Here, we present cDNAs synthesized from the silk glands of six mygalomorph species, a mesothele, and a non-orbicularian araneomorph, and uncover a surprisingly rich silk gene diversity. In particular, we find ECP homologs in the mesothele, suggesting that ECPs were present in the common ancestor of extant spiders, and originally were not specialized to complex with tubuliform spidroins. Furthermore, gene-tree/species-tree reconciliation analysis reveals that numerous spidroin gene duplications occurred after the split between Mesothelae and Opisthothelae (Mygalomorphae plus Araneomorphae. We use the spidroin gene tree to reconstruct the evolution of amino acid

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

    Science.gov (United States)

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

    2015-06-08

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

  7. Teaching the fundamentals of biological data integration using classroom games.

    Directory of Open Access Journals (Sweden)

    Maria Victoria Schneider

    Full Text Available This article aims to introduce the nature of data integration to life scientists. Generally, the subject of data integration is not discussed outside the field of computational science and is not covered in any detail, or even neglected, when teaching/training trainees. End users (hereby defined as wet-lab trainees, clinicians, lab researchers will mostly interact with bioinformatics resources and tools through web interfaces that mask the user from the data integration processes. However, the lack of formal training or acquaintance with even simple database concepts and terminology often results in a real obstacle to the full comprehension of the resources and tools the end users wish to access. Understanding how data integration works is fundamental to empowering trainees to see the limitations as well as the possibilities when exploring, retrieving, and analysing biological data from databases. Here we introduce a game-based learning activity for training/teaching the topic of data integration that trainers/educators can adopt and adapt for their classroom. In particular we provide an example using DAS (Distributed Annotation Systems as a method for data integration.

  8. The preliminary assessment and isolation of entomopathogenic fungi to be used in biological control with twospotted spider mite [Tetranychus urticae (acari, tetranychidae)] from East Anatolia

    Science.gov (United States)

    Örtücü, Serkan; Algur, Ömer Faruk

    2017-04-01

    This study was conducted to isolation entomopathogenic fungi for possible use in biocontrol of two-spotted spider mite Tetranychus urticae Koch. and to determine their pathogenicity. For this purpose, plant leaves infected with T. urticae were collected from Erzurum, Kars and Ardahan. At laboratory, the internal and external mycoflora of T.urticae individuals on plant leaves were determined. As a result of isolation, twenty-five different fungi species belonging to the genera Acremonium, Alternaria, Aspergillus, Beauveria, Cladosporium, Gliocladium, Humicola, Penicillium, Trichoderma, Isaria, Ulocladium and Verticillium were obtained. Pathogenicity of this forty-five isolate belonging to twenty-five species were evaluated. As a test organism, T. urticae was used and suspensions (1 × 108conidia ml-1) were prepared in Tween 80. 2ml suspension of a single dose was sprayed onto down side of bean leaf discs using hand sprayer. Mortality was recorded daily for 7 days. A total of twelve isolates belonging to three species were determined to be pathogen against T.urticae. According to scale used: AT020 Isaria farinosa and AT025 Cladosporium cladosporioides were determined as least pathogen, AT037 and AT101 Beauveria bassiana, and AT019 and AT026 C. cladosporioides, and AT035 and AT036 I. farinosa as moderate pathogen, AT007, AT021, AT034 and AT076 B. bassiana as highly pathogen. The other thirty-three isolates found that not pathogenic against T.urticae.

  9. Graduate Curriculum for Biological Information Specialists: A Key to Integration of Scale in Biology

    Directory of Open Access Journals (Sweden)

    Carole L. Palmer

    2007-12-01

    Full Text Available Scientific data problems do not stand in isolation. They are part of a larger set of challenges associated with the escalation of scientific information and changes in scholarly communication in the digital environment. Biologists in particular are generating enormous sets of data at a high rate, and new discoveries in the biological sciences will increasingly depend on the integration of data across multiple scales. This work will require new kinds of information expertise in key areas. To build this professional capacity we have developed two complementary educational programs: a Biological Information Specialist (BIS masters degree and a concentration in Data Curation (DC. We believe that BISs will be central in the development of cyberinfrastructure and information services needed to facilitate interdisciplinary and multi-scale science. Here we present three sample cases from our current research projects to illustrate areas in which we expect information specialists to make important contributions to biological research practice.

  10. Integrative biology approach identifies cytokine targeting strategies for psoriasis.

    Science.gov (United States)

    Perera, Gayathri K; Ainali, Chrysanthi; Semenova, Ekaterina; Hundhausen, Christian; Barinaga, Guillermo; Kassen, Deepika; Williams, Andrew E; Mirza, Muddassar M; Balazs, Mercedesz; Wang, Xiaoting; Rodriguez, Robert Sanchez; Alendar, Andrej; Barker, Jonathan; Tsoka, Sophia; Ouyang, Wenjun; Nestle, Frank O

    2014-02-12

    Cytokines are critical checkpoints of inflammation. The treatment of human autoimmune disease has been revolutionized by targeting inflammatory cytokines as key drivers of disease pathogenesis. Despite this, there exist numerous pitfalls when translating preclinical data into the clinic. We developed an integrative biology approach combining human disease transcriptome data sets with clinically relevant in vivo models in an attempt to bridge this translational gap. We chose interleukin-22 (IL-22) as a model cytokine because of its potentially important proinflammatory role in epithelial tissues. Injection of IL-22 into normal human skin grafts produced marked inflammatory skin changes resembling human psoriasis. Injection of anti-IL-22 monoclonal antibody in a human xenotransplant model of psoriasis, developed specifically to test potential therapeutic candidates, efficiently blocked skin inflammation. Bioinformatic analysis integrating both the IL-22 and anti-IL-22 cytokine transcriptomes and mapping them onto a psoriasis disease gene coexpression network identified key cytokine-dependent hub genes. Using knockout mice and small-molecule blockade, we show that one of these hub genes, the so far unexplored serine/threonine kinase PIM1, is a critical checkpoint for human skin inflammation and potential future therapeutic target in psoriasis. Using in silico integration of human data sets and biological models, we were able to identify a new target in the treatment of psoriasis.

  11. Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

    DEFF Research Database (Denmark)

    Schoof, Erwin; Erler, Janine

    understanding of molecular processes which are fundamental to tumorigenesis. In Article 1, we propose a novel framework for how cancer mutations can be studied by taking into account their effect at the protein network level. In Article 2, we demonstrate how global, quantitative data on phosphorylation dynamics...... can be generated using MS, and how this can be modeled using a computational framework for deciphering kinase-substrate dynamics. This framework is described in depth in Article 3, and covers the design of KinomeXplorer, which allows the prediction of kinases responsible for modulating observed...... phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...

  12. Broadening Participation in the Society for Integrative and Comparative Biology.

    Science.gov (United States)

    Wilga, Cheryl A D; Nishiguchi, Michele; Tsukimura, Brian

    2017-07-01

    The goal of the Society for Integrative and Comparative Biology's Broadening Participation Committee (SICB BPC) is to increase the number of underrepresented group (URG) members within the society and to expand their capabilities as future researchers and leaders within SICB. Our short-term 10-year goal was to increase the recruitment and retention of URG members in the society by 10%. Our long-term 25-year goal is to increase the membership of URG in the society through recruitment and retention until the membership demographic mirrors that of the US Census. Our plans to accomplish this included establishment of a formal standing committee, establishment of a moderate budget to support BPC activities, hosting professional development workshops, hosting diversity and mentor socials, and obtaining grant funds to supplement our budget. This paper documents broadening participation activities in the society, discusses the effectiveness of these activities, and evaluates BPC goals after 5 years of targeted funded activities. Over the past 5 years, the number of URG members rose by 5.2% to a total of 16.2%, members who report ethnicity and gender increased by 25.2% and 18%, respectively, and the number of members attending BPC activities has increased to 33% by 2016. SICB has made significant advances in broadening participation, not only through increased expenditures, but also with a commitment by its members and leadership to increase diversity. Most members realize that increasing diversity will both improve the Society's ability to develop different approaches to tackling problems within integrative biology, and help solve larger global issues that are evident throughout science and technology fields. In addition, having URG members as part of the executive committee would provide other URG members role models within the society, as well as have a voice in the leadership that represents diversity and inclusion for all scientists. © The Author 2017. Published by

  13. Integrated MEMS/NEMS Resonant Cantilevers for Ultrasensitive Biological Detection

    Directory of Open Access Journals (Sweden)

    Xinxin Li

    2009-01-01

    Full Text Available The paper reviews the recent researches implemented in Chinese Academy of Sciences, with achievements on integrated resonant microcantilever sensors. In the resonant cantilevers, the self-sensing elements and resonance exciting elements are both top-down integrated with silicon micromachining techniques. Quite a lot of effort is focused on optimization of the resonance mode and sensing structure for improvement of sensitivity. On the other hand, to enable the micro-cantilevers specifically sensitive to bio/chemical molecules, sensing materials are developed and modified on the cantilever surface with a self-assembled monolayer (SAM based bottom-up construction and surface functionalization. To improve the selectivity of the sensors and depress environmental noise, multiple and localized surface modifications are developed. The achieved volume production capability and satisfactory detecting resolution to trace-level biological antigen of alpha-fetoprotein (AFP give the micro-cantilever sensors a great promise for rapid and high-resoluble detection.

  14. Animal coloration: sexy spider scales.

    Science.gov (United States)

    Taylor, Lisa A; McGraw, Kevin J

    2007-08-07

    Many male jumping spiders display vibrant colors that are used in visual communication. A recent microscopic study on a jumping spider from Singapore shows that three-layered 'scale sandwiches' of chitin and air are responsible for producing their brilliant iridescent body coloration.

  15. Spider Movement, UV Reflectance and Size, but Not Spider Crypsis, Affect the Response of Honeybees to Australian Crab Spiders

    Science.gov (United States)

    Llandres, Ana L.; Rodríguez-Gironés, Miguel A.

    2011-01-01

    According to the crypsis hypothesis, the ability of female crab spiders to change body colour and match the colour of flowers has been selected because flower visitors are less likely to detect spiders that match the colour of the flowers used as hunting platform. However, recent findings suggest that spider crypsis plays a minor role in predator detection and some studies even showed that pollinators can become attracted to flowers harbouring Australian crab spider when the UV contrast between spider and flower increases. Here we studied the response of Apis mellifera honeybees to the presence of white or yellow Thomisus spectabilis Australian crab spiders sitting on Bidens alba inflorescences and also the response of honeybees to crab spiders that we made easily detectable painting blue their forelimbs or abdomen. To account for the visual systems of crab spider's prey, we measured the reflectance properties of the spiders and inflorescences used for the experiments. We found that honeybees did not respond to the degree of matching between spiders and inflorescences (either chromatic or achromatic contrast): they responded similarly to white and yellow spiders, to control and painted spiders. However spider UV reflection, spider size and spider movement determined honeybee behaviour: the probability that honeybees landed on spider-harbouring inflorescences was greatest when the spiders were large and had high UV reflectance or when spiders were small and reflected little UV, and honeybees were more likely to reject inflorescences if spiders moved as the bee approached the inflorescence. Our study suggests that only the large, but not the small Australian crab spiders deceive their preys by reflecting UV light, and highlights the importance of other cues that elicited an anti-predator response in honeybees. PMID:21359183

  16. Spider movement, UV reflectance and size, but not spider crypsis, affect the response of honeybees to Australian crab spiders.

    Science.gov (United States)

    Llandres, Ana L; Rodríguez-Gironés, Miguel A

    2011-02-16

    According to the crypsis hypothesis, the ability of female crab spiders to change body colour and match the colour of flowers has been selected because flower visitors are less likely to detect spiders that match the colour of the flowers used as hunting platform. However, recent findings suggest that spider crypsis plays a minor role in predator detection and some studies even showed that pollinators can become attracted to flowers harbouring Australian crab spider when the UV contrast between spider and flower increases. Here we studied the response of Apis mellifera honeybees to the presence of white or yellow Thomisus spectabilis Australian crab spiders sitting on Bidens alba inflorescences and also the response of honeybees to crab spiders that we made easily detectable painting blue their forelimbs or abdomen. To account for the visual systems of crab spider's prey, we measured the reflectance properties of the spiders and inflorescences used for the experiments. We found that honeybees did not respond to the degree of matching between spiders and inflorescences (either chromatic or achromatic contrast): they responded similarly to white and yellow spiders, to control and painted spiders. However spider UV reflection, spider size and spider movement determined honeybee behaviour: the probability that honeybees landed on spider-harbouring inflorescences was greatest when the spiders were large and had high UV reflectance or when spiders were small and reflected little UV, and honeybees were more likely to reject inflorescences if spiders moved as the bee approached the inflorescence. Our study suggests that only the large, but not the small Australian crab spiders deceive their preys by reflecting UV light, and highlights the importance of other cues that elicited an anti-predator response in honeybees.

  17. Integration of ecological-biological thresholds in conservation decision making.

    Science.gov (United States)

    Mavrommati, Georgia; Bithas, Kostas; Borsuk, Mark E; Howarth, Richard B

    2016-12-01

    In the Anthropocene, coupled human and natural systems dominate and only a few natural systems remain relatively unaffected by human influence. On the one hand, conservation criteria based on areas of minimal human impact are not relevant to much of the biosphere. On the other hand, conservation criteria based on economic factors are problematic with respect to their ability to arrive at operational indicators of well-being that can be applied in practice over multiple generations. Coupled human and natural systems are subject to economic development which, under current management structures, tends to affect natural systems and cross planetary boundaries. Hence, designing and applying conservation criteria applicable in real-world systems where human and natural systems need to interact and sustainably coexist is essential. By recognizing the criticality of satisfying basic needs as well as the great uncertainty over the needs and preferences of future generations, we sought to incorporate conservation criteria based on minimal human impact into economic evaluation. These criteria require the conservation of environmental conditions such that the opportunity for intergenerational welfare optimization is maintained. Toward this end, we propose the integration of ecological-biological thresholds into decision making and use as an example the planetary-boundaries approach. Both conservation scientists and economists must be involved in defining operational ecological-biological thresholds that can be incorporated into economic thinking and reflect the objectives of conservation, sustainability, and intergenerational welfare optimization. © 2016 Society for Conservation Biology.

  18. Crab spiders (Araeneae: Philodromidae, Thomisidae) of Ramsey County, Minnesota.

    Science.gov (United States)

    Daniel. T. Jennings; Bruce Cutler

    1996-01-01

    Crab spiders of 2 families, 10 genera, and 35 species were collected over a 31-year period in Ramsey County, Minnesota. Rarely collected species included Philodromus keyserlingi, Xysticus pellax, X. chippewa, X. banksi and X. alboniger. Identification source(s), season and collection frequency, and biology are summarized for each species.

  19. Integration and macroevolutionary patterns in the pollination biology of conifers.

    Science.gov (United States)

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

    2015-06-01

    Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  20. High School Students' Attitudes Towards Spiders: A cross-cultural comparison

    Science.gov (United States)

    Prokop, Pavol; Tolarovičová, Andrea; Camerik, Anne M.; Peterková, Viera

    2010-08-01

    Spiders are traditionally considered to be among the least popular of animals. Current evidence suggests that a negative attitude towards spiders could be influenced by both cultural and evolutionary pressures. Some researchers suggest that science education activities could positively influence students' perceptions of spiders. Their evidence is, however, ambivalent. Using a five-point score Likert-type questionnaire in which the items were developed in a similar way to four of Kellert's categories of attitude (scientistic, negativistic, naturalistic, and ecologistic) towards invertebrates, we compared the level of knowledge of and attitudes towards spiders of high school students from two countries, Slovakia (n = 354) and South Africa (n = 382). The students represented different cultures and followed dissimilar science education curricula. Only among the Slovakian students there was a statistically significant but low correlation between knowledge and attitude (r = 0.30). The South African students scored higher in the categories of scientistic, naturalistic, and ecologistic attitudes. Comparison of attitude towards spiders of indigenous Africans from coeducational Catholic schools revealed that South African students have greater fear of spiders than Slovakian students, supporting the biological preparedness hypothesis. This hypothesis predicts a greater fear of spiders in South Africa than in Europe since several South African spiders possess venoms that are dangerous to humans. The results of this study are discussed from science education, cultural, and evolutionary perspectives.

  1. A spider elevator

    Energy Technology Data Exchange (ETDEWEB)

    Butylkin, A.V.; Butylkin, V.A.; Izosimov, A.M.

    1983-01-01

    A spider elevator is proposed which contains a body, a wedge clamp with wedges hinged to each other, a subassembly for holding the wedge clamp in the open and closed positions and a mechanism for changing the wedge clamp, which is made in the form of levers with ears for cleats and installed in the body with the capability of turning. To increase reliability in the operational mode through using the external force for clamping the pipe, the free ends of the levers are hinged with the body by a power cylinder.

  2. Integrated Ecological River Health Assessments, Based on Water Chemistry, Physical Habitat Quality and Biological Integrity

    Directory of Open Access Journals (Sweden)

    Ji Yoon Kim

    2015-11-01

    Full Text Available This study evaluated integrative river ecosystem health using stressor-based models of physical habitat health, chemical water health, and biological health of fish and identified multiple-stressor indicators influencing the ecosystem health. Integrated health responses (IHRs, based on star-plot approach, were calculated from qualitative habitat evaluation index (QHEI, nutrient pollution index (NPI, and index of biological integrity (IBI in four different longitudinal regions (Groups I–IV. For the calculations of IHRs values, multi-metric QHEI, NPI, and IBI models were developed and their criteria for the diagnosis of the health were determined. The longitudinal patterns of the river were analyzed by a self-organizing map (SOM model and the key major stressors in the river were identified by principal component analysis (PCA. Our model scores of integrated health responses (IHRs suggested that mid-stream and downstream regions were impaired, and the key stressors were closely associated with nutrient enrichment (N and P and organic matter pollutions from domestic wastewater disposal plants and urban sewage. This modeling approach of IHRs may be used as an effective tool for evaluations of integrative ecological river health..

  3. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  4. Integrated anaerobic/aerobic biological treatment for intensive swine production.

    Science.gov (United States)

    Bortone, Giuseppe

    2009-11-01

    Manure processing could help farmers to effectively manage nitrogen (N) surplus load. Many pig farms have to treat wastewater. Piggery wastewater treatment is a complex challenge, due to the high COD and N concentrations and low C/N ratio. Anaerobic digestion (AD) could be a convenient pre-treatment, particularly from the energetic view point and farm income, but this causes further reduction of C/N ratio and makes denitrification difficult. N removal can only be obtained integrating anaerobic/aerobic treatment by taking into account the best use of electron donors. Experiences gained in Italy during development of integrated biological treatment approaches for swine manure, from bench to full scale, are reported in this paper. Solid/liquid separation as pre-treatment of raw manure is an efficient strategy to facilitate liquid fraction treatment without significantly lowering C/N ratio. In Italy, two full scale SBRs showed excellent efficiency and reliability. Current renewable energy policy and incentives makes economically attractive the application of AD to the separated solid fraction using high solid anaerobic digester (HSAD) technology. Economic evaluation showed that energy production can reduce costs up to 60%, making sustainable the overall treatment.

  5. Biomimetic Spider Leg Joints: A Review from Biomechanical Research to Compliant Robotic Actuators

    Directory of Open Access Journals (Sweden)

    Stefan Landkammer

    2016-07-01

    Full Text Available Due to their inherent compliance, soft actuated joints are becoming increasingly important for robotic applications, especially when human-robot-interactions are expected. Several of these flexible actuators are inspired by biological models. One perfect showpiece for biomimetic robots is the spider leg, because it combines lightweight design and graceful movements with powerful and dynamic actuation. Building on this motivation, the review article focuses on compliant robotic joints inspired by the function principle of the spider leg. The mechanism is introduced by an overview of existing biological and biomechanical research. Thereupon a classification of robots that are bio-inspired by spider joints is presented. Based on this, the biomimetic robot applications referring to the spider principle are identified and discussed.

  6. Pegasys: software for executing and integrating analyses of biological sequences

    Directory of Open Access Journals (Sweden)

    Lett Drew

    2004-04-01

    Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

  7. Spiders from Mars?

    Science.gov (United States)

    2003-01-01

    MGS MOC Release No. MOC2-426, 19 July 2003No, this is not a picture of a giant, martian spider web. This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a plethora of polygonal features on the floor of a northern hemisphere impact crater near 65.6oN, 327.7oW. The picture was acquired during spring, after the seasonal carbon dioxide frost cap had largely migrated through the region. At the time the picture was taken, remnants of seasonal frost remained on the crater rim and on the edges of the troughs that bound each of the polygons. Frost often provides a helpful hint as to where polygons and patterned ground occur. The polygons, if they were on Earth, would indicate the presence of freeze-thaw cycles in ground ice. Although uncertain, the same might be true of Mars. Sunlight illuminates the scene from the lower left.

  8. Remote monitoring of vibrational information in spider webs

    Science.gov (United States)

    Mortimer, B.; Soler, A.; Siviour, C. R.; Vollrath, F.

    2018-06-01

    Spiders are fascinating model species to study information-acquisition strategies, with the web acting as an extension of the animal's body. Here, we compare the strategies of two orb-weaving spiders that acquire information through vibrations transmitted and filtered in the web. Whereas Araneus diadematus monitors web vibration directly on the web, Zygiella x-notata uses a signal thread to remotely monitor web vibration from a retreat, which gives added protection. We assess the implications of these two information-acquisition strategies on the quality of vibration information transfer, using laser Doppler vibrometry to measure vibrations of real webs and finite element analysis in computer models of webs. We observed that the signal thread imposed no biologically relevant time penalty for vibration propagation. However, loss of energy (attenuation) was a cost associated with remote monitoring via a signal thread. The findings have implications for the biological use of vibrations by spiders, including the mechanisms to locate and discriminate between vibration sources. We show that orb-weaver spiders are fascinating examples of organisms that modify their physical environment to shape their information-acquisition strategy.

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

    Science.gov (United States)

    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. Integrated self-powered microchip biosensor for endogenous biological cyanide.

    Science.gov (United States)

    Deng, Liu; Chen, Chaogui; Zhou, Ming; Guo, Shaojun; Wang, Erkang; Dong, Shaojun

    2010-05-15

    In this work we developed a fully integrated biofuel cell on a microchip, which consisted of glucose dehydrogenase supported (carbon nanotubes/thionine/gold nanoparticles)(8) multilayer as the anode, and the (carbon nanotubes/polylysine/laccase)(15) multilayer as the cathode. The as-obtained biofuel cell produced open circuit potential 620 mV and power density 302 microW cm(-2), showing great potential as a small power resource of portable electronics. Most importantly, for the first time we demonstrated the feasibility of developing a self-powered biosensor based on the inhibitive effect on microchip enzyme biofuel cell. With cyanide employed as the model analyte, this method showed a linear range of 3.0 x 10(-7) to 5.0 x 10(-4) M and a detection limit with 1.0 x 10(-7) M under the optimal conditions. The detection limit was lower than the acceptable cyanide concentration in drinking water (1.9 x 10(-6) M) according to the World Health Organization (WHO). This self-powered sensor was successfully used to detect the cyanide concentration in a real sample, cassava, which is the main carbohydrate resource in South America and Africa. This presented biosensor combined with a resistor and a multimeter demonstrated the general applicability as a fast and simple detection method in the determination of endogenous biological cyanide.

  11. Record breaking achievements by spiders and the scientists who study them.

    Science.gov (United States)

    Mammola, Stefano; Michalik, Peter; Hebets, Eileen A; Isaia, Marco

    2017-01-01

    Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students-as well as scientists themselves-into the biology of spiders, we compiled a list of 99 record breaking achievements by spiders (the "Spider World Records"). We chose a world-record style format, as this is known to be an effective way to intrigue readers of all ages. We highlighted, for example, the largest and smallest spiders, the largest prey eaten, the fastest runners, the highest fliers, the species with the longest sperm, the most venomous species, and many more. We hope that our compilation will inspire science educators to embrace the biology of spiders as a resource that engages students in science learning. By making these achievements accessible to non-arachnologists and arachnologists alike, we suggest that they could be used: (i) by educators to draw in students for science education, (ii) to highlight gaps in current organismal knowledge, and (iii) to suggest novel avenues for future research efforts. Our contribution is not meant to be comprehensive, but aims to raise public awareness on spiders, while also providing an initial database of their record breaking achievements.

  12. Sclerotherapy of Varicose Veins and Spider Veins

    Science.gov (United States)

    ... Index A-Z Sclerotherapy of Varicose Veins and Spider Veins Sclerotherapy uses injections from a very fine, ... Sclerotherapy? What is Sclerotherapy of Varicose Veins and Spider Veins? Sclerotherapy is a minimally invasive treatment used ...

  13. Application of 3 kinds of practical electromagnetic spiders in electromagnetic spider web

    OpenAIRE

    Jiang Min

    2016-01-01

    Electromagnetic spider web the launch circuit has introduced a lot, but in the center position of the utility of the spider generally have 3 kinds of circuits respectively, the use of single-chip microcomputer circuit of the low energy consumption spider by multi-channel transmission, single circuit receiver circuit. Direct use of the 3 channels of the spider and the use of PLC circuit spider, depending on the actual situation were placed.

  14. Application of 3 kinds of practical electromagnetic spiders in electromagnetic spider web

    Directory of Open Access Journals (Sweden)

    Jiang Min

    2016-01-01

    Full Text Available Electromagnetic spider web the launch circuit has introduced a lot, but in the center position of the utility of the spider generally have 3 kinds of circuits respectively, the use of single-chip microcomputer circuit of the low energy consumption spider by multi-channel transmission, single circuit receiver circuit. Direct use of the 3 channels of the spider and the use of PLC circuit spider, depending on the actual situation were placed.

  15. Spider phylogenomics: untangling the Spider Tree of Life

    Directory of Open Access Journals (Sweden)

    Nicole L. Garrison

    2016-02-01

    Full Text Available Spiders (Order Araneae are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results

  16. Spider phylogenomics: untangling the Spider Tree of Life

    Science.gov (United States)

    Garrison, Nicole L.; Rodriguez, Juanita; Agnarsson, Ingi; Coddington, Jonathan A.; Griswold, Charles E.; Hamilton, Christopher A.; Hedin, Marshal; Kocot, Kevin M.; Ledford, Joel M.

    2016-01-01

    Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the “usual suspect” genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the

  17. Approach and avoidance in fear of spiders

    NARCIS (Netherlands)

    Rinck, M.; Becker, E.S.

    2007-01-01

    We examined attitudes towards spiders by employing an Approach-Avoidance Task, in which participants respond to pictures by pulling a joystick towards themselves or by pushing it away from themselves. For spider fearfuls, this stimulus–response assignment is either compatible (push spiders away) or

  18. Spider and burnable poison rod combinations

    International Nuclear Information System (INIS)

    Edwards, G.T.; Schluderberg, D.C.

    1980-01-01

    An improved design of burnable poison rods and associated spiders used in fuel assemblies of pressurized water power reactor cores, is described. The rods are joined to the spider arms in a manner which is proof against the reactor core environment and yet allows the removal of the rods from the spider simply, swiftly and delicately. (U.K.)

  19. Redefining Perineural Invasion: Integration of Biology With Clinical Outcome.

    Science.gov (United States)

    Schmitd, Ligia B; Beesley, Lauren J; Russo, Nickole; Bellile, Emily L; Inglehart, Ronald C; Liu, Min; Romanowicz, Genevieve; Wolf, Gregory T; Taylor, Jeremy M G; D'Silva, Nisha J

    2018-05-22

    A diagnosis of perineural invasion (PNI), defined as cancer within or surrounding at least 33% of the nerve, leads to selection of aggressive treatment in squamous cell carcinoma (SCC). Recent mechanistic studies show that cancer and nerves interact prior to physical contact. The purpose of this study was to explore cancer-nerve interactions relative to clinical outcome. Biopsy specimens from 71 patients with oral cavity SCC were stained with hematoxylin and eosin and immunohistochemical (IHC; cytokeratin, S100, GAP43, Tuj1) stains. Using current criteria, PNI detection was increased with IHC. Overall survival (OS) tended to be poor for patients with PNI (P = .098). OS was significantly lower for patients with minimum tumor-nerve distance smaller than 5 μm (P = .011). The estimated relative death rate decreased as the nerve-tumor distance increased; there was a gradual drop off in death rate from distance equal to zero that stabilized around 500 μm. In PNI-negative patients, nerve diameter was significantly related to OS (HR 2.88, 95%CI[1.11,7.49]). Among PNI-negative nerves, larger nerve-tumor distance and smaller nerve diameter were significantly related to better OS, even when adjusting for T-stage and age (HR 0.82, 95% CI[0.72,0.92]; HR 1.27, 95% CI[1.00,1.62], respectively). GAP43, a marker for neuronal outgrowth, stained less than Tuj1 in nerves at greater distances from tumor (OR 0.76, 95% CI[0.73,0.79]); more GAP43 staining was associated with PNI. Findings from a small group of patients suggest that nerve parameters other than presence of PNI can influence outcome and that current criteria of PNI need to be re-evaluated to integrate recent biological discoveries. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Web building and silk properties functionally covary among species of wolf spider.

    Science.gov (United States)

    Lacava, Mariángeles; Camargo, Arley; Garcia, Luis F; Benamú, Marco A; Santana, Martin; Fang, Jian; Wang, Xungai; Blamires, Sean J

    2018-04-15

    Although phylogenetic studies have shown covariation between the properties of spider major ampullate (MA) silk and web building, both spider webs and silks are highly plastic so we cannot be sure whether these traits functionally covary or just vary across environments that the spiders occupy. As MaSp2-like proteins provide MA silk with greater extensibility, their presence is considered necessary for spider webs to effectively capture prey. Wolf spiders (Lycosidae) are predominantly non-web building, but a select few species build webs. We accordingly collected MA silk from two web-building and six non-web-building species found in semirural ecosystems in Uruguay to test whether the presence of MaSp2-like proteins (indicated by amino acid composition, silk mechanical properties and silk nanostructures) was associated with web building across the group. The web-building and non-web-building species were from disparate subfamilies so we estimated a genetic phylogeny to perform appropriate comparisons. For all of the properties measured, we found differences between web-building and non-web-building species. A phylogenetic regression model confirmed that web building and not phylogenetic inertia influences silk properties. Our study definitively showed an ecological influence over spider silk properties. We expect that the presence of the MaSp2-like proteins and the subsequent nanostructures improves the mechanical performance of silks within the webs. Our study furthers our understanding of spider web and silk co-evolution and the ecological implications of spider silk properties. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

  1. Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

    Science.gov (United States)

    Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

    2007-01-01

    Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

  2. Brown spider dermonecrotic toxin directly induces nephrotoxicity

    International Nuclear Information System (INIS)

    Chaim, Olga Meiri; Sade, Youssef Bacila; Bertoni da Silveira, Rafael; Toma, Leny; Kalapothakis, Evanguedes; Chavez-Olortegui, Carlos; Mangili, Oldemir Carlos; Gremski, Waldemiro; Dietrich, Carl Peter von; Nader, Helena B.; Sanches Veiga, Silvio

    2006-01-01

    Brown spider (Loxosceles genus) venom can induce dermonecrotic lesions at the bite site and systemic manifestations including fever, vomiting, convulsions, disseminated intravascular coagulation, hemolytic anemia and acute renal failure. The venom is composed of a mixture of proteins with several molecules biochemically and biologically well characterized. The mechanism by which the venom induces renal damage is unknown. By using mice exposed to Loxosceles intermedia recombinant dermonecrotic toxin (LiRecDT), we showed direct induction of renal injuries. Microscopic analysis of renal biopsies from dermonecrotic toxin-treated mice showed histological alterations including glomerular edema and tubular necrosis. Hyalinization of tubules with deposition of proteinaceous material in the tubule lumen, tubule epithelial cell vacuoles, tubular edema and epithelial cell lysis was also observed. Leukocytic infiltration was neither observed in the glomerulus nor the tubules. Renal vessels showed no sign of inflammatory response. Additionally, biochemical analyses showed such toxin-induced changes in renal function as urine alkalinization, hematuria and azotemia with elevation of blood urea nitrogen levels. Immunofluorescence with dermonecrotic toxin antibodies and confocal microscopy analysis showed deposition and direct binding of this toxin to renal intrinsic structures. By immunoblotting with a hyperimmune dermonecrotic toxin antiserum on renal lysates from toxin-treated mice, we detected a positive signal at the region of 33-35 kDa, which strengthens the idea that renal failure is directly induced by dermonecrotic toxin. Immunofluorescence reaction with dermonecrotic toxin antibodies revealed deposition and binding of this toxin directly in MDCK epithelial cells in culture. Similarly, dermonecrotic toxin treatment caused morphological alterations of MDCK cells including cytoplasmic vacuoles, blebs, evoked impaired spreading and detached cells from each other and from

  3. Multiple origins of subsociality in crab spiders (Thomisidae).

    Science.gov (United States)

    Ruch, Jasmin; Riehl, Torben; May-Collado, Laura J; Agnarsson, Ingi

    2015-01-01

    Determining factors that facilitate the transition from a solitary to a social lifestyle is a major challenge in evolutionary biology, especially in taxa that are usually aggressive towards conspecifics. Most spiders live solitarily and few species are known to be social. Nevertheless, sociality has evolved multiple times across several families and nearly all studied social lineages have originated from a periodically social (subsocial) ancestor. Group-living crab spiders (Thomisidae) are exclusively found in Australia and differ from most other social spiders because they lack a communal capture web. Three of the group-living species were placed in the genus Diaea and another in the genus Xysticus. Most Australian thomisids are, however, difficult to identify as most descriptions are old and of poor quality, and the genera Diaea and Xysticus may not correspond to monophyletic groups. Here, we clarify the phylogenetic relationships of the four group-living Australian thomisids and conclude that amongst these subsociality has evolved two to three times independently. The subsocial Xysticus bimaculatus is not closely related to any of the social Diaea and an independent origin of subsociality is likely in this case. The presented data indicates that within Diaea two origins of subsociality are possible. Our results help to understand the evolution of sociality in thomisids and support the hypothesis that permanent sociality in spiders has evolved multiple times relatively recently from subsocial ancestors. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

    Science.gov (United States)

    Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

    2014-11-01

    The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

  5. On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education

    Science.gov (United States)

    Feser, Jason; Vasaly, Helen; Herrera, Jose

    2013-01-01

    In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and the…

  6. Ecotoxicological effects of buprofezin on fecundity, growth, development, and predation of the wolf spider Pirata piratoides (Schenkel).

    Science.gov (United States)

    Deng, Lingling; Xu, Muqi; Cao, Hong; Dai, Jiayin

    2008-11-01

    The toxicological effects of buprofezin, an insect growth regulator, on the fecundity, development, and pest control potential of the wolf spider Pirata piratoides (Schenkel) (Araneae: Lycosidae) were investigated in the laboratory. It was shown that buprofezin had low toxicity to P. piratoides and that the median lethal dosage (LD(50)) 48 h and 10% lethal dosage (LD(10)) after topical application for female spiders were 653 and 316 mg buprofezin/mg fresh weight of spider, respectively. Buprofezin significantly reduced the percent hatching of spiders' eggs but had only a slight effect on egg production. No negative effects on the development and growth were observed. However, spider predation rates were strongly affected: Insecticide-treated females predated on fewer prey than the controls, and their predation rate did not recover even 5 days after insecticide application. This indicated that their pest control potential might be influenced by buprofezin, and the use of buprofezin in biological control of insects is discussed.

  7. Toward an interactive article: integrating journals and biological databases

    Directory of Open Access Journals (Sweden)

    Marygold Steven J

    2011-05-01

    Full Text Available Abstract Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to

  8. Reconstitutable control rod spider assembly

    International Nuclear Information System (INIS)

    Shallenberger, J.M.; Ferian, S.J.

    1990-01-01

    A reconstitutable control rod/spider assembly includes a hollow connecting finger of the spider having a pair of opposing flat segments formed on the interior thereof and engaging a pair of opposing flat sectors formed on the exterior of a stem extending form the upper end of control rod. The stem also has an externally-threaded portion engaging a nut and a pilot aligning portion for the nut. The nut has a radially flexible and expandable thread-defining element captured in its bore. The segments and sectors allow the rod to be removed and reattached after turning through 180 0 to allow more even wear on the rod. (author)

  9. Comparação econômica entre controle biológico e químico para o manejo de ácaro-vermelho em macieira Economic comparison of biological and chemical control in the management of red spider mites in apple orchard

    Directory of Open Access Journals (Sweden)

    Lino Bittencourt Monteiro

    2006-12-01

    Full Text Available O ácaro-vermelho da macieira, Panonychus ulmi (Acari: Tetranychidae, é uma importante praga na cultura da macieira em Fraiburgo - SC, e o controle biológico aplicado foi implantado em meados dos anos 90. O objetivo deste trabalho foi demonstrar os benefícios econômicos da utilização do controle biológico no manejo do ácaro-vermelho. A avaliação foi realizada em dois pomares comerciais de macieiras. Em um deles, foi implantado o controle biológico aplicado de ácaros, baseado na liberação do ácaro predador Neoseiulus californicus (Acari: Phytoseiidae, seleção de inseticidas e manejo de ervas invasoras, e o outro pomar seguiu o manejo convencional de artrópodes, baseado na aplicação de produtos químicos para o controle de insetos, ácaros fitófagos e ervas invasoras. A análise econômica mostrou que os custos com mão-de-obra e máquinas foram semelhantes em ambos os pomares, entretanto os custos com acaricidas foram significativamente inferiores no pomar onde o manejo foi o controle biológico, demonstrando que, apesar da necessidade de investimentos em instalações para a criação do ácaro predador e custos de manutenção das mesmas, a estratégia biológica foi economicamente viável.Red spider mite, Panonychus ulmi (Acari: Tetranychidae is a significant pest in apple tree in Fraiburgo, Santa Catarina (SC and applied biological control was implemented in the mid-nineties. The objective of this study was to demonstrate the economic benefits of biological control in the management of red spider mite. The assessment was carried out in two commercial orchards, one of which was subjected to biological control of spider mite by releasing the predator Neoseiulus californicus, insecticide selection and weed management, and the other to conventional arthropod management, based on the application of chemicals to control insects, phytofagous mites and weed. Economic analysis showed that the costs for labor and machines were

  10. Analysis of transcriptomes of three orb-web spider species reveals gene profiles involved in silk and toxin.

    Science.gov (United States)

    Zhao, Ying-Jun; Zeng, Yan; Chen, Lei; Dong, Yang; Wang, Wen

    2014-12-01

    As an ancient arthropod with a history of 390 million years, spiders evolved numerous morphological forms resulting from adaptation to different environments. The venom and silk of spiders, which have promising commercial applications in agriculture, medicine and engineering fields, are of special interests to researchers. However, little is known about their genomic components, which hinders not only understanding spider biology but also utilizing their valuable genes. Here we report on deep sequenced and de novo assembled transcriptomes of three orb-web spider species, Gasteracantha arcuata, Nasoonaria sinensis and Gasteracantha hasselti which are distributed in tropical forests of south China. With Illumina paired-end RNA-seq technology, 54 871, 101 855 and 75 455 unigenes for the three spider species were obtained, respectively, among which 9 300, 10 001 and 10 494 unique genes are annotated, respectively. From these annotated unigenes, we comprehensively analyzed silk and toxin gene components and structures for the three spider species. Our study provides valuable transcriptome data for three spider species which previously lacked any genetic/genomic data. The results have laid the first fundamental genomic basis for exploiting gene resources from these spiders. © 2013 Institute of Zoology, Chinese Academy of Sciences.

  11. The ITER Neutral Beam Test Facility towards SPIDER operation

    Science.gov (United States)

    Toigo, V.; Dal Bello, S.; Gaio, E.; Luchetta, A.; Pasqualotto, R.; Zaccaria, P.; Bigi, M.; Chitarin, G.; Marcuzzi, D.; Pomaro, N.; Serianni, G.; Agostinetti, P.; Agostini, M.; Antoni, V.; Aprile, D.; Baltador, C.; Barbisan, M.; Battistella, M.; Boldrin, M.; Brombin, M.; Dalla Palma, M.; De Lorenzi, A.; Delogu, R.; De Muri, M.; Fellin, F.; Ferro, A.; Gambetta, G.; Grando, L.; Jain, P.; Maistrello, A.; Manduchi, G.; Marconato, N.; Pavei, M.; Peruzzo, S.; Pilan, N.; Pimazzoni, A.; Piovan, R.; Recchia, M.; Rizzolo, A.; Sartori, E.; Siragusa, M.; Spada, E.; Spagnolo, S.; Spolaore, M.; Taliercio, C.; Valente, M.; Veltri, P.; Zamengo, A.; Zaniol, B.; Zanotto, L.; Zaupa, M.; Boilson, D.; Graceffa, J.; Svensson, L.; Schunke, B.; Decamps, H.; Urbani, M.; Kushwah, M.; Chareyre, J.; Singh, M.; Bonicelli, T.; Agarici, G.; Garbuglia, A.; Masiello, A.; Paolucci, F.; Simon, M.; Bailly-Maitre, L.; Bragulat, E.; Gomez, G.; Gutierrez, D.; Mico, G.; Moreno, J.-F.; Pilard, V.; Chakraborty, A.; Baruah, U.; Rotti, C.; Patel, H.; Nagaraju, M. V.; Singh, N. P.; Patel, A.; Dhola, H.; Raval, B.; Fantz, U.; Fröschle, M.; Heinemann, B.; Kraus, W.; Nocentini, R.; Riedl, R.; Schiesko, L.; Wimmer, C.; Wünderlich, D.; Cavenago, M.; Croci, G.; Gorini, G.; Rebai, M.; Muraro, A.; Tardocchi, M.; Hemsworth, R.

    2017-08-01

    SPIDER is one of two projects of the ITER Neutral Beam Test Facility under construction in Padova, Italy, at the Consorzio RFX premises. It will have a 100 keV beam source with a full-size prototype of the radiofrequency ion source for the ITER neutral beam injector (NBI) and also, similar to the ITER diagnostic neutral beam, it is designed to operate with a pulse length of up to 3600 s, featuring an ITER-like magnetic filter field configuration (for high extraction of negative ions) and caesium oven (for high production of negative ions) layout as well as a wide set of diagnostics. These features will allow a reproduction of the ion source operation in ITER, which cannot be done in any other existing test facility. SPIDER realization is well advanced and the first operation is expected at the beginning of 2018, with the mission of achieving the ITER heating and diagnostic NBI ion source requirements and of improving its performance in terms of reliability and availability. This paper mainly focuses on the preparation of the first SPIDER operations—integration and testing of SPIDER components, completion and implementation of diagnostics and control and formulation of operation and research plan, based on a staged strategy.

  12. IntegromeDB: an integrated system and biological search engine.

    Science.gov (United States)

    Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

    2012-01-19

    With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

  13. THE EXECUTION OF PLANNED DETOURS BY SPIDER-EATING PREDATORS

    Science.gov (United States)

    Cross, Fiona R.; Jackson, Robert R.

    2016-01-01

    Many spiders from the salticid subfamily Spartaeinae specialize at preying on other spiders and they adopt complex strategies when targeting these dangerous prey. We tested 15 of these spider-eating spartaeine species for the capacity to plan detours ahead of time. Each trial began with the test subject on top of a tower from which it could view two boxes: one containing prey and the other not containing prey. The distance between the tower and the boxes was too far to reach by leaping and the tower sat on a platform surrounded by water. As the species studied are known to avoid water, the only way they could reach the prey without getting wet was by taking one of two circuitous walkways from the platform: one leading to the prey (‘correct’) and one not leading to the prey (‘incorrect’). After leaving the tower, the test subject could not see the prey and sometimes it had to walk past the incorrect walkway before reaching the correct walkway. Yet all 15 species chose the correct walkway significantly more often than the incorrect walkway. We propose that these findings exemplify genuine cognition based on representation. PMID:26781057

  14. Atomic force microscope with integrated optical microscope for biological applications

    OpenAIRE

    Putman, Constant A.J.; Putman, C.A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Segerink, Franciscus B.; Greve, Jan

    1992-01-01

    Since atomic force microscopy (AFM) is capable of imaging nonconducting surfaces, the technique holds great promises for high‐resolution imaging of biological specimens. A disadvantage of most AFMs is the fact that the relatively large sample surface has to be scanned multiple times to pinpoint a specific biological object of interest. Here an AFM is presented which has an incorporated inverted optical microscope. The optical image from the optical microscope is not obscured by the cantilever...

  15. Integrating biological redesign: where synthetic biology came from and where it needs to go.

    Science.gov (United States)

    Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

    2014-03-27

    Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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.

  17. The Spider and the Fly

    Science.gov (United States)

    Mellinger, Keith E.; Viglione, Raymond

    2012-01-01

    The Spider and the Fly puzzle, originally attributed to the great puzzler Henry Ernest Dudeney, and now over 100 years old, asks for the shortest path between two points on a particular square prism. We explore a generalization, find that the original solution only holds in certain cases, and suggest how this discovery might be used in the…

  18. BIOLOGÍA Y ECOLOGÍA DE LA ARAÑA PLATEADA Argiope argentata (Fabricius, 1775 (ARANEIDAE EN UN SECTOR XERÓFILO DEL NORESTE DE LA PENÍNSULA DE ARAYA, VENEZUELA | BIOLOGY AND ECOLOGY OF SILVER SPIDER Argiope argentata (Fabricius, 1775 (ARANEIDAE XERIC SECTOR IN NORTHEAST PENINSULA ARAYA, VENEZUELA

    Directory of Open Access Journals (Sweden)

    Robert Velásquez Escalante

    2016-08-01

    Full Text Available Despite the important role they play in ecosystems spiders as predators of invertebrates in the country, they have been little studied. In order to present some aspects of the biology and ecological role in ecosystems of northeastern Venezuela, two populations of Argiope argentata were studied (in mangrove and dry forest in the vicinity of Guayacán. Direct capture was used by manually collected as unique method of sampling and extensive observations of the bodies were performed in the field. In the cobwebs we sought: male and female, wrapped preys and web decoration; the height of the cloth on the ground and used to secure the substrate was determined. Xerófilo habitat in 25 spiders were observed, while in the mangrove were 75, most females (60 and only eight males. Cobwebs (n = 86, they are mainly found in plants of Avicennia sp. and Prosopis sp. Which they were built in the middle and lower vegetation (40-80 cm were the most successful in capturing prey (all insects, mainly Diptera and have a cross web decoration. These preliminary results contribute, no doubt, to the knowledge of the natural history of populations Argiope Araya peninsula.

  19. VIPR III VADR SPIDER Structural Design and Analysis

    Science.gov (United States)

    Li, Wesley; Chen, Tony

    2016-01-01

    In support of the National Aeronautics and Space Administration (NASA) Vehicle Integrated Propulsion Research (VIPR) Phase III team to evaluate the volcanic ash environment effects on the Pratt & Whitney F117-PW-100 turbofan engine, NASA Armstrong Flight Research Center has successfully performed structural design and analysis on the Volcanic Ash Distribution Rig (VADR) and the Structural Particulate Integration Device for Engine Research (SPIDER) for the ash ingestion test. Static and dynamic load analyses were performed to ensure no structural failure would occur during the test. Modal analysis was conducted, and the results were used to develop engine power setting avoidance zones. These engine power setting avoidance zones were defined to minimize the dwell time when the natural frequencies of the VADR/SPIDER system coincided with the excitation frequencies of the engine which was operating at various revolutions per minute. Vortex-induced vibration due to engine suction air flow during the ingestion test was also evaluated, but was not a concern.

  20. KinomeXplorer: an integrated platform for kinome biology studies

    DEFF Research Database (Denmark)

    Horn, Heiko; Schoof, Erwin; Kim, Jinho

    2014-01-01

    A letter to the editor is presented related to the KinomeXplorer, an integrated platform providing workflows to efficiently analyze phosphorylation dependent interaction networks or kinase signaling networks....

  1. Synthetic Spider Silk Production on a Laboratory Scale

    Science.gov (United States)

    Hsia, Yang; Gnesa, Eric; Pacheco, Ryan; Kohler, Kristin; Jeffery, Felicia; Vierra, Craig

    2012-01-01

    As society progresses and resources become scarcer, it is becoming increasingly important to cultivate new technologies that engineer next generation biomaterials with high performance properties. The development of these new structural materials must be rapid, cost-efficient and involve processing methodologies and products that are environmentally friendly and sustainable. Spiders spin a multitude of different fiber types with diverse mechanical properties, offering a rich source of next generation engineering materials for biomimicry that rival the best manmade and natural materials. Since the collection of large quantities of natural spider silk is impractical, synthetic silk production has the ability to provide scientists with access to an unlimited supply of threads. Therefore, if the spinning process can be streamlined and perfected, artificial spider fibers have the potential use for a broad range of applications ranging from body armor, surgical sutures, ropes and cables, tires, strings for musical instruments, and composites for aviation and aerospace technology. In order to advance the synthetic silk production process and to yield fibers that display low variance in their material properties from spin to spin, we developed a wet-spinning protocol that integrates expression of recombinant spider silk proteins in bacteria, purification and concentration of the proteins, followed by fiber extrusion and a mechanical post-spin treatment. This is the first visual representation that reveals a step-by-step process to spin and analyze artificial silk fibers on a laboratory scale. It also provides details to minimize the introduction of variability among fibers spun from the same spinning dope. Collectively, these methods will propel the process of artificial silk production, leading to higher quality fibers that surpass natural spider silks. PMID:22847722

  2. Biological removal of algae in an integrated pond system

    CSIR Research Space (South Africa)

    Meiring, PGJ

    1995-01-01

    Full Text Available A system of oxidation ponds in series with a biological trickling filter is described. It was known that this arrangement was incapable of reducing effectively the levels of algae present in the pond liquid even though nitrification was effected...

  3. Atomic force microscope with integrated optical microscope for biological applications

    NARCIS (Netherlands)

    Putman, Constant A.J.; Putman, C.A.J.; van der Werf, Kees; de Grooth, B.G.; van Hulst, N.F.; Segerink, Franciscus B.; Greve, Jan

    1992-01-01

    Since atomic force microscopy (AFM) is capable of imaging nonconducting surfaces, the technique holds great promises for high‐resolution imaging of biological specimens. A disadvantage of most AFMs is the fact that the relatively large sample surface has to be scanned multiple times to pinpoint a

  4. An Integrative Systems Biology Approach to Understanding Pulmonary Diseases

    NARCIS (Netherlands)

    Auffray, Charles; Adcock, Ian M.; Chung, Kian Fan; Djukanovic, Ratko; Pison, Christophe; Sterk, Peter J.

    2010-01-01

    Chronic inflammatory pulmonary diseases such as COPD and asthma are highly prevalent and associated with a major health burden worldwide. Despite a wealth of biologic and clinical information on normal and pathologic airway structure and function, the primary causes and mechanisms of disease remain

  5. DEMONSTRATION OF AN INTEGRATED, PASSIVE BIOLOGICAL TREATMENT PROCESS FOR AMD

    Science.gov (United States)

    An innovative, cost-effective, biological treatment process has been designed by MSE Technology Applications, Inc. to treat acid mine drainage (AMD). A pilot-scale demonstration is being conducted under the Mine Waste Technology Program using water flowing from an abandoned mine ...

  6. Biological soil crusts as an integral component of desert environments

    Science.gov (United States)

    Belnap, Jayne; Weber, Bettina

    2013-01-01

    The biology and ecology of biological soil crusts, a soil surface community of mosses, lichens, cyanobacteria, green algae, fungi, and bacteria, have only recently been a topic of research. Most efforts began in the western U.S. (Cameron, Harper, Rushforth, and St. Clair), Australia (Rogers), and Israel (Friedmann, Evenari, and Lange) in the late 1960s and 1970s (e.g., Friedmann et al. 1967; Evenari 1985reviewed in Harper and Marble 1988). However, these groups worked independently of each other and, in fact, were often not aware of each other’s work. In addition, biological soil crust communities were seen as more a novelty than a critical component of dryland ecosystems. Since then, researchers have investigated many different aspects of these communities and have shown that although small to microscopic, biological soil crusts are critical in many ecological processes of deserts. They often cover most of desert soil surfaces and substantially mediate inputs and outputs from desert soils (Belnap et al. 2003). They can be a large source of biodiversity for deserts, as they can contain more species than the surrounding vascular plant community (Rosentreter 1986). These communities are important in reducing soil erosion and increasing soil fertility through the capture of dust and the fixation of atmospheric nitrogen and carbon into forms available to other life forms (Elbert et al. 2012). Because of their many effects on soil characteristics, such as external and internal morphological characteristics, aggregate stability, soil moisture, and permeability, they also affect seed germination and establishment and local hydrological cycles. Covering up to 70% of the surface area in many arid and semi-arid regions around the world (Belnap and Lange 2003), biological soil crusts are a key component within desert environments.

  7. DNA barcodes for assessment of the biological integrity of aquatic ecosystems

    Science.gov (United States)

    Water quality regulations and aquatic ecosystem monitoring increasingly rely on direct assessments of biological integrity. Because these aquatic “bioassessments” evaluate the incidence and abundance of sensitive aquatic species, they are able to measure cumulative ecosystem eff...

  8. Biological data - Integrated acoustic and trawl survey of Pacific hake off the Pacific Coast

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Integrated acoustic and trawl surveys are used to assess the distribution, biomass, and biology of Pacific hake along the Pacific coasts of the United States and...

  9. Specialised use of working memory by Portia africana, a spider-eating salticid.

    Science.gov (United States)

    Cross, Fiona R; Jackson, Robert R

    2014-03-01

    Using expectancy-violation methods, we investigated the role of working memory in the predatory strategy of Portia africana, a salticid spider from Kenya that preys by preference on other spiders. One of this predator's tactics is to launch opportunistic leaping attacks on to other spiders in their webs. Focussing on this particular tactic, our experiments began with a test spider on a ramp facing a lure (dead prey spider mounted on a cork disc) that could be reached by leaping. After the test spider faced the lure for 30 s, we blocked the test spider's view of the lure by lowering an opaque shutter before the spider leapt. When the shutter was raised 90 s later, either the same lure came into view again (control) or a different lure came into view (experimental: different prey type in same orientation or same prey type in different orientation). We recorded attack frequency (number of test spiders that leapt at the lure) and attack latency (time elapsing between shutter being raised and spiders initiating a leap). Attack latencies in control trials were not significantly different from attack latencies in experimental trials, regardless of whether it was prey type or prey orientation that changed in the experimental trials. However, compared with test spiders in the no-change control trials, significantly fewer test spiders leapt when prey type changed. There was no significant effect on attack frequency when prey orientation changed. These findings suggest that this predator represents prey type independently of prey orientation.

  10. The evolution of sociality in spiders

    DEFF Research Database (Denmark)

    Lubin, Yael; Bilde, T.

    2007-01-01

    . Anelosimus (Theridiidae) C. Sociality in Spiders: An Evolutionary Dead End? V. Evolution and Maintenance of Sociality in Spiders: Relevant Models A. Kin Selection 1. Kin Recognition 2. Inbreeding and Kin Selection B. Multilevel Selection (Group Selection) C. Ecological Benefits D. Ecological Constraints E......I. Introducing Social Spiders II. Social and Subsocial Species: A Survey of Behavioral Traits III. Inbred Sociality in Spiders A. Cooperation Versus Competition: A Balancing Act B. Do Social Spiders Have Division of Labor? C. Colony Foundation: Propagule Dispersal Versus Fission D. Female......-Biased Colony Sex Ratios: Primary and Operational Sex Ratios E. Mating System: Inbreeding and Its Population-Genetic Consequences F. "Boom and Bust" Colony Dynamics IV. Phylogenetic Relationships Among Social Spider Species A. Common Features of Social Evolution B. Case Studies 1. Stegodyphus (Eresidae) 2...

  11. Radiation effect onto biodiversity of spiders

    International Nuclear Information System (INIS)

    Mehrabova, M.A.; Naghiyev, J.A; Huseynov, N.I; Topchiyeva, Sh.A.; Hasanov, N.H.

    2010-01-01

    At present time spiders are one of the considerably diverse groups of living organisms in fauna of Azerbayjan Republic. They play an important in environmental chain, being the main group of wild arthropodas in most biocoenoses. Therefore, it's not surprised that recently an increased interest has being observed to the study of spiders as indicators of environmental conditions. Spiders have been collected in polluted areas, their identification and sampling of soil, water and plants has been conducted. The degree of radionuclides' impact on the number and distribution of spiders and their venom in the observed zones of Azerbaijan has been revealed and preliminarily predicted. The number of the collected spiders equals to 292 which has been determined later at an electronic identifier Spinnen Mitteleuropas. The radionuclides in spiders have been determined at Canberra facility. Different natural radioactive elements were revealed in the investigated samples.

  12. Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops

    Directory of Open Access Journals (Sweden)

    Hafiz Sohaib Ahmed Saqib

    2017-10-01

    Full Text Available Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies.

  13. Lean Big Data integration in systems biology and systems pharmacology.

    Science.gov (United States)

    Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan

    2014-09-01

    Data sets from recent large-scale projects can be integrated into one unified puzzle that can provide new insights into how drugs and genetic perturbations applied to human cells are linked to whole-organism phenotypes. Data that report how drugs affect the phenotype of human cell lines and how drugs induce changes in gene and protein expression in human cell lines can be combined with knowledge about human disease, side effects induced by drugs, and mouse phenotypes. Such data integration efforts can be achieved through the conversion of data from the various resources into single-node-type networks, gene-set libraries, or multipartite graphs. This approach can lead us to the identification of more relationships between genes, drugs, and phenotypes as well as benchmark computational and experimental methods. Overall, this lean 'Big Data' integration strategy will bring us closer toward the goal of realizing personalized medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Application of integrative genomics and systems biology to conventional and in vitro reproductive traits in cattle

    DEFF Research Database (Denmark)

    Mazzoni, Gianluca; Pedersen, Hanne S.; de Oliveira Junior, Gerson A.

    2017-01-01

    by both conventional and ARTs such as OPU-IVP. The integration of systems biology information across different biological layers generates a complete view of the different molecular networks that control complex traits and can provide a strong contribution to the understanding of traits related to ARTs....

  15. Campus Eco Tours: An Integrative & Interactive Field Project for Undergraduate Biology Students

    Science.gov (United States)

    Boes, Katie E.

    2013-01-01

    Outdoor areas within or near college campuses offer an opportunity for biology students to observe the natural world and apply concepts from class. Here, I describe an engaging and integrative project where undergraduate non-major biology students work in teams to develop and present professional "eco tours." This project takes place over multiple…

  16. Integr8: enhanced inter-operability of European molecular biology databases.

    Science.gov (United States)

    Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

    2003-01-01

    The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

  17. But what about the Empress of Racnoss? The allocation of attention to spiders and Doctor Who in a visual search task is predicted by fear and expertise.

    Science.gov (United States)

    Purkis, Helena M; Lester, Kathryn J; Field, Andy P

    2011-12-01

    If there is a spider in the room, then the spider phobic in your group is most likely to point it out to you. This phenomenon is believed to arise because our attentional systems are hardwired to attend to threat in our environment, and, to a spider phobic, spiders are threatening. However, an alternative explanation is simply that attention is quickly drawn to the stimulus of most personal relevance in the environment. Our research examined whether positive stimuli with no biological or evolutionary relevance could be allocated preferential attention. We compared attention to pictures of spiders with pictures from the TV program Doctor Who, for people who varied in both their love of Doctor Who and their fear of spiders. We found a double dissociation: interference from spider and Doctor-Who-related images in a visual search task was predicted by spider fear and Doctor Who expertise, respectively. As such, allocation of attention reflected the personal relevance of the images rather than their threat content. The attentional system believed to have a causal role in anxiety disorders is therefore likely to be a general system that responds not to threat but to stimulus relevance; hence, nonevolutionary images, such as those from Doctor Who, captured attention as quickly as fear-relevant spider images. Where this leaves the Empress of Racnoss, we are unsure. (c) 2011 APA, all rights reserved.

  18. Integrative Physiology 2.0’: integration of systems biology into physiology and its application to cardiovascular homeostasis

    Science.gov (United States)

    Kuster, Diederik W D; Merkus, Daphne; van der Velden, Jolanda; Verhoeven, Adrie J M; Duncker, Dirk J

    2011-01-01

    Since the completion of the Human Genome Project and the advent of the large scaled unbiased ‘-omics’ techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of single genes or proteins, towards a more holistic approach by studying networks and interactions between individual components of networks. From a conceptual standpoint, systems biology elicits a ‘back to the future’ experience for any integrative physiologist. However, many of the new techniques and modalities employed by systems biologists yield tremendous potential for integrative physiologists to expand their tool arsenal to (quantitatively) study complex biological processes, such as cardiac remodelling and heart failure, in a truly holistic fashion. We therefore advocate that systems biology should not become/stay a separate discipline with ‘-omics’ as its playing field, but should be integrated into physiology to create ‘Integrative Physiology 2.0’. PMID:21224228

  19. Parasitism of Trombidium brevimanum larvae on agrobiont linyphiid spiders from Germany.

    Science.gov (United States)

    Tomić, Vladimir; Mąkol, Joanna; Stamenković, Srdjan; Büchs, Wolfgang; Prescher, Sabine; Sivčev, Ivan; Graora, Draga; Sivčev, Lazar; Gotlin-Čuljak, Tatjana; Dudić, Boris

    2015-08-01

    An experiment on three differently-managed agricultural fields in Ahlum, Germany, which aimed at establishing the impact of different management systems on the biodiversity of predators and decomposers, yielded a significant number of spiders parasitized by larvae of Trombidium brevimanum (Actinotrichida, Parasitengona, Trombidiidae). Spider data from the whole sampling period (September 2010-July 2012), indicated that ectoparasitic larvae were recorded only on spiders in pitfall traps in the period of June-July 2011. In this period, only eight species of Linyphiidae--out of 42 species assigned to nine spider families recorded from the study area--were parasitized by mites; considerable levels of parasitism were recorded on Erigone atra, E. dentipalpis, and Oedothorax apicatus. The highest prevalence of parasitism was recorded on the organic field for E. atra (29%), while on the integrated and conventional fields significantly fewer parasitized spiders were observed. The preferred attachment sites on the spider host were regions with softer cuticle, especially regions on the carapace and on the abdomen, adjacent to the pedicel.

  20. Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

  1. Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

    DEFF Research Database (Denmark)

    Pfreundt, Andrea; Svendsen, Winnie Edith; Dimaki, Maria

    2016-01-01

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project...

  2. INTEGRATED MANAGEMENT OF CHROMOLAENA ODORATA EMPHASIZING THE CLASSICAL BIOLOGICAL CONTROL

    Directory of Open Access Journals (Sweden)

    SOEKISMAN TJITROSEMITO

    1998-01-01

    Full Text Available Chromolaena odorata, Siam weed, a very important weed of Java Island (Indonesia is native to Central and South America. In the laboratory it showed rapid growth (1.15 g/g/week in the first 8 weeks of its growth. The biomass was mainly as leaves (LAR : 317.50 cm'/g total weight. It slowed down in the following month as the biomass was utilized for stem and branch formation. This behavior supported the growth of C. odorata into a very dense stand. It flowered, fruited during the dry season, and senesced following maturation of seeds from inflorescence branches. These branches dried out, but soon the stem resumed aggressive growth following the wet season. Leaf biomass was affected by the size of the stem in its early phase of regrowth, but later on it was more affected by the number of branches. The introduction of Pareuchaetes pseudoinsulata to Indonesia, was successful only in North Sumatera. In Java it has not been reported to establish succesfully. The introduction of another biological control agent, Procecidochares conneca to Indonesia was shown to be sp ecific and upon release in West Java it established immediately. It spread exponentia lly in the first 6 months of its release. Field monitoring continues to eval uate the impact of the agents. Other biocontrol agents (Actmole anteas and Conotrachelus wilt be introduced to Indonesia in 1997 through ACIAR Project on the Biological Control of Chromolaena odorata in Indonesia and Papua New Guinea.

  3. Ion transport through biological membranes an integrated theoretical approach

    CERN Document Server

    Mackey, Michael C

    1975-01-01

    This book illustrates some of the ways physics and mathematics have been, and are being, used to elucidate the underlying mechan­ isms of passive ion movement through biological membranes in general, and the membranes of excltable cells in particular. I have made no effort to be comprehensive in my introduction of biological material and the reader interested in a brief account of single cell electro­ physlology from a physically-oriented biologists viewpoint will find the chapters by Woodbury (1965) an excellent introduction. Part I is introductory in nature, exploring the basic electrical properties of inexcitable and excitable cell plasma membranes. Cable theory is utilized to illustrate the function of the non-decrementing action potential as a signaling mechanism for the long range trans­ mission of information in the nervous system, and to gain some in­ sight into the gross behaviour of neurons. The detailed analysis of Hodgkin and Huxley on the squid giant axon membrane ionic conductance properties...

  4. Bayesian integration of position and orientation cues in perception of biological and non-biological dynamic forms

    Directory of Open Access Journals (Sweden)

    Steven Matthew Thurman

    2014-02-01

    Full Text Available Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic

  5. BioInt: an integrative biological object-oriented application framework and interpreter.

    Science.gov (United States)

    Desai, Sanket; Burra, Prasad

    2015-01-01

    BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

  6. Integrated modelling of physical, chemical and biological weather

    DEFF Research Database (Denmark)

    Kurganskiy, Alexander

    . This is an online-coupled meteorology-chemistry model where chemical constituents and different types of aerosols are an integrated part of the dynamical model, i.e., these constituents are transported in the same way as, e.g., water vapor and cloud water, and, at the same time, the aerosols can interactively...... impact radiation and cloud micro-physics. The birch pollen modelling study has been performed for domains covering Europe and western Russia. Verification of the simulated birch pollen concentrations against in-situ observations showed good agreement obtaining the best score for two Danish sites...

  7. Integration of biological networks and gene expression data using Cytoscape

    DEFF Research Database (Denmark)

    Cline, M.S.; Smoot, M.; Cerami, E.

    2007-01-01

    of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules......Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context...... and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape....

  8. Gravity Reception and Cardiac Function in the Spider

    Science.gov (United States)

    Finck, A.

    1985-01-01

    The following features of the arachnid gravity system were studied. (1) the absolute threshold to hyper-gz is quite low indicating fine proprioreceptive properties of the lyriform organ, the Gz/vibration detector; (2) the neurogenic heart of the spider is a good dependent variable for assessing its behavior to Gz and other stimuli which produce mechanical effects on the exoskeleton; (3) Not only is the cardiac response useful but it is now understood to be an integral part of the system which compensates for the consequences of gravity in the spider (an hydraulic leg extension); and (4) a theoretical model was proposed in which a mechanical amplifier, the leg lever, converts a weak force (at the tarsus) to a strong force (at the patella), capable of compressing the exoskeleton and consequently the lyriform receptor.

  9. A Usages of Herb Extracts by Stream Integrated with Micro-organism to Control Insect Pests and Phytophagus Mites by Biological Control

    Energy Technology Data Exchange (ETDEWEB)

    Uraisakul, Kanok [Rajamangala University of Technology Suvarnabhumi Phranakhonsiayathaya, Hantra Campus, Phranakhonsiayathaya (Thailand); Piadang, Nattaya [Office of Atoms for Peace, Bangkok (Thailand)

    2006-09-15

    A usages of herb extracts by stream integrated rith micro-organism to control insect pests and phytophagus mites by biological control was compared with insecticide to investigate the responses of chili tree and kieffer lime tree. Moreover, herb extracts were tested in controlling insect pests. Herb extracts were selected from many effective kinds such as: Azadirachta indica, Hyptis suaveolens, Citronella grass, Eucalyptus, Stemona, Galangal, Zingiber, cassumunar Roxb. Chronmolaena oderatum, Derris elyptica, Ginger, Annona seed, Malueraca sp., Andrographis paniculata, Veronia aquarrosa, Garlic, Thevetia peruviana, and Tobacco. The experiment was set at Herb Laboratory Ayutthaya Campus, Rajamangala University of Technology, Suvarnabhumi during August 2004 to June 2006. From testing herb extracts at 100 ppm. On Chili germination, the result was that the Chromolaena extracts made highest germination of 69.50%, Citronella grass at 500 ppm., made highest germination of chili seed at 86.00% within 12 days. Garlic extracts could kill 75.90% of aphids in 24 hrs., maximized in this experiments. Malueraca extracts at 500 ppm. Could kill 92.65% of chili aphids similar to the activity of insecticides action in 24 hrs. However at 5,000 ppm. It found that chemical treatment gave difference results from herbal treatments. Annona extracts could kill 64.58% of chili aphids better that others treatments. There are 18 treatment of time at 6 hrs. , 15 hrs., and 24 hrs., respectively. The results found that at 6 hrs., Kelthane could kill 93.75% of red spider mite. At 15 hrs. Stemona could kill 95.50% of red spider mite. At 24 hrs. Stemona or Chromolaena could kill 100% of red spider mite equally, Chrolaena could kill more than 83% of chili thrips at 24 hrs. Annona extracts could harvest the maximum of fruit fresh weight and numbers of fruits. After cutting leaves for producing new leaves, spraying herbal extracts was not different in statistic; however, Eucalyptus extracts, Neem plus

  10. A Usages of Herb Extracts by Stream Integrated with Micro-organism to Control Insect Pests and Phytophagus Mites by Biological Control

    International Nuclear Information System (INIS)

    Uraisakul, Kanok; Piadang, Nattaya

    2006-09-01

    A usages of herb extracts by stream integrated rith micro-organism to control insect pests and phytophagus mites by biological control was compared with insecticide to investigate the responses of chili tree and kieffer lime tree. Moreover, herb extracts were tested in controlling insect pests. Herb extracts were selected from many effective kinds such as: Azadirachta indica, Hyptis suaveolens, Citronella grass, Eucalyptus, Stemona, Galangal, Zingiber, cassumunar Roxb. Chronmolaena oderatum, Derris elyptica, Ginger, Annona seed, Malueraca sp., Andrographis paniculata, Veronia aquarrosa, Garlic, Thevetia peruviana, and Tobacco. The experiment was set at Herb Laboratory Ayutthaya Campus, Rajamangala University of Technology, Suvarnabhumi during August 2004 to June 2006. From testing herb extracts at 100 ppm. On Chili germination, the result was that the Chromolaena extracts made highest germination of 69.50%, Citronella grass at 500 ppm., made highest germination of chili seed at 86.00% within 12 days. Garlic extracts could kill 75.90% of aphids in 24 hrs., maximized in this experiments. Malueraca extracts at 500 ppm. Could kill 92.65% of chili aphids similar to the activity of insecticides action in 24 hrs. However at 5,000 ppm. It found that chemical treatment gave difference results from herbal treatments. Annona extracts could kill 64.58% of chili aphids better that others treatments. There are 18 treatment of time at 6 hrs. , 15 hrs., and 24 hrs., respectively. The results found that at 6 hrs., Kelthane could kill 93.75% of red spider mite. At 15 hrs. Stemona could kill 95.50% of red spider mite. At 24 hrs. Stemona or Chromolaena could kill 100% of red spider mite equally, Chrolaena could kill more than 83% of chili thrips at 24 hrs. Annona extracts could harvest the maximum of fruit fresh weight and numbers of fruits. After cutting leaves for producing new leaves, spraying herbal extracts was not different in statistic; however, Eucalyptus extracts, Neem plus

  11. Probabilistic Inference of Biological Networks via Data Integration

    Directory of Open Access Journals (Sweden)

    Mark F. Rogers

    2015-01-01

    Full Text Available There is significant interest in inferring the structure of subcellular networks of interaction. Here we consider supervised interactive network inference in which a reference set of known network links and nonlinks is used to train a classifier for predicting new links. Many types of data are relevant to inferring functional links between genes, motivating the use of data integration. We use pairwise kernels to predict novel links, along with multiple kernel learning to integrate distinct sources of data into a decision function. We evaluate various pairwise kernels to establish which are most informative and compare individual kernel accuracies with accuracies for weighted combinations. By associating a probability measure with classifier predictions, we enable cautious classification, which can increase accuracy by restricting predictions to high-confidence instances, and data cleaning that can mitigate the influence of mislabeled training instances. Although one pairwise kernel (the tensor product pairwise kernel appears to work best, different kernels may contribute complimentary information about interactions: experiments in S. cerevisiae (yeast reveal that a weighted combination of pairwise kernels applied to different types of data yields the highest predictive accuracy. Combined with cautious classification and data cleaning, we can achieve predictive accuracies of up to 99.6%.

  12. Seeds integrate biological information about conspecific and allospecific neighbours.

    Science.gov (United States)

    Yamawo, Akira; Mukai, Hiromi

    2017-06-28

    Numerous organisms integrate information from multiple sources and express adaptive behaviours, but how they do so at different developmental stages remains to be identified. Seeds, which are the embryonic stage of plants, need to make decisions about the timing of emergence in response to environmental cues related to survival. We investigated the timing of emergence of Plantago asiatica (Plantaginaceae) seed while manipulating the presence of Trifolium repens seed and the relatedness of neighbouring P. asiatica seed. The relatedness of neighbouring P. asiatica seed and the presence of seeds of T. repens did not on their own influence the timing of P. asiatica emergence. However, when encountering a T. repens seed, a P. asiatica seed emerged faster in the presence of a sibling seed than in the presence of a non-sibling seed. Water extracts of seeds gave the same result. We show that P. asiatica seeds integrate information about the relatedness of neighbouring P. asiatica seeds and the presence of seeds of a different species via water-soluble chemicals and adjust their emergence behaviour in response. These findings suggest the presence of kin-dependent interspecific interactions. © 2017 The Author(s).

  13. Tea saponin reduces the damage of Ectropis obliqua to tea crops, and exerts reduced effects on the spiders Ebrechtella tricuspidata and Evarcha albaria compared to chemical insecticides

    Directory of Open Access Journals (Sweden)

    Chi Zeng

    2018-03-01

    % diafenthiuron EC (43.33% and 36.67%, respectively. The highest controlling efficacy of 30% TS was 77.02% at 5 d after treatment, which showed no difference to 10% bifenthrin EC or 50% diafenthiuron SC. 30% TS was placed in the class N (harmless or slightly harmful of IOBC (International Organization of Biological Control categories for natural enemies, namely spiders. Conclusions Our results indicate that TS is a botanical insecticide that has a good controlling efficacy in E. obliqua larvae, which suggests it has promise as application in the integrated pest management (IPM envisaged for tea crops.

  14. Carbon sequestration, biological diversity, and sustainable development: Integrated forest management

    Energy Technology Data Exchange (ETDEWEB)

    Cairns, M.A. (Environmental Research Lab., Corvallis, OR (United States)); Meganck, R.A. (United Nations Environment Programme for the Wider Caribbean, Kingston (Jamaica))

    Tropical deforestation provides a significant contribution to anthropogenic increases in atmospheric CO[sub 2] concentration that may lead to global warming. Forestation and other forest management options to sequester CO[sub 2] in the tropical latitudes may fail unless they address local economic, social, environmental, and political needs of people in the developing world. Forest management is discussed in terms of three objectives: Carbon sequestration, sustainable development, and biodiversity conservation. An integrated forest management strategy of land-use planning is proposed to achieve these objectives and is centered around: Preservation of primary forest, intensified use of nontimber resources, agroforestry, and selective use of plantation forestry. 89 refs., 1 fig., 1 tab.

  15. Treatment of atrazine by integrating photocatalytic and biological processes

    International Nuclear Information System (INIS)

    Chan, C.Y.; Tao, S.; Dawson, R.; Wong, P.K.

    2004-01-01

    This research examines the degradation of atrazine by photocatalytic oxidation (PCO) under different experimental conditions. Deisopropylatrazine, deethylatrazine and deethyldeisopropylatrazine were formed as major intermediates based on gas chromatography-mass spectrometry. The reaction mixture was found to be toxic towards two bioassays, i.e. the Microtox[reg] and amphipods survival tests even when atrazine was completely degraded by PCO within 2 h under optimized conditions. The results indicate that adding H 2 O 2 could significantly enhance the degradation of atrazine by PCO. Ammeline, ammelide and cyanuric acid (CA) became the major intermediates/products as detected by high performance liquid chromatography from 6th to the 40th h of PCO treatment. After 72 h PCO treatment, only CA was detectable in the reaction mixture. Further degradation of CA was carried out by a newly isolated CA-degrading bacterium, Sphingomonas capsulata. The photochemical pretreatment integrated with microbial degradation lead to the complete degradation and detoxification of atrazine

  16. Value-Based Medicine and Integration of Tumor Biology.

    Science.gov (United States)

    Brooks, Gabriel A; Bosserman, Linda D; Mambetsariev, Isa; Salgia, Ravi

    2017-01-01

    Clinical oncology is in the midst of a genomic revolution, as molecular insights redefine our understanding of cancer biology. Greater awareness of the distinct aberrations that drive carcinogenesis is also contributing to a growing armamentarium of genomically targeted therapies. Although much work remains to better understand how to combine and sequence these therapies, improved outcomes for patients are becoming manifest. As we welcome this genomic revolution in cancer care, oncologists also must grapple with a number of practical problems. Costs of cancer care continue to grow, with targeted therapies responsible for an increasing proportion of spending. Rising costs are bringing the concept of value into sharper focus and challenging the oncology community with implementation of value-based cancer care. This article explores the ways that the genomic revolution is transforming cancer care, describes various frameworks for considering the value of genomically targeted therapies, and outlines key challenges for delivering on the promise of personalized cancer care. It highlights practical solutions for the implementation of value-based care, including investment in biomarker development and clinical trials to improve the efficacy of targeted therapy, the use of evidence-based clinical pathways, team-based care, computerized clinical decision support, and value-based payment approaches.

  17. Integrating fluid dynamic and biologic effects on staphylococci bacteria biofilms

    Science.gov (United States)

    Sherman, Erica; Endres, Jennifer; Bayles, Kenneth; Wei, Timothy

    2017-11-01

    Staphylococcus aureus bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. In previous work on biofilm growth and evolution in steady, laminar microchannel flows, it has been established that tower formation occurs around a very limited range of applied shear stresses centered on 0.6 dynes/cm2. Quantifying cell density characteristics as a function of time during biofilm formation reveals indicators of tower development hours before towers actually form and become visible. The next step in this research is to explore biological factors that might explain why this specific shear is so important. Additional studies with mutants, e.g. ica-A, that have been tied to tower formation have been conducted. The shear dependence of these mutants and their correlation to the behavior of wild type S. aureus is examined.

  18. Making United States Integrated Ocean Observing System (U.S. IOOS) inclusive of marine biological resources

    Science.gov (United States)

    Moustahfid, H.; Potemra, J.; Goldstein, P.; Mendelssohn, R.; Desrochers, A.

    2011-01-01

    An important Data Management and Communication (DMAC) goal is to enable a multi-disciplinary view of the ocean environment by facilitating discovery and integration of data from various sources, projects and scientific domains. United States Integrated Ocean Observing System (U.S. IOOS) DMAC functional requirements are based upon guidelines for standardized data access services, data formats, metadata, controlled vocabularies, and other conventions. So far, the data integration effort has focused on geophysical U.S. IOOS core variables such as temperature, salinity, ocean currents, etc. The IOOS Biological Observations Project is addressing the DMAC requirements that pertain to biological observations standards and interoperability applicable to U.S. IOOS and to various observing systems. Biological observations are highly heterogeneous and the variety of formats, logical structures, and sampling methods create significant challenges. Here we describe an informatics framework for biological observing data (e.g. species presence/absence and abundance data) that will expand information content and reconcile standards for the representation and integration of these biological observations for users to maximize the value of these observing data. We further propose that the approach described can be applied to other datasets generated in scientific observing surveys and will provide a vehicle for wider dissemination of biological observing data. We propose to employ data definition conventions that are well understood in U.S. IOOS and to combine these with ratified terminologies, policies and guidelines. ?? 2011 MTS.

  19. Science Education Resources on the Web--Spiders.

    Science.gov (United States)

    Thirunarayanan, M. O.

    1997-01-01

    Lists Web sites containing information on spiders and offers brief descriptions of the information available at those sites. The 11 sites provide information on taxonomy of spiders, anatomy, different ways spiders use silk, Internet mailing lists, folk literature and art, bibliographies, night collection, and spiders commonly found in the state of…

  20. Tangled in a sparse spider web

    DEFF Research Database (Denmark)

    Dimitrov, Dimitar Stefanov; Lopardo, Lara; Giribet, Gonzalo

    2012-01-01

    In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA ...

  1. Lignin valorization through integrated biological funneling and chemical catalysis

    Science.gov (United States)

    Linger, Jeffrey G.; Vardon, Derek R.; Guarnieri, Michael T.; Karp, Eric M.; Hunsinger, Glendon B.; Franden, Mary Ann; Johnson, Christopher W.; Chupka, Gina; Strathmann, Timothy J.; Pienkos, Philip T.; Beckham, Gregg T.

    2014-01-01

    Lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on Earth after cellulose. In production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. In nature, however, some organisms have evolved metabolic pathways that enable the utilization of lignin-derived aromatic molecules as carbon sources. Aromatic catabolism typically occurs via upper pathways that act as a “biological funnel” to convert heterogeneous substrates to central intermediates, such as protocatechuate or catechol. These intermediates undergo ring cleavage and are further converted via the β-ketoadipate pathway to central carbon metabolism. Here, we use a natural aromatic-catabolizing organism, Pseudomonas putida KT2440, to demonstrate that these aromatic metabolic pathways can be used to convert both aromatic model compounds and heterogeneous, lignin-enriched streams derived from pilot-scale biomass pretreatment into medium chain-length polyhydroxyalkanoates (mcl-PHAs). mcl-PHAs were then isolated from the cells and demonstrated to be similar in physicochemical properties to conventional carbohydrate-derived mcl-PHAs, which have applications as bioplastics. In a further demonstration of their utility, mcl-PHAs were catalytically converted to both chemical precursors and fuel-range hydrocarbons. Overall, this work demonstrates that the use of aromatic catabolic pathways enables an approach to valorize lignin by overcoming its inherent heterogeneity to produce fuels, chemicals, and materials. PMID:25092344

  2. Human evolution. Evolution of early Homo: an integrated biological perspective.

    Science.gov (United States)

    Antón, Susan C; Potts, Richard; Aiello, Leslie C

    2014-07-04

    Integration of evidence over the past decade has revised understandings about the major adaptations underlying the origin and early evolution of the genus Homo. Many features associated with Homo sapiens, including our large linear bodies, elongated hind limbs, large energy-expensive brains, reduced sexual dimorphism, increased carnivory, and unique life history traits, were once thought to have evolved near the origin of the genus in response to heightened aridity and open habitats in Africa. However, recent analyses of fossil, archaeological, and environmental data indicate that such traits did not arise as a single package. Instead, some arose substantially earlier and some later than previously thought. From ~2.5 to 1.5 million years ago, three lineages of early Homo evolved in a context of habitat instability and fragmentation on seasonal, intergenerational, and evolutionary time scales. These contexts gave a selective advantage to traits, such as dietary flexibility and larger body size, that facilitated survival in shifting environments. Copyright © 2014, American Association for the Advancement of Science.

  3. An integrated platform for assessing biologics (Conference Presentation)

    Science.gov (United States)

    Schein, Perry; O'Dell, Dakota; Erickson, David

    2016-04-01

    Protein therapeutics are a rapidly growing portion of the pharmaceuticals market and have many significant advantages over traditional small molecule drugs. As this market expands, however, critical regulatory and quality control issues remain, most notably the problem of protein aggregation. Individual target proteins often aggregate into larger masses which trigger an immune response in the body, which can reduce the efficacy of the drug for its intended purpose, or cause serious anaphylactic side-effects. Although detecting and minimizing aggregate formation is critical to ensure an effective product, aggregation dynamics are often highly complicated and there is little hope of reliable prediction and prevention from first principles. This problem is compounded for aggregates in the subvisible range of 100 nm to 10 micrometers where traditional techniques for detecting aggregates have significant limitations. Here, we present an integrated optofluidic platform for detecting nanoscale protein aggregates and characterizing interactions between these aggregates and a reference surface. By delivering light to a solution of proteins with an optical waveguide, scattered light from individual protein aggregates can be detected and analyzed to determine the force profile between each particle and the waveguide surface. Unlike existing methods which only determine size or charge, our label-free screening technique can directly measure the surface interaction forces between single aggregates and the glass substrate. This direct measurement capability may allow for better empirical predictions of the stability of protein aggregates during drug manufacturing and storage.

  4. Can Plant Defence Mechanisms Provide New Approaches for the Sustainable Control of the Two-Spotted Spider Mite Tetranychus urticae?

    Directory of Open Access Journals (Sweden)

    Blas Agut

    2018-02-01

    Full Text Available Tetranychus urticae (T. urticae Koch is a cosmopolitan, polyphagous mite which causes economic losses in both agricultural and ornamental plants. Some traits of T. urticae hamper its management, including a short life cycle, arrhenotokous parthenogenesis, its haplodiploid sex determination system, and its extraordinary ability to adapt to different hosts and environmental conditions. Currently, the use of chemical and biological control are the major control methods used against this mite. In recent years, some studies have focused on plant defence mechanisms against herbivores. Various families of plant compounds (such as flavonoids, glucosinolates, or acyl sugars have been shown to behave as acaricides. Plants can be induced upon appropriate stimuli to increase their resistance against spider mites. This knowledge, together with the understanding of mechanisms by which T. urticae detoxifies and adapts to pesticides, may complement the control of this pest. Herein, we describe plant volatile compounds (VOCs with repellent activity, and new findings about defence priming against spider mites, which interfere with the T. urticae performance. The use of VOCs and defence priming can be integrated into current management practices and reduce the damage caused by T. urticae in the field by implementing new, more sustainable crop management tools.

  5. Selfishness, warfare and economics; or integration, cooperation and biology

    Directory of Open Access Journals (Sweden)

    Emiliano Jesus Salvucci

    2012-05-01

    Full Text Available The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. Modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related with the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: Viruses are recognized as a macroorganism with a huge collection of genes, most unknown, that constitute the major planet's gene pool with a fundamental role in evolution. The hologenome theory considers an organism and all of its associated symbiotic microbes as a result of symbiopoiesis. Microbes, helmints, that normally are understood as parasites, are cohabitants and they have cohabited with their host and drives the evolution and existence of the partners. Each organism is a result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus and eukaryotic DNA and the interaction of its own genome with the genome of its microbiota resulting in an intertwined metabolism (a superorganism along evolution. These new interpretations are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.

  6. The biology of lysine acetylation integrates transcriptional programming and metabolism

    Directory of Open Access Journals (Sweden)

    Mujtaba Shiraz

    2011-03-01

    Full Text Available Abstract The biochemical landscape of lysine acetylation has expanded from a small number of proteins in the nucleus to a multitude of proteins in the cytoplasm. Since the first report confirming acetylation of the tumor suppressor protein p53 by a lysine acetyltransferase (KAT, there has been a surge in the identification of new, non-histone targets of KATs. Added to the known substrates of KATs are metabolic enzymes, cytoskeletal proteins, molecular chaperones, ribosomal proteins and nuclear import factors. Emerging studies demonstrate that no fewer than 2000 proteins in any particular cell type may undergo lysine acetylation. As described in this review, our analyses of cellular acetylated proteins using DAVID 6.7 bioinformatics resources have facilitated organization of acetylated proteins into functional clusters integral to cell signaling, the stress response, proteolysis, apoptosis, metabolism, and neuronal development. In addition, these clusters also depict association of acetylated proteins with human diseases. These findings not only support lysine acetylation as a widespread cellular phenomenon, but also impel questions to clarify the underlying molecular and cellular mechanisms governing target selectivity by KATs. Present challenges are to understand the molecular basis for the overlapping roles of KAT-containing co-activators, to differentiate between global versus dynamic acetylation marks, and to elucidate the physiological roles of acetylated proteins in biochemical pathways. In addition to discussing the cellular 'acetylome', a focus of this work is to present the widespread and dynamic nature of lysine acetylation and highlight the nexus that exists between epigenetic-directed transcriptional regulation and metabolism.

  7. The observation of biology implemented by integrated religion values in integrated Islamic school (Decriptive Study in X Integrated Senior Hight School Tasikmalaya)

    Science.gov (United States)

    Nurjanah, E.; Adisendjaja, Y. H.; Kusumastuti, M. N.

    2018-05-01

    The learning Integrated Religious value is one of the efforts to increase the motivation of learning and building the student character. This study aims to describe the application of Biology learning integrated religion values in Integrated Islamic School. Research methods used in this research is descriptive. Participants in this study involved the headmaster, headmaster of curriculum, biology teachers, boarding school teachers, the lead of boarding schools, and students. The instruments used are interview, observation and the student questionnaire about learning biology. The results showed that learning in X school consists of two curriculums, there was the curriculum of national education and curriculum of boarding school. The curriculum of national education referred to 2013 curriculum and boarding school curriculum referred to the curriculum of Salafi boarding school (Kitab Kuning). However, in its learning process not delivered integrated. The main obstacle to implementing the learning integrated religious values are 1) the background of general teacher education did not know of any connection between biology subject and subject that are studied in boarding school; 2) schools did not form the teaching team; 3) unavailability of materials integrated religious values.

  8. Verified spider bites in Oregon (USA) with the intent to assess hobo spider venom toxicity.

    Science.gov (United States)

    McKeown, Nathanael; Vetter, Richard S; Hendrickson, Robert G

    2014-06-01

    This study compiled 33 verified spider bites from the state of Oregon (USA). The initial goal was to amass a series of bites by the hobo spider to assess whether it possesses toxic venom, a supposition which is currently in a contested state. None of the 33 bites from several spider species developed significant medical symptoms nor did dermonecrosis occur. The most common biters were the yellow sac spider, Cheiracanthium mildei (N = 10) and orb-weavers of the genus Araneus (N = 6). There were 10 bites from three genera of funnel web spiders of the family Agelenidae including one hobo spider bite and one from the congeneric giant house spider which is readily confused as a hobo spider. The hobo spider bite resulted in pain, redness, twitching in the calf muscle and resolved in 12 h. Also generated from this study were possibly the first records of bites from spiders of the genera Callobius (Amaurobiidae) and Antrodiaetus (Antrodiaetidae), both with minor manifestations. Published by Elsevier Ltd.

  9. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    Science.gov (United States)

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  10. Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila

    OpenAIRE

    Kuntner, Matja?; Coddington, Jonathan A.

    2009-01-01

    Background More than 41,000 spider species are known with about 400?500 added each year, but for some well-known groups, such as the giant golden orbweavers, Nephila, the last valid described species dates from the 19th century. Nephila are renowned for being the largest web-spinning spiders, making the largest orb webs, and are model organisms for the study of extreme sexual size dimorphism (SSD) and sexual biology. Here, we report on the discovery of a new, giant Nephila species from Africa...

  11. Structure to function: Spider silk and human collagen

    Science.gov (United States)

    Rabotyagova, Olena S.

    Nature has the ability to assemble a variety of simple molecules into complex functional structures with diverse properties. Collagens, silks and muscles fibers are some examples of fibrous proteins with self-assembling properties. One of the great challenges facing Science is to mimic these designs in Nature to find a way to construct molecules that are capable of organizing into functional supra-structures by self-assembly. In order to do so, a construction kit consisting of molecular building blocks along with a complete understanding on how to form functional materials is required. In this current research, the focus is on spider silk and collagen as fibrous protein-based biopolymers that can shed light on how to generate nanostructures through the complex process of self-assembly. Spider silk in fiber form offers a unique combination of high elasticity, toughness, and mechanical strength, along with biological compatibility and biodegrability. Spider silk is an example of a natural block copolymer, in which hydrophobic and hydrophilic blocks are linked together generating polymers that organize into functional materials with extraordinary properties. Since silks resemble synthetic block copolymer systems, we adopted the principles of block copolymer design from the synthetic polymer literature to build block copolymers based on spider silk sequences. Moreover, we consider spider silk to be an important model with which to study the relationships between structure and properties in our system. Thus, the first part of this work was dedicated to a novel family of spider silk block copolymers, where we generated a new family of functional spider silk-like block copolymers through recombinant DNA technology. To provide fundamental insight into relationships between peptide primary sequence, block composition, and block length and observed morphological and structural features, we used these bioengineered spider silk block copolymers to study secondary structure

  12. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

    Science.gov (United States)

    Kohl, Kevin D

    2017-10-01

    Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  13. Integrating biological and social values when prioritizing places for biodiversity conservation.

    Science.gov (United States)

    Whitehead, Amy L; Kujala, Heini; Ives, Christopher D; Gordon, Ascelin; Lentini, Pia E; Wintle, Brendan A; Nicholson, Emily; Raymond, Christopher M

    2014-08-01

    The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes. © 2014 Society for Conservation Biology.

  14. Sperm dynamics in spiders (Araneae): ultrastructural analysis of the sperm activation process in the garden spider Argiope bruennichi (Scopoli, 1772).

    Science.gov (United States)

    Vöcking, Oliver; Uhl, Gabriele; Michalik, Peter

    2013-01-01

    Storage of sperm inside the female genital tract is an integral phase of reproduction in many animal species. The sperm storage site constitutes the arena for sperm activation, sperm competition and female sperm choice. Consequently, to understand animal mating systems information on the processes that occur from sperm transfer to fertilization is required. Here, we focus on sperm activation in spiders. Male spiders produce sperm whose cell components are coiled within the sperm cell and that are surrounded by a proteinaceous sheath. These inactive and encapsulated sperm are transferred to the female spermathecae where they are stored for later fertilization. We analyzed the ultrastructural changes of sperm cells during residency time in the female genital system of the orb-web spider Argiope bruennichi. We found three clearly distinguishable sperm conditions: encapsulated sperm (secretion sheath present), decapsulated (secretion sheath absent) and uncoiled sperm (cell components uncoiled, presumably activated). After insemination, sperm remain in the encapsulated condition for several days and become decapsulated after variable periods of time. A variable portion of the decapsulated sperm transforms rapidly to the uncoiled condition resulting in a simultaneous occurrence of decapsulated and uncoiled sperm. After oviposition, only decapsulated and uncoiled sperm are left in the spermathecae, strongly suggesting that the activation process is not reversible. Furthermore, we found four different types of secretion in the spermathecae which might play a role in the decapsulation and activation process.

  15. [Engineered spider silk: the intelligent biomaterial of the future. Part I].

    Science.gov (United States)

    Florczak, Anna; Piekoś, Konrad; Kaźmierska, Katarzyna; Mackiewicz, Andrzej; Dams-Kozłowska, Hanna

    2011-06-17

    The unique properties of spider silk such as strength, extensibility, toughness, biocompatibility and biodegradability are the reasons for the recent development in silk biomaterial technology. For a long time scientific progress was impeded by limited access to spider silk. However, the development of the molecular biology strategy was a breaking point in synthetic spider silk protein design. The sequences of engineered spider silk are based on the consensus motives of the corresponding natural equivalents. Moreover, the engineered silk proteins may be modified in order to gain a new function. The strategy of the hybrid proteins constructed on the DNA level combines the sequence of engineered silk, which is responsible for the biomaterial structure, with the sequence of polypeptide which allows functionalization of the silk biomaterial. The functional domains may comprise receptor binding sites, enzymes, metal or sugar binding sites and others. Currently, advanced research is being conducted, which on the one hand focuses on establishing the particular silk structure and understanding the process of silk thread formation in nature. On the other hand, there are attempts to improve methods of engineered spider silk protein production. Due to acquired knowledge and recent progress in synthetic protein technology, the engineered silk will turn into intelligent biomaterial of the future, while its industrial production scale will trigger a biotechnological revolution.

  16. Distinct spinning patterns gain differentiated loading tolerance of silk thread anchorages in spiders with different ecology.

    Science.gov (United States)

    Wolff, Jonas O; van der Meijden, Arie; Herberstein, Marie E

    2017-07-26

    Building behaviour in animals extends biological functions beyond bodies. Many studies have emphasized the role of behavioural programmes, physiology and extrinsic factors for the structure and function of buildings. Structure attachments associated with animal constructions offer yet unrealized research opportunities. Spiders build a variety of one- to three-dimensional structures from silk fibres. The evolution of economic web shapes as a key for ecological success in spiders has been related to the emergence of high performance silks and thread coating glues. However, the role of thread anchorages has been widely neglected in those models. Here, we show that orb-web (Araneidae) and hunting spiders (Sparassidae) use different silk application patterns that determine the structure and robustness of the joint in silk thread anchorages. Silk anchorages of orb-web spiders show a greater robustness against different loading situations, whereas the silk anchorages of hunting spiders have their highest pull-off resistance when loaded parallel to the substrate along the direction of dragline spinning. This suggests that the behavioural 'printing' of silk into attachment discs along with spinneret morphology was a prerequisite for the evolution of extended silk use in a three-dimensional space. This highlights the ecological role of attachments in the evolution of animal architectures. © 2017 The Author(s).

  17. Learned predation risk management by spider mites

    Directory of Open Access Journals (Sweden)

    Thomas eHackl

    2014-09-01

    Full Text Available Predation is a prime selective force shaping prey behavior. Investment in anti-predator behavior is traded-off against time and energy for other fitness-enhancing activities such as foraging or reproduction. To optimize this benefit/cost trade-off, prey should be able to innately and/or by experience modulate their behavior to the level of predation risk. Here, we assessed learned predation risk management in the herbivorous two-spotted spider mite Tetranychus urticae. We exposed spider mites coming from benign (naïve or high immediate predation risk (experienced environments to latent and/or no risk and assessed their site choice, activity and oviposition. Benign environments were characterized by the absence of any predator cues, high immediate risk environments by killed spider mites, physical presence of the predatory mite Phytoseiulus persimilis and associated chemosensory traces left on the surface, and latent risk environments by only predator traces. In the no-choice experiment both naïve and experienced spider mites laid their first egg later on leaves with than without predator traces. Irrespective of predator traces presence/absence, experienced mites laid their first egg earlier than naïve ones did. Naïve spider mites were more active, indicating higher restlessness, and laid fewer eggs on leaves with predator traces, whereas experienced mites were less active and laid similar numbers of eggs on leaves with and without predator traces. In the choice experiment both naïve and experienced spider mites preferentially resided and oviposited on leaves without predator traces but experienced mites were less active than naïve ones. Overall, our study suggests that spider mites experienced with high predation risk behave bolder under latent risk than naïve spider mites. Since predator traces alone do not indicate immediate risk, we argue that the attenuated anti-predator response of experienced spider mites represents adaptive learned

  18. Promoting Student Learning through the Integration of Lab and Lecture: The Seamless Biology Curriculum

    Science.gov (United States)

    Burrowes, Patricia; Nazario, Gladys

    2008-01-01

    The authors engaged in an education experiment to determine if the integration of lab and lecture activities in zoology and botany proved beneficial to student learning and motivation toward biology. Their results revealed that this strategy positively influenced students' academic achievement, conceptual understanding, and ability to apply…

  19. Understanding Spider-Man: Your Everyday Superhero

    OpenAIRE

    Falk, Nicklas; Blomsterberg, Sofie Amalie; Suciu, Alice Sabrina; Pedersen, Mads Peter; Lucas, Vilhelm

    2014-01-01

    This project focuses on the understanding of Spider-Man, and the morals and ethics that lie behind the choices he makes. Through the Dimensions Philosophy & Science/Text & Sign, this understanding is concluded by looking at ethical theories and comic book analysis. Based on the Ultimate Spider-Man comic book series, the aim is to clarify who Spider-Man is and what causes him to act in certain ways; before and after his realization of power. Some theories used to investigate these area...

  20. Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

    Science.gov (United States)

    Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

    2017-01-01

    Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

  1. Camels, Cormorants, and Kangaroo Rats: Integration and Synthesis in Organismal Biology After World War II.

    Science.gov (United States)

    Hagen, Joel B

    2015-01-01

    During the decades following World War II diverse groups of American biologists established a variety of distinctive approaches to organismal biology. Rhetorically, organismal biology could be used defensively to distinguish established research traditions from perceived threats from newly emerging fields such as molecular biology. But, organismal biologists were also interested in integrating biological disciplines and using a focus on organisms to synthesize levels of organization from molecules and cells to populations and communities. Part of this broad movement was the development of an area of research variously referred to as physiological ecology, environmental physiology, or ecophysiology. This area of research was distinctive in its self-conscious blend of field and laboratory practices and its explicit integration with other areas of biology such as ecology, animal behavior, and evolution in order to study adaptation. Comparing the intersecting careers of Knut Schmidt-Nielsen and George Bartholomew highlights two strikingly different approaches to physiological ecology. These alternative approaches to studying the interactions of organisms and environments also differed in important ways from the organismal biology championed by leading figures in the modern synthesis.

  2. A data integration approach for cell cycle analysis oriented to model simulation in systems biology

    Directory of Open Access Journals (Sweden)

    Mosca Ettore

    2007-08-01

    Full Text Available Abstract Background The cell cycle is one of the biological processes most frequently investigated in systems biology studies and it involves the knowledge of a large number of genes and networks of protein interactions. A deep knowledge of the molecular aspect of this biological process can contribute to making cancer research more accurate and innovative. In this context the mathematical modelling of the cell cycle has a relevant role to quantify the behaviour of each component of the systems. The mathematical modelling of a biological process such as the cell cycle allows a systemic description that helps to highlight some features such as emergent properties which could be hidden when the analysis is performed only from a reductionism point of view. Moreover, in modelling complex systems, a complete annotation of all the components is equally important to understand the interaction mechanism inside the network: for this reason data integration of the model components has high relevance in systems biology studies. Description In this work, we present a resource, the Cell Cycle Database, intended to support systems biology analysis on the Cell Cycle process, based on two organisms, yeast and mammalian. The database integrates information about genes and proteins involved in the cell cycle process, stores complete models of the interaction networks and allows the mathematical simulation over time of the quantitative behaviour of each component. To accomplish this task, we developed, a web interface for browsing information related to cell cycle genes, proteins and mathematical models. In this framework, we have implemented a pipeline which allows users to deal with the mathematical part of the models, in order to solve, using different variables, the ordinary differential equation systems that describe the biological process. Conclusion This integrated system is freely available in order to support systems biology research on the cell cycle and

  3. The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

    Science.gov (United States)

    Jacobsen, B J; Zidack, N K; Larson, B J

    2004-11-01

    ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

  4. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  5. Behavioural responses of two-spotted spider mites induced by predator-borne and prey-borne cues.

    Science.gov (United States)

    Gyuris, Enikő; Szép, Erna; Kontschán, Jenő; Hettyey, Attila; Tóth, Zoltán

    2017-11-01

    Applying predatory mites as biological control agents is a well established method against spider mites which are major pests worldwide. Although antipredator responses can influence the outcome of predator-prey interactions, we have limited information about what cues spider mites use to adjust their behavioural antipredator responses. We experimentally exposed two-spotted spider mites (Tetranychus urticae) to different predator-borne cues (using a specialist predator, Phytoseiulus persimilis, or a generalist predator, Amblyseius swirskii), conspecific prey-borne cues, or both, and measured locomotion and egg-laying activity. The reactions to predator species compared to each other manifested in reversed tendencies: spider mites increased their locomotion activity in the presence of P. persimilis, whereas they decreased it when exposed to A. swirskii. The strongest response was triggered by the presence of a killed conspecific: focal spider mites decreased their locomotion activity compared to the control group. Oviposition activity was not affected by either treatment. Our results point out that spider mites may change their behaviour in response to predators, and also to the presence of killed conspecifics, but these effects were not enhanced when both types of cues were present. The effect of social contacts among prey conspecifics on predator-induced behavioural defences is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Non-webbuilding spiders: prey specialists or generalists?

    Science.gov (United States)

    Nentwig, Wolfgang

    1986-07-01

    Feeding experiments were performed with seven species of non-webbuilding spiders and a variety of prey taxa. Some species were generally polyphagous whereas other spiders restricted their prey to a few groups. At one end of the spectrum of prey specialization the thomisid Misumena vatia is limited to a few taxa of possible prey (Table 1). The literature of prey records of non-webbuilding spiders is reviewed (Table 2) with special emphasis on oligophagous or monophagous spiders. Monophagous spiders are generally rare and have specialized on only a few prey taxa: social insects (ants, bees, termites) and spiders.

  7. Almost a spider: a 305-million-year-old fossil arachnid and spider origins.

    Science.gov (United States)

    Garwood, Russell J; Dunlop, Jason A; Selden, Paul A; Spencer, Alan R T; Atwood, Robert C; Vo, Nghia T; Drakopoulos, Michael

    2016-03-30

    Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasierigen. et sp. nov. from the Late Carboniferous (Stephanian,ca 305-299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian-Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies. © 2016 The Authors.

  8. Influence of Crop Management and Environmental Factors on Wolf Spider Assemblages (Araneae: Lycosidae) in an Australian Cotton Cropping System.

    Science.gov (United States)

    Rendon, Dalila; Whitehouse, Mary E A; Hulugalle, Nilantha R; Taylor, Phillip W

    2015-02-01

    Wolf spiders (Lycosidae) are the most abundant ground-hunting spiders in the Australian cotton (Gossypium hirsutum L.) agroecosystems. These spiders have potential in controlling pest bollworms, Helicoverpa spp. (Lepidoptera: Noctuidae) in minimum-tilled fields. A study was carried out during a wet growing season (2011-2012) in Narrabri, New South Wales, Australia, to determine how different crop rotations and tillage affect wolf spider assemblages in cotton fields. Spider abundance and species richness did not differ significantly between simple plots (no winter crop) and complex plots (cotton-wheat Triticum aestivum L.-vetch Vicia benghalensis L. rotation). However, the wolf spider biodiversity, as expressed by the Shannon-Weaver and Simpson's indices, was significantly higher in complex plots. Higher biodiversity reflected a more even distribution of the most dominant species (Venatrix konei Berland, Hogna crispipes Koch, and Tasmanicosa leuckartii Thorell) and the presence of more rare species in complex plots. T. leuckartii was more abundant in complex plots and appears to be sensitive to farming disturbances, whereas V. konei and H. crispipes were similarly abundant in the two plot types, suggesting higher resilience or recolonizing abilities. The demographic structure of these three species varied through the season, but not between plot types. Environmental variables had a significant effect on spider assemblage, but effects of environment and plot treatment were overshadowed by the seasonal progression of cotton stages. Maintaining a high density and even distribution of wolf spiders that prey on Helicoverpa spp. should be considered as a conservation biological control element when implementing agronomic and pest management strategies. © The Author 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

    Science.gov (United States)

    Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

    2016-02-01

    The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

  10. Edge effect on weevils and spiders

    OpenAIRE

    Horváth, R.; Magura, T.; Péter, G.; Tóthmérész, B.

    2002-01-01

    The edge effect on weevils and spiders was tested along oak forest – meadow transects using sweep-net samples at the Síkfökút Project in Hungary. For spiders the species richness was significantly higher in the forest edge than either in the meadow or the forest interior. For weevils the species richness of the forest edge was higher than that of the meadow, but the difference was not statistically significant whereas the species richness of the forest...

  11. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

    Directory of Open Access Journals (Sweden)

    Christley Scott

    2010-08-01

    Full Text Available Abstract Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent advent of programming for graphical processing units (GPU opens up the possibility of developing more integrative, detailed and predictive biological models while at the same time decreasing the computational cost to simulate those models. Results We construct a 3D model of epidermal development and provide a set of GPU algorithms that executes significantly faster than sequential central processing unit (CPU code. We provide a parallel implementation of the subcellular element method for individual cells residing in a lattice-free spatial environment. Each cell in our epidermal model includes an internal gene network, which integrates cellular interaction of Notch signaling together with environmental interaction of basement membrane adhesion, to specify cellular state and behaviors such as growth and division. We take a pedagogical approach to describing how modeling methods are efficiently implemented on the GPU including memory layout of data structures and functional decomposition. We discuss various programmatic issues and provide a set of design guidelines for GPU programming that are instructive to avoid common pitfalls as well as to extract performance from the GPU architecture. Conclusions We demonstrate that GPU algorithms represent a significant technological advance for the simulation of complex biological models. We further demonstrate with our epidermal model that the integration of multiple complex modeling methods for heterogeneous multicellular biological processes is both feasible and computationally tractable using this new technology. We hope that the provided algorithms and source code will be a

  12. Tav4SB: integrating tools for analysis of kinetic models of biological systems.

    Science.gov (United States)

    Rybiński, Mikołaj; Lula, Michał; Banasik, Paweł; Lasota, Sławomir; Gambin, Anna

    2012-04-05

    Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project's Web page: http://bioputer.mimuw.edu.pl/tav4sb/. The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

  13. Spiders do have melanin after all.

    Science.gov (United States)

    Hsiung, Bor-Kai; Blackledge, Todd A; Shawkey, Matthew D

    2015-11-01

    Melanin pigments are broadly distributed in nature - from bacteria to fungi to plants and animals. However, many previous attempts to identify melanins in spiders were unsuccessful, suggesting that these otherwise ubiquitous pigments were lost during spider evolution. Yet, spiders exhibit many dark colours similar to those produced by melanins in other organisms, and the low solubility of melanins makes isolation and characterization difficult. Therefore, whether melanins are truly absent or have simply not yet been detected is an open question. Raman spectroscopy provides a reliable way to detect melanins in situ, without the need for isolation. In this study, we document the presence of eumelanin in diverse species of spiders using confocal Raman microspectroscopy. Comparisons of spectra with theoretically calculated data falsify the previous hypothesis that dark colours are produced solely by ommochromes in spiders. Our data indicate that melanins are present in spiders and further supporting that they are present in most living organisms. © 2015. Published by The Company of Biologists Ltd.

  14. Genus-specificity of araneophagy of linyphiid spiders and spiders of other families (Arachnida, Araneae)

    NARCIS (Netherlands)

    Heuts, B.; Brunt, T.

    2009-01-01

    We found genus specificity of predation by spiders on other spiders in captivity which surpass them in body size (araneophagy). Adult specimens of three species of the linyphiid genus Walckenaeria which were successively tested for araneophagy (in the laboratory) in the order of first species

  15. Ant mimicry lessens predation on a North American jumping spider by larger salticid spiders.

    Science.gov (United States)

    Durkee, Caitlin A; Weiss, Martha R; Uma, Divya B

    2011-10-01

    Ant-like appearance (myrmecomorphy) has evolved >70 times in insects and spiders, accounting for >2,000 species of myrmecomorphic arthropods. Most myrmecomorphic spiders are considered to be Batesian mimics; that is, a palatable spider avoids predation through resemblance to an unpalatable ant-although this presumption has been tested in relatively few cases. Here we explicitly examined the extent to which Peckhamia picata (Salticidae), a North American ant-mimicking jumping spider, is protected from four species of jumping spider predators, relative to nonmimetic salticids and model ants. In addition, we conducted focused behavioral observations on one salticid predator, Thiodina puerpera, to determine the point at which the predators' behaviors toward model, mimic, and nonmimic diverge. We also examined the behaviors of Peckhamia in the presence of Thiodina. We found that mimetic jumping spiders were consumed less than a third as often as nonmimetic jumping spiders, suggesting that Peckhamia does indeed gain protection as a result of its resemblance to ants, and so can be considered a Batesian mimic. Furthermore, our focal predator did not consume any ant-mimicking spiders, and seemed to categorize Peckhamia with its model ant early in the hunting sequence. Such early determination of prey versus nonprey may be the result of speed-accuracy trade-offs in predator decision-making.

  16. Cognitive bias in spider-phobic children: Comparison of a pictorial and a linguistic spider Stroop.

    NARCIS (Netherlands)

    Kindt, M.; Brosschot, J.F.

    1999-01-01

    Examined the relation between spider fear in children and cognitive processing bias toward threatening information. It was investigated whether spider fear in children is related to a cognitive bias for threatening pictures and words. Pictorial and linguistic Stroop stimuli were administered to 28

  17. Measurement of the Ecological Integrity of Cerrado Streams Using Biological Metrics and the Index of Habitat Integrity

    Directory of Open Access Journals (Sweden)

    Deusiano Florêncio dos Reis

    2017-01-01

    Full Text Available Generally, aquatic communities reflect the effects of anthropogenic changes such as deforestation or organic pollution. The Cerrado stands among the most threatened ecosystems by human activities in Brazil. In order to evaluate the ecological integrity of the streams in a preserved watershed in the Northern Cerrado biome corresponding to a mosaic of ecosystems in transition to the Amazonia biome in Brazil, biological metrics related to diversity, structure, and sensitivity of aquatic macroinvertebrates were calculated. Sampling included collections along stretches of 200 m of nine streams and measurements of abiotic variables (temperature, electrical conductivity, pH, total dissolved solids, dissolved oxygen, and discharge and the Index of Habitat Integrity (HII. The values of the abiotic variables and the HII indicated that most of the streams have good ecological integrity, due to high oxygen levels and low concentrations of dissolved solids and electric conductivity. Two streams showed altered HII scores mainly related to small dams for recreational and domestic use, use of Cerrado natural pasture for cattle raising, and spot deforestation in bathing areas. However, this finding is not reflected in the biological metrics that were used. Considering all nine streams, only two showed satisfactory ecological quality (measured by Biological Monitoring Working Party (BMWP, total richness, and EPT (Ephemeroptera, Plecoptera, and Trichoptera richness, only one of which had a low HII score. These results indicate that punctual measures of abiotic parameters do not reveal the long-term impacts of anthropic activities in these streams, including related fire management of pasture that annually alters the vegetation matrix and may act as a disturbance for the macroinvertebrate communities. Due to this, biomonitoring of low order streams in Cerrado ecosystems of the Northern Central Brazil by different biotic metrics and also physical attributes of the

  18. Evaluation of the design effects of different agropastoral systems on the diversity and density of spiders

    Directory of Open Access Journals (Sweden)

    Melina S. Almada

    2017-04-01

    Full Text Available Sustainable agro-ecological design is challenging when the goal is self-regulation of the system. The objective of this study was to evaluate if the agropastoral design system affects the spider community, as spiders are the main predators in these production systems, and to determine those designs which maximize the diversity and density of spiders. The study was conducted during 2009/2010, at the Experimental Research Station of Agriculture (EEA-INTA Reconquista (Santa Fe, Argentina where we considered four different designs: C1 (five agricultural fields, C2 (three agricultural fields and four livestock fields, C3 (six agricultural fields and one livestock field and C4 (five agricultural fields and one forest area. In each design, the spiders were collected by pitfall traps and suction samples with a G-Vac (garden-vacuum. The designs proposed were considered on the basis of environmental heterogeneity. The C4 treatment had the greatest number of species, followed by C2, C3 and C1 (183, 178, 144 and 142 species, respectively, and C2 presented the greatest abundance of spiders followed by C4, C3 and C1 (n=5708, 4785, 4271 and 3448, respectively. Eight guilds were present in C3 and C4. This study is the first to evaluate the diversity of spiders in agropastoral systems in Argentina. Our results show that designs that include more fields with livestock or equal to those for agriculture, as well as forest areas, increase environmental heterogeneity. Therefore, the presence of a biological controller and dominant predatory group will be possible with sustainable designs that have environmental heterogeneity, contributing to improved pest control in agricultural systems.

  19. An RNA Virome Associated to the Golden Orb-Weaver Spider Nephila clavipes

    Directory of Open Access Journals (Sweden)

    Humberto J. Debat

    2017-10-01

    Full Text Available The golden orb-weaver spider Nephila clavipes, known for its sexual size dimorphism, is abundant and widespread in the New World. The first annotated genome of orb-weaver spiders, exploring N. clavipes, has recently been reported. The study, focused primarily on the diversity of silk specific genes, shed light into the complex evolutionary history of spiders. Furthermore, a robust transcriptome analysis provided a massive resource for N. clavipes RNA survey. Here, I present evidence of viral sequences corresponding to the first 10 extant virus species associated to N. clavipes and indeed, nephilids. The putatively new species are linked to ssRNA positive-strand viruses, such as Picornavirales, and to ssRNA negative-strand and dsRNA viruses. In addition, I detected sequence data of new strains of two recently reported arthropod viruses, which complemented and extended the corresponding sequence references. The identified viruses appear to be complete, potentially functional, and presenting the typical architecture and consistent viral domains. The intrinsic nature of the detected sequences and their absence in the recently generated genome assembly, suggest that they correspond to bona fide RNA virus sequences. The available RNA data allowed for the first time to address a tissue/organ specific analysis of virus loads/presence in spiders, suggesting a complex spatial and differential distribution of the tentative viruses, encompassing the spider brain and also silk and venom glands. Until recently, the virus landscape associated to spiders remained elusive. The discovered viruses described here provide only a fragmented glimpse of the potential magnitude of the Aranea virosphere. Future studies should focus not only on complementing and expanding these findings, but also on addressing the potential ecological role of these viruses, which might influence the biology of these outstanding arthropod species.

  20. Methods of integrating Islamic values in teaching biology for shaping attitude and character

    Science.gov (United States)

    Listyono; Supardi, K. I.; Hindarto, N.; Ridlo, S.

    2018-03-01

    Learning is expected to develop the potential of learners to have the spiritual attitude: moral strength, self-control, personality, intelligence, noble character, as well as the skills needed by themselves, society, and nation. Implementation of role and morale in learning is an alternative way which is expected to answer the challenge. The solution offered is to inject student with religious material Islamic in learning biology. The content value of materials teaching biology includes terms of practical value, religious values, daily life value, socio-political value, and the value of art. In Islamic religious values (Qur'an and Hadith) various methods can touch human feelings, souls, and generate motivation. Integrating learning with Islamic value can be done by the deductive or inductive approach. The appropriate method of integration is the amtsal (analog) method, hiwar (dialog) method, targhib & tarhib (encouragement & warning) method, and example method (giving a noble role model / good example). The right strategy in integrating Islamic values is outlined in the design of lesson plan. The integration of Islamic values in lesson plan will facilitate teachers to build students' character because Islamic values can be implemented in every learning steps so students will be accustomed to receiving the character value in this integrated learning.

  1. PathJam: a new service for integrating biological pathway information

    Directory of Open Access Journals (Sweden)

    Glez-Peña Daniel

    2010-03-01

    Full Text Available Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

  2. Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

    Science.gov (United States)

    Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

    2017-01-01

    Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

  3. Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

    Science.gov (United States)

    Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

    2011-01-01

    Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

  4. Spinning gland transcriptomics from two main clades of spiders (order: Araneae--insights on their molecular, anatomical and behavioral evolution.

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    Full Text Available Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade. Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i anatomical differentiation of spinning glands and (ii behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution.

  5. Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

    Science.gov (United States)

    Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

    2013-01-01

    Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

  6. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

    Directory of Open Access Journals (Sweden)

    Lo Kenneth

    2012-08-01

    Full Text Available Abstract Background Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge. Results We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models. Conclusions We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.

  7. Biologic and clinical aspects of integration of different bone substitutes in oral surgery: a literature review.

    Science.gov (United States)

    Zizzari, Vincenzo Luca; Zara, Susi; Tetè, Giulia; Vinci, Raffaele; Gherlone, Enrico; Cataldi, Amelia

    2016-10-01

    Many bone substitutes have been proposed for bone regeneration, and researchers have focused on the interactions occurring between grafts and host tissue, as the biologic response of host tissue is related to the origin of the biomaterial. Bone substitutes used in oral and maxillofacial surgery could be categorized according to their biologic origin and source as autologous bone graft when obtained from the same individual receiving the graft; homologous bone graft, or allograft, when harvested from an individual other than the one receiving the graft; animal-derived heterologous bone graft, or xenograft, when derived from a species other than human; and alloplastic graft, made of bone substitute of synthetic origin. The aim of this review is to describe the most commonly used bone substitutes, according to their origin, and to focus on the biologic events that ultimately lead to the integration of a biomaterial with the host tissue. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Improving integrative searching of systems chemical biology data using semantic annotation.

    Science.gov (United States)

    Chen, Bin; Ding, Ying; Wild, David J

    2012-03-08

    Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  9. Biological and psychological rhythms: an integrative approach to rhythm disturbances in autistic disorder.

    Science.gov (United States)

    Botbol, Michel; Cabon, Philippe; Kermarrec, Solenn; Tordjman, Sylvie

    2013-09-01

    Biological rhythms are crucial phenomena that are perfect examples of the adaptation of organisms to their environment. A considerable amount of work has described different types of biological rhythms (from circadian to ultradian), individual differences in their patterns and the complexity of their regulation. In particular, the regulation and maturation of the sleep-wake cycle have been thoroughly studied. Its desynchronization, both endogenous and exogenous, is now well understood, as are its consequences for cognitive impairments and health problems. From a completely different perspective, psychoanalysts have shown a growing interest in the rhythms of psychic life. This interest extends beyond the original focus of psychoanalysis on dreams and the sleep-wake cycle, incorporating central theoretical and practical psychoanalytic issues related to the core functioning of the psychic life: the rhythmic structures of drive dynamics, intersubjective developmental processes and psychic containment functions. Psychopathological and biological approaches to the study of infantile autism reveal the importance of specific biological and psychological rhythmic disturbances in this disorder. Considering data and hypotheses from both perspectives, this paper proposes an integrative approach to the study of these rhythmic disturbances and offers an etiopathogenic hypothesis based on this integrative approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Conservation Biology and Traditional Ecological Knowledge: Integrating Academic Disciplines for Better Conservation Practice

    Directory of Open Access Journals (Sweden)

    Joshua A. Drew

    2006-12-01

    Full Text Available Conservation biology and environmental anthropology are disciplines that are both concerned with the identification and preservation of diversity, in one case biological and in the other cultural. Both conservation biology and the study of traditional ecoloigcal knowledge function at the nexus of the social and natural worlds, yet historically there have been major impediments to integrating the two. Here we identify linguistic, cultural, and epistemological barriers between the two disciplines. We argue that the two disciplines are uniquely positioned to inform each other and to provide critical insights and new perspectives on the way these sciences are practiced. We conclude by synthesizing common themes found in conservation success stories, and by making several suggestions on integration. These include cross-disciplinary publication, expanding memberships in professional societies and conducting multidisciplinary research based on similar interests in ecological process, taxonomy, or geography. Finally, we argue that extinction threats, be they biological or cultural/linguistic are imminent, and that by bringing these disciplines together we may be able to forge synergistic conservation programs capable of protecting the vivid splendor of life on Earth.

  11. Improving integrative searching of systems chemical biology data using semantic annotation

    Directory of Open Access Journals (Sweden)

    Chen Bin

    2012-03-01

    Full Text Available Abstract Background Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. Results We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i simplifies the process of building SPARQL queries, (ii enables useful new kinds of queries on the data and (iii makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Availability Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  12. Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

    Science.gov (United States)

    Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. © 2016 K. Hoffman, S. Leupen, et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. IS IT POSSIBLE TO INTEGRATE BASIC BIOLOGICAL DISCIPLINES IN A PRIVATE INSTITUTION?

    Directory of Open Access Journals (Sweden)

    L.A. Azzalis

    2008-05-01

    Full Text Available Basic biological disciplines as biochemistry, genetic and molecular biology have grown faster than any of other sciences. Moreover, those disciplines contribute to the understanding and treatment of an elevated number of illnesses. On the other hand, teachers cannot assure the graduating students that each particular discipline  is essential.  Furthermore,  those disciplines are often studied separately without any interdisciplinary integration between them.  The new curriculum proposed at Anhembi Morumbi University  - a private institution placed at São Paulo city  - incorporates learning blocks that  have been designed to integrate basic biological disciplines and clinical contents from the beginning in order to provide the stimulation and motivation to guide the  student through his learning.  The educational trend has concentrated on the following steps: 1 Biochemistry, genetic, cellular and molecular biology teachers´ from that institution have elaborated a new discipline  that was named Biologic Process. The aim of this new discipline was integrate basic biological sciences in a single content;  2  Selecting problems that could be discussed in the light of biochemistry, genetic and molecular contents; e.g. sickle cell anemia; 3 Developing  an innovative instructional method that challenges students “learn to learn” different from problem-based learning , economically unavailable at any particular university,  and  4 Assessments that measure knowledge, skills, attitudes and beliefs.  We believe that the future pedagogical system in  private health university will be a combination of “classical”  presentation of contents combined with actively involved students in the educational process and instruction based on either hypothetical  or real clinical cases in order to create  the stimulus for  the student continues to  integrate basic and clinical investigation.

  14. Energetics, scaling and sexual size dimorphism of spiders.

    Science.gov (United States)

    Grossi, B; Canals, M

    2015-03-01

    The extreme sexual size dimorphism in spiders has motivated studies for many years. In many species the male can be very small relative to the female. There are several hypotheses trying to explain this fact, most of them emphasizing the role of energy in determining spider size. The aim of this paper is to review the role of energy in sexual size dimorphism of spiders, even for those spiders that do not necessarily live in high foliage, using physical and allometric principles. Here we propose that the cost of transport or equivalently energy expenditure and the speed are traits under selection pressure in male spiders, favoring those of smaller size to reduce travel costs. The morphology of the spiders responds to these selective forces depending upon the lifestyle of the spiders. Climbing and bridging spiders must overcome the force of gravity. If bridging allows faster dispersal, small males would have a selective advantage by enjoying more mating opportunities. In wandering spiders with low population density and as a consequence few male-male interactions, high speed and low energy expenditure or cost of transport should be favored by natural selection. Pendulum mechanics show the advantages of long legs in spiders and their relationship with high speed, even in climbing and bridging spiders. Thus small size, compensated by long legs should be the expected morphology for a fast and mobile male spider.

  15. Spider diffraction: a comparison of curved and straight legs

    International Nuclear Information System (INIS)

    Richter, J.L.

    1984-01-01

    It has been known for some time that, if curved legs rather than the usual straight ones are used in the spider that supports the secondary optics in certain telescopes, the visible diffraction effect is reduced. Fraunhofer theory is used to calculate the diffraction effects due to the curved leg spider. Calculated and photographic diffraction patterns are compared for straight and curved leg spiders

  16. Acute Generalized Exanthematous Pustulosis (AGEP Triggered by a Spider Bite

    Directory of Open Access Journals (Sweden)

    Michael Makris

    2009-01-01

    Discussion: A spider bite may represent a possible causative factor of AGEP. A spider's venom contains sphingomyelinase that stimulates the release of IL8 and GM-CSF, which are involved in AGEP pathogenesis. Whether or not the con-current use of antibiotics has an effect in AGEP appearance when combined with a spider's venom, cannot be excluded.

  17. [Problems of world outlook and methodology of science integration in biological studies].

    Science.gov (United States)

    Khododova, Iu D

    1981-01-01

    Problems of worldoutlook and methodology of the natural-science knowledge are considered basing on the analysis of tendencies in the development of the membrane theory of cell processes and the use of principles of biological membrane functioning when solving some scientific and applied problems pertaining to different branches of chemistry and biology. The notion scientific knowledge integration is defined as interpenetration of approaches, methods and ideas of different branches of knowledge and enrichment on this basis of their content resulting in knowledge augmentation in each field taken separately. These processes are accompanied by appearance of new branches of knowledge - sciences "on junction" and their subsequent differentiations. The analysis of some gnoseological situations shows that integration of sciences contributes to coordination and some agreement of thinking styles of different specialists, puts forward keen personality of a scientist demanding, in particular, his high professional mobility. Problems of scientific activity organization are considered, which involve social sciences into the integration processes. The role of philosophy in the integration processes is emphasized.

  18. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Kempa Stefan

    2009-05-01

    Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  19. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

    Science.gov (United States)

    May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

    2009-05-04

    The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  20. Multi-omic data integration enables discovery of hidden biological regularities

    DEFF Research Database (Denmark)

    Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin

    2016-01-01

    Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi- level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration...... of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule. Second, we show that genome- scale models, based on genomic and bibliomic data......, enable quantitative synchronization of disparate data types. Integrating omics data with models enabled the discovery of two novel regularities: condition invariant in vivo turnover rates of enzymes and the correlation of protein structural motifs and translational pausing. These regularities can...

  1. Remembering the object you fear: brain potentials during recognition of spiders in spider-fearful individuals.

    Science.gov (United States)

    Michalowski, Jaroslaw M; Weymar, Mathias; Hamm, Alfons O

    2014-01-01

    In the present study we investigated long-term memory for unpleasant, neutral and spider pictures in 15 spider-fearful and 15 non-fearful control individuals using behavioral and electrophysiological measures. During the initial (incidental) encoding, pictures were passively viewed in three separate blocks and were subsequently rated for valence and arousal. A recognition memory task was performed one week later in which old and new unpleasant, neutral and spider pictures were presented. Replicating previous results, we found enhanced memory performance and higher confidence ratings for unpleasant when compared to neutral materials in both animal fearful individuals and controls. When compared to controls high animal fearful individuals also showed a tendency towards better memory accuracy and significantly higher confidence during recognition of spider pictures, suggesting that memory of objects prompting specific fear is also facilitated in fearful individuals. In line, spider-fearful but not control participants responded with larger ERP positivity for correctly recognized old when compared to correctly rejected new spider pictures, thus showing the same effects in the neural signature of emotional memory for feared objects that were already discovered for other emotional materials. The increased fear memory for phobic materials observed in the present study in spider-fearful individuals might result in an enhanced fear response and reinforce negative beliefs aggravating anxiety symptomatology and hindering recovery.

  2. Flee or fight: ontogenetic changes in the behavior of cobweb spiders in encounters with spider-hunting wasps.

    Science.gov (United States)

    Uma, Divya B; Weiss, Martha R

    2012-12-01

    An animal's body size plays a predominant role in shaping its interspecific interactions, and, in encounters between two predators, often determines which shall be predator and which shall be prey. Spiders are top predators of insects, yet can fall prey to mud-dauber wasps that provision their larval nests with paralyzed spiders. Here we examined predator-prey interactions between Chalybion californicum (Saussure) (Sphecidae), a mud-dauber wasp, and Parasteatoda tepidariorum C. L. Koch (Theridiidae), a cobweb spider. We examined whether a spider's size influences its response to an attacking wasp, and report a size-dependent change in spider behavior: small-sized spiders fled, whereas medium- and large-sized spiders fought in response to wasp attacks. From the wasps' perspective, we examined whether spider size influences a wasp's hunting behavior and capture success. We found that wasps commonly approached small spiders, but were much less likely to approach medium and large spiders. However, wasp capture success did not vary with spider size. We also report a strategy used by Chalybion wasps toward cobweb spiders that is consistent with an interpretation of aggressive mimicry.

  3. Conservation systematics of the shield-backed trapdoor spiders of the nigrum-group (Mygalomorphae, Idiopidae, Idiosoma): integrative taxonomy reveals a diverse and threatened fauna from south-western Australia.

    Science.gov (United States)

    Rix, Michael G; Huey, Joel A; Cooper, Steven J B; Austin, Andrew D; Harvey, Mark S

    2018-01-01

    The aganippine shield-backed trapdoor spiders of the monophyletic nigrum -group of Idiosoma Ausserer s. l. are revised, and 15 new species are described from Western Australia and the Eyre Peninsula of South Australia: I. arenaceum Rix & Harvey, sp. n. , I. corrugatum Rix & Harvey, sp. n. , I. clypeatum Rix & Harvey, sp. n. , I. dandaragan Rix & Harvey, sp. n. , I. formosum Rix & Harvey, sp. n. , I. gardneri Rix & Harvey, sp. n. , I. gutharuka Rix & Harvey, sp. n. , I. incomptum Rix & Harvey, sp. n. , I. intermedium Rix & Harvey, sp. n. , I. jarrah Rix & Harvey, sp. n. , I. kopejtkaorum Rix & Harvey, sp. n. , I. kwongan Rix & Harvey, sp. n. , I. mcclementsorum Rix & Harvey, sp. n. , I. mcnamarai Rix & Harvey, sp. n. , and I. schoknechtorum Rix & Harvey, sp. n. Two previously described species from south-western Western Australia, I. nigrum Main, 1952 and I. sigillatum (O. P.-Cambridge, 1870), are re-illustrated and re-diagnosed, and complementary molecular data for 14 species and seven genes are analysed with Bayesian methods. Members of the nigrum -group are of long-standing conservation significance, and I. nigrum is the only spider in Australia to be afforded threatened species status under both State and Commonwealth legislation. Two other species, I. formosum Rix & Harvey, sp. n. and I. kopejtkaorum Rix & Harvey, sp. n. , are also formally listed as Endangered under Western Australian State legislation. Here we significantly relimit I. nigrum to include only those populations from the central and central-western Wheatbelt bioregion, and further document the known diversity and conservation status of all known species.

  4. Conservation systematics of the shield-backed trapdoor spiders of the nigrum-group (Mygalomorphae, Idiopidae, Idiosoma: integrative taxonomy reveals a diverse and threatened fauna from south-western Australia

    Directory of Open Access Journals (Sweden)

    Michael G. Rix

    2018-05-01

    Full Text Available The aganippine shield-backed trapdoor spiders of the monophyletic nigrum-group of Idiosoma Ausserer s. l. are revised, and 15 new species are described from Western Australia and the Eyre Peninsula of South Australia: I. arenaceum Rix & Harvey, sp. n., I. corrugatum Rix & Harvey, sp. n., I. clypeatum Rix & Harvey, sp. n., I. dandaragan Rix & Harvey, sp. n., I. formosum Rix & Harvey, sp. n., I. gardneri Rix & Harvey, sp. n., I. gutharuka Rix & Harvey, sp. n., I. incomptum Rix & Harvey, sp. n., I. intermedium Rix & Harvey, sp. n., I. jarrah Rix & Harvey, sp. n., I. kopejtkaorum Rix & Harvey, sp. n., I. kwongan Rix & Harvey, sp. n., I. mcclementsorum Rix & Harvey, sp. n., I. mcnamarai Rix & Harvey, sp. n., and I. schoknechtorum Rix & Harvey, sp. n. Two previously described species from south-western Western Australia, I. nigrum Main, 1952 and I. sigillatum (O. P.-Cambridge, 1870, are re-illustrated and re-diagnosed, and complementary molecular data for 14 species and seven genes are analysed with Bayesian methods. Members of the nigrum-group are of long-standing conservation significance, and I. nigrum is the only spider in Australia to be afforded threatened species status under both State and Commonwealth legislation. Two other species, I. formosum Rix & Harvey, sp. n. and I. kopejtkaorum Rix & Harvey, sp. n., are also formally listed as Endangered under Western Australian State legislation. Here we significantly relimit I. nigrum to include only those populations from the central and central-western Wheatbelt bioregion, and further document the known diversity and conservation status of all known species.

  5. Conservation systematics of the shield-backed trapdoor spiders of the nigrum-group (Mygalomorphae, Idiopidae, Idiosoma): integrative taxonomy reveals a diverse and threatened fauna from south-western Australia

    Science.gov (United States)

    Rix, Michael G.; Huey, Joel A.; Cooper, Steven J.B.; Austin, Andrew D.; Harvey, Mark S.

    2018-01-01

    Abstract The aganippine shield-backed trapdoor spiders of the monophyletic nigrum-group of Idiosoma Ausserer s. l. are revised, and 15 new species are described from Western Australia and the Eyre Peninsula of South Australia: I. arenaceum Rix & Harvey, sp. n., I. corrugatum Rix & Harvey, sp. n., I. clypeatum Rix & Harvey, sp. n., I. dandaragan Rix & Harvey, sp. n., I. formosum Rix & Harvey, sp. n., I. gardneri Rix & Harvey, sp. n., I. gutharuka Rix & Harvey, sp. n., I. incomptum Rix & Harvey, sp. n., I. intermedium Rix & Harvey, sp. n., I. jarrah Rix & Harvey, sp. n., I. kopejtkaorum Rix & Harvey, sp. n., I. kwongan Rix & Harvey, sp. n., I. mcclementsorum Rix & Harvey, sp. n., I. mcnamarai Rix & Harvey, sp. n., and I. schoknechtorum Rix & Harvey, sp. n. Two previously described species from south-western Western Australia, I. nigrum Main, 1952 and I. sigillatum (O. P.-Cambridge, 1870), are re-illustrated and re-diagnosed, and complementary molecular data for 14 species and seven genes are analysed with Bayesian methods. Members of the nigrum-group are of long-standing conservation significance, and I. nigrum is the only spider in Australia to be afforded threatened species status under both State and Commonwealth legislation. Two other species, I. formosum Rix & Harvey, sp. n. and I. kopejtkaorum Rix & Harvey, sp. n., are also formally listed as Endangered under Western Australian State legislation. Here we significantly relimit I. nigrum to include only those populations from the central and central-western Wheatbelt bioregion, and further document the known diversity and conservation status of all known species. PMID:29773959

  6. Nephila clavipes spiders (Araneae: Nephilidae) keep track of captured prey counts: testing for a sense of numerosity in an orb-weaver.

    Science.gov (United States)

    Rodríguez, Rafael L; Briceño, R D; Briceño-Aguilar, Eduardo; Höbel, Gerlinde

    2015-01-01

    Nephila clavipes golden orb-web spiders accumulate prey larders on their webs and search for them if they are removed from their web. Spiders that lose larger larders (i.e., spiders that lose larders consisting of more prey items) search for longer intervals, indicating that the spiders form memories of the size of the prey larders they have accumulated, and use those memories to regulate recovery efforts when the larders are pilfered. Here, we ask whether the spiders represent prey counts (i.e., numerosity) or a continuous integration of prey quantity (mass) in their memories. We manipulated larder sizes in treatments that varied in either prey size or prey numbers but were equivalent in total prey quantity (mass). We then removed the larders to elicit searching and used the spiders' searching behavior as an assay of their representations in memory. Searching increased with prey quantity (larder size) and did so more steeply with higher prey counts than with single prey of larger sizes. Thus, Nephila spiders seem to track prey quantity in two ways, but to attend more to prey numerosity. We discuss alternatives for continuous accumulator mechanisms that remain to be tested against the numerosity hypothesis, and the evolutionary and adaptive significance of evidence suggestive of numerosity in a sit-and-wait invertebrate predator.

  7. Fish predation by semi-aquatic spiders: a global pattern.

    Directory of Open Access Journals (Sweden)

    Martin Nyffeler

    Full Text Available More than 80 incidences of fish predation by semi-aquatic spiders--observed at the fringes of shallow freshwater streams, rivers, lakes, ponds, swamps, and fens--are reviewed. We provide evidence that fish predation by semi-aquatic spiders is geographically widespread, occurring on all continents except Antarctica. Fish predation by spiders appears to be more common in warmer areas between 40° S and 40° N. The fish captured by spiders, usually ranging from 2-6 cm in length, are among the most common fish taxa occurring in their respective geographic area (e.g., mosquitofish [Gambusia spp.] in the southeastern USA, fish of the order Characiformes in the Neotropics, killifish [Aphyosemion spp.] in Central and West Africa, as well as Australian native fish of the genera Galaxias, Melanotaenia, and Pseudomugil. Naturally occurring fish predation has been witnessed in more than a dozen spider species from the superfamily Lycosoidea (families Pisauridae, Trechaleidae, and Lycosidae, in two species of the superfamily Ctenoidea (family Ctenidae, and in one species of the superfamily Corinnoidea (family Liocranidae. The majority of reports on fish predation by spiders referred to pisaurid spiders of the genera Dolomedes and Nilus (>75% of observed incidences. There is laboratory evidence that spiders from several more families (e.g., the water spider Argyroneta aquatica [Cybaeidae], the intertidal spider Desis marina [Desidae], and the 'swimming' huntsman spider Heteropoda natans [Sparassidae] predate fish as well. Our finding of such a large diversity of spider families being engaged in fish predation is novel. Semi-aquatic spiders captured fish whose body length exceeded the spiders' body length (the captured fish being, on average, 2.2 times as long as the spiders. Evidence suggests that fish prey might be an occasional prey item of substantial nutritional importance.

  8. Fish predation by semi-aquatic spiders: a global pattern.

    Science.gov (United States)

    Nyffeler, Martin; Pusey, Bradley J

    2014-01-01

    More than 80 incidences of fish predation by semi-aquatic spiders--observed at the fringes of shallow freshwater streams, rivers, lakes, ponds, swamps, and fens--are reviewed. We provide evidence that fish predation by semi-aquatic spiders is geographically widespread, occurring on all continents except Antarctica. Fish predation by spiders appears to be more common in warmer areas between 40° S and 40° N. The fish captured by spiders, usually ranging from 2-6 cm in length, are among the most common fish taxa occurring in their respective geographic area (e.g., mosquitofish [Gambusia spp.] in the southeastern USA, fish of the order Characiformes in the Neotropics, killifish [Aphyosemion spp.] in Central and West Africa, as well as Australian native fish of the genera Galaxias, Melanotaenia, and Pseudomugil). Naturally occurring fish predation has been witnessed in more than a dozen spider species from the superfamily Lycosoidea (families Pisauridae, Trechaleidae, and Lycosidae), in two species of the superfamily Ctenoidea (family Ctenidae), and in one species of the superfamily Corinnoidea (family Liocranidae). The majority of reports on fish predation by spiders referred to pisaurid spiders of the genera Dolomedes and Nilus (>75% of observed incidences). There is laboratory evidence that spiders from several more families (e.g., the water spider Argyroneta aquatica [Cybaeidae], the intertidal spider Desis marina [Desidae], and the 'swimming' huntsman spider Heteropoda natans [Sparassidae]) predate fish as well. Our finding of such a large diversity of spider families being engaged in fish predation is novel. Semi-aquatic spiders captured fish whose body length exceeded the spiders' body length (the captured fish being, on average, 2.2 times as long as the spiders). Evidence suggests that fish prey might be an occasional prey item of substantial nutritional importance.

  9. iTools: a framework for classification, categorization and integration of computational biology resources.

    Directory of Open Access Journals (Sweden)

    Ivo D Dinov

    2008-05-01

    Full Text Available The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long

  10. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.

    Science.gov (United States)

    Ciaccio, Mark F; Finkle, Justin D; Xue, Albert Y; Bagheri, Neda

    2014-07-01

    An organism's ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue-signal-response networks. However, selecting a strategy that answers a specific biological question requires knowledge both of the type of data being collected, and of the strengths and weaknesses of different computational regimes. We broadly explore several computational approaches, and we evaluate their accuracy in predicting a given response. Specifically, we describe how statistical algorithms can be used in the context of integrative and comparative biology to elucidate the genomic, proteomic, and/or cellular networks responsible for robust physiological response. As a case study, we apply this strategy to a dataset of quantitative levels of protein abundance from the mussel, Mytilus galloprovincialis, to uncover the temperature-dependent signaling network. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  11. Inbreeding avoidance in spiders: evidence for rescue effect in fecundity of female spiders with outbreeding opportunity

    DEFF Research Database (Denmark)

    Bilde, T.; Maklakov, A.A.; Schilling, Nadia

    2007-01-01

    avoidance can be because of low risk of inbreeding, variation in tolerance to inbreeding or high costs of outbreeding. We examined the relationship between inbreeding depression and inbreeding avoidance adaptations under two levels of inbreeding in the spider Oedothorax apicatus, asking whether preference...... for unrelated sperm via pre- and/or post-copulatory mechanisms could restore female fitness when inbreeding depression increases. Using inbred isofemale lines we provided female spiders with one or two male spiders of different relatedness in five combinations: one male sib; one male nonsib; two male sibs; two...

  12. Protocols for the delivery of small molecules to the two-spotted spider mite, Tetranychus urticae.

    Directory of Open Access Journals (Sweden)

    Takeshi Suzuki

    Full Text Available The two-spotted spider mite, Tetranychus urticae, is a chelicerate herbivore with an extremely wide host range and an extraordinary ability to develop pesticide resistance. Due to its responsiveness to natural and synthetic xenobiotics, the spider mite is becoming a prime pest herbivore model for studies of the evolution of host range, plant-herbivore interactions and mechanisms of xenobiotic resistance. The spider mite genome has been sequenced and its transcriptional responses to developmental and various biotic and abiotic cues have been documented. However, to identify biological and evolutionary roles of T. urticae genes and proteins, it is necessary to develop methods for the efficient manipulation of mite gene function or protein activity. Here, we describe protocols developed for the delivery of small molecules into spider mites. Starting with mite maintenance and the preparation of the experimental mite populations of developmentally synchronized larvae and adults, we describe 3 methods for delivery of small molecules including artificial diet, leaf coating, and soaking. The presented results define critical steps in these methods and demonstrate that they can successfully deliver tracer dyes into mites. Described protocols provide guidelines for high-throughput setups for delivery of experimental compounds that could be used in reverse genetics platforms to modulate gene expression or protein activity, or for screens focused on discovery of new molecules for mite control. In addition, described protocols could be adapted for other Tetranychidae and related species of economic importance such as Varroa, dust and poultry mites.

  13. Background colour matching by a crab spider in the field: a community sensory ecology perspective.

    Science.gov (United States)

    Defrize, Jérémy; Théry, Marc; Casas, Jérôme

    2010-05-01

    The question of whether a species matches the colour of its natural background in the perspective of the correct receiver is complex to address for several reasons; however, the answer to this question may provide invaluable support for functional interpretations of colour. In most cases, little is known about the identity and visual sensory abilities of the correct receiver and the precise location at which interactions take place in the field, in particular for mimetic systems. In this study, we focused on Misumena vatia, a crab spider meeting the criteria for assessing crypsis better than many other models, and claimed to use colour changes for both aggressive and protective crypsis. We carried out a systematic field survey to quantitatively assess the exactness of background colour matching in M. vatia with respect to the visual system of many of its receivers within the community. We applied physiological models of bird, bee and blowfly colour vision, using flower and spider spectral reflectances measured with a spectroradiometer. We observed that crypsis at long distance is systematically achieved, exclusively through achromatic contrast, in both bee and bird visions. At short distance, M. vatia is mostly chromatically detectable, whatever the substrate, for bees and birds. However, spiders can be either poorly discriminable or quite visible depending on the substrate for bees. Spiders are always chromatically undetectable for blowflies. We discuss the biological relevance of these results in both defensive and aggressive contexts of crypsis within a community sensory perspective.

  14. Spider assemblages associated with different crop stages of irrigated rice agroecosystems from eastern Uruguay.

    Science.gov (United States)

    Bao, Leticia; Ginella, Juaquín; Cadenazzi, Mónica; Castiglioni, Enrique A; Martínez, Sebastián; Casales, Luis; Caraballo, María P; Laborda, Álvaro; Simo, Miguel

    2018-01-01

    The rice crop and associated ecosystems constitute a rich mosaic of habitats that preserve a rich biological diversity. Spiders are an abundant and successful group of natural predators that are considered efficient in the biocontrol of the major insect pests in agroecosystems. Spider diversity in different stages of the rice crop growth from eastern Uruguay was analysed. Field study was developed on six rice farms with rotation system with pasture, installed during intercropping stage as cover crop. Six rice crops distributed in three locations were sampled with pitfall and entomological vaccum suction machine. Sixteen families, representing six guilds, were collected. Lycosidae, Linyphiidae, Anyphaenidae and Tetragnathidae were the most abundant families (26%, 25%, 20% and 12%, respectively) and comprised more than 80% of total abundance. Other hunters (29%), sheet web weavers (25%) and ground hunters (24%) were the most abundant guilds. Species composition along different crop stages was significantly different according to the ANOSIM test. The results showed higher spider abundance and diversity along the crop and intercrop stages. This study represents the first contribution to the knowledge of spider diversity associated with rice agroecosystem in the country.

  15. Double Deception: Ant-Mimicking Spiders Elude Both Visually- and Chemically-Oriented Predators

    Science.gov (United States)

    Uma, Divya; Durkee, Caitlin; Herzner, Gudrun; Weiss, Martha

    2013-01-01

    Biological mimicry is often multimodal, in that a mimic reinforces its resemblance to another organism via different kinds of signals that can be perceived by a specific target audience. In this paper we describe a novel scenario, in which a mimic deceives at least two distinct audiences, each of which relies primarily on a different sensory modality for decision-making. We have previously shown that Peckhamia picata, a myrmecomorphic spider that morphologically and behaviorally resembles the ant Camponotus nearcticus, experiences reduced predation by visually-oriented jumping spiders. Here we report that Peckhamia also faces reduced aggression from spider-hunting sphecid wasps as well as from its model ant, both of which use chemical cues to identify prey. We also report that Peckhamia does not chemically resemble its model ants, and that its total cuticular hydrocarbons are significantly lower than those of the ants and non-mimic spiders. Although further studies are needed to clarify the basis of Peckhamia's chemically-mediated protection, to our knowledge, such ‘double deception,’ in which a single organism sends misleading visual cues to one set of predators while chemically misleading another set, has not been reported; however, it is likely to be common among what have until now been considered purely visual mimics. PMID:24236152

  16. Citrus-orchard ground harbours a diverse, well-established and abundant ground-dwelling spider fauna

    Energy Technology Data Exchange (ETDEWEB)

    Monzo, C.; Molla, O.; Vanaclocha, P.; Monton, H.; Melic, A.; Castanera, P.; Urbaneja, A.

    2011-07-01

    Ground-dwelling spider assemblages comprise one of the most representative predatory groups to be found in many crops. There is some evidence of the role that ground-dwelling spiders play in controlling certain citrus pests; however, there are almost no studies about the abundance and composition of this predatory group in citrus orchards. A three-year survey conducted using pitfall traps in three citrus orchards in Eastern Spain yielded more than five-thousand ground-dwelling spiders belonging to more than 50 species and 20 families. Wandering families such as Lycosidae, Gnaphosidae and Zodariidae were the most numerous in terms of captures. The generalist predator Pardosa cribata Simon (Araneae: Lycosidae) was the most common species, representing a quarter of all captures, followed by Zodarion cesari Pekar. (Araneae: Zodariidae) and Trachyzelotes fuscipes (Koch) (Araneae: Gnaphosidae). Spiders were active throughout the year with a peak population in summer. The species abundance data for the three spider assemblages sampled fitted a log normal statistical model which is consistent with a well-established community. The presence of a cover crop provided higher abundance of alternative prey and consequently higher abundance and diversity of ground-dwelling spiders. This work demonstrates that the citrus-orchard ground harbours a diverse and abundant ground-dwelling spider fauna, which is also active throughout the year. A challenge for future studies will be to establish conservation management strategies for these predators, that will improve biological control of those citrus pests that inhabit or spend part of their life cycle on the orchard floor. (Author) 49 refs.

  17. A review on machine learning principles for multi-view biological data integration.

    Science.gov (United States)

    Li, Yifeng; Wu, Fang-Xiang; Ngom, Alioune

    2018-03-01

    Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.

  18. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  19. Optically probing torsional superelasticity in spider silks

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P. [Department of Physical Sciences, IISER Mohali, Sector 81, Manauli, Mohali 140306 (India)

    2013-11-11

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10{sup 2−3} rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices.

  20. Optically probing torsional superelasticity in spider silks

    International Nuclear Information System (INIS)

    Kumar, Bhupesh; Thakur, Ashish; Panda, Biswajit; Singh, Kamal P.

    2013-01-01

    We investigate torsion mechanics of various spider silks using a sensitive optical technique. We find that spider silks are torsionally superelastic in that they can reversibly withstand great torsion strains of over 10 2−3 rotations per cm before failure. Among various silks from a spider, we find the failure twist-strain is greatest in the sticky capture silk followed by dragline and egg-case silk. Our in situ laser-diffraction measurements reveal that torsional strains on the silks induce a nano-scale transverse compression in its diameter that is linear and reversible. These unique torsional properties of the silks could find applications in silk-based materials and devices

  1. Edge effect on weevils and spiders

    Directory of Open Access Journals (Sweden)

    R. Horváth

    2002-05-01

    Full Text Available The edge effect on weevils and spiders was tested along oak forest – meadow transects using sweep-net samples at the Síkfökút Project in Hungary. For spiders the species richness was significantly higher in the forest edge than either in the meadow or the forest interior. For weevils the species richness of the forest edge was higher than that of the meadow, but the difference was not statistically significant whereas the species richness of the forest interior was significantly lower than that of the forest edge and the meadow. The composition of the spider assemblage of the edge was more similar to the forest, while the composition of weevils in the edge was more similar to the meadow. Our results based on two invertebrate groups operating on different trophic levels suggest that there is a significant edge effect for the studied taxa resulting in higher species richness in the edge.

  2. Dietary and prey-capture adaptations by which Zodarion germanicum, an ant-eating spider (Araneae: Zodariidae), specialises on the Formicinae

    DEFF Research Database (Denmark)

    Pekár, S.; Toft, Søren; Hrusková, M.

    2008-01-01

    There has been considerable recent interest in the biology of spiders that specialise on ants as prey, but previous studies have tended to envisage the level of adaptation as being to ants as a group. In this paper, we provide evidence that Zodarion germanicum is a spider that has dietary and venom...... adaptations by which it targets a particular subset of ants, the subfamily Formicinae. We reared spiders from first instar in the laboratory on three different diets: formicine ants only, myrmicine ants only and mixed (both formicine and myrmicine ants). Fitness-related life-history parameters were determined......, and we found that the spiders on the formicine-only diet lived longer and grew at a faster rate. Lipid, carbon and nitrogen compositions of ants were analysed, but we found no evidence of formicines differing from myrmicines in macro-nutrient content. This suggests that effects on longevity and growth...

  3. Adaptation of sensor morphology: an integrative view of perception from biologically inspired robotics perspective

    Science.gov (United States)

    Nurzaman, Surya G.

    2016-01-01

    Sensor morphology, the morphology of a sensing mechanism which plays a role of shaping the desired response from physical stimuli from surroundings to generate signals usable as sensory information, is one of the key common aspects of sensing processes. This paper presents a structured review of researches on bioinspired sensor morphology implemented in robotic systems, and discusses the fundamental design principles. Based on literature review, we propose two key arguments: first, owing to its synthetic nature, biologically inspired robotics approach is a unique and powerful methodology to understand the role of sensor morphology and how it can evolve and adapt to its task and environment. Second, a consideration of an integrative view of perception by looking into multidisciplinary and overarching mechanisms of sensor morphology adaptation across biology and engineering enables us to extract relevant design principles that are important to extend our understanding of the unfinished concepts in sensing and perception. PMID:27499843

  4. CHOmine: an integrated data warehouse for CHO systems biology and modeling.

    Science.gov (United States)

    Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

    2017-01-01

    The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

  5. Polymer micro-grippers with an integrated force sensor for biological manipulation

    International Nuclear Information System (INIS)

    Mackay, R E; Le, H R; Clark, S; Williams, J A

    2013-01-01

    The development of a novel micro-system integrating SU-8 polymer micro-grippers with a tensile force sensor for handling and characterizing the mechanical properties of delicate biological materials, such as fibrils, is presented. The micro-grippers are actuated by the electro-thermal effect and have gripping forces comparable to the common ‘hot-and-cold-arm’ grippers. A robust finite element model was developed to investigate system performance and validated experimentally. A new micro-mechanical calibration method using a piezoelectric manipulator with a micro-force measurement system was successfully applied to test the structure. Both FEA simulation and micro-mechanical testing results indicated that the system could fulfil the requirements for micro-object manipulation within a biological environment. (paper)

  6. Using reefcheck monitoring database to develop the coral reef index of biological integrity

    DEFF Research Database (Denmark)

    Nguyen, Hai Yen T.; Pedersen, Ole; Ikejima, Kou

    2009-01-01

    The coral reef indices of biological integrity was constituted based on the reef check monitoring data. Seventy six minimally disturbed sites and 72 maximallv disturbed sites in shallow water and 39 minimally disturbed sites and 37 maximally disturbed sites in deep water were classified based...... on the high-end and low-end percentages and ratios of hard coral, dead coral and fieshy algae. A total of 52 candidate metrics was identified and compiled, Eight and four metrics were finally selected to constitute the shallow and deep water coral reef indices respectively. The rating curve was applied.......05) and coral damaged by other factors -0.283 (pcoral reef indices were sensitive responses to stressors and can be capable to use as the coral reef biological monitoring tool....

  7. Aquatic subsidies transport anthropogenic nitrogen to riparian spiders

    Energy Technology Data Exchange (ETDEWEB)

    Akamatsu, Fumikazu, E-mail: f-akamt55@pwri.go.jp [Department of Environmental Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Toda, Hideshige [Department of Environmental Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan)

    2011-05-15

    Stable nitrogen isotopic composition ({delta}{sup 15}N) of aquatic biota increases with anthropogenic N inputs such as sewage and livestock waste downstream. Increase in {delta}{sup 15}N of riparian spiders downstream may reflect the anthropogenic pollution exposure through predation on aquatic insects. A two-source mixing model based on stable carbon isotopic composition showed the greatest dependence on aquatic insects (84%) by horizontal web-building spiders, followed by intermediate (48%) and low (31%) dependence by cursorial and vertical web-building spiders, respectively. The spider body size was negatively correlated with the dietary proportion of aquatic insects and spider {delta}{sup 15}N. The aquatic subsidies transported anthropogenic N to smaller riparian spiders downstream. This transport of anthropogenic N was regulated by spider's guild designation and body size. - Highlights: > {delta}{sup 15}N of aquatic insects increases downstream with anthropogenic nitrogen inputs. > {delta}{sup 15}N of riparian spiders increases with a high dietary proportion of aquatic insects and smaller spider body size. > The aquatic subsidies transport anthropogenic nitrogen to smaller riparian spiders downstream. - Smaller spiders assimilate anthropogenic nitrogen through the predation on aquatic subsides.

  8. Aquatic subsidies transport anthropogenic nitrogen to riparian spiders

    International Nuclear Information System (INIS)

    Akamatsu, Fumikazu; Toda, Hideshige

    2011-01-01

    Stable nitrogen isotopic composition (δ 15 N) of aquatic biota increases with anthropogenic N inputs such as sewage and livestock waste downstream. Increase in δ 15 N of riparian spiders downstream may reflect the anthropogenic pollution exposure through predation on aquatic insects. A two-source mixing model based on stable carbon isotopic composition showed the greatest dependence on aquatic insects (84%) by horizontal web-building spiders, followed by intermediate (48%) and low (31%) dependence by cursorial and vertical web-building spiders, respectively. The spider body size was negatively correlated with the dietary proportion of aquatic insects and spider δ 15 N. The aquatic subsidies transported anthropogenic N to smaller riparian spiders downstream. This transport of anthropogenic N was regulated by spider's guild designation and body size. - Highlights: → δ 15 N of aquatic insects increases downstream with anthropogenic nitrogen inputs. → δ 15 N of riparian spiders increases with a high dietary proportion of aquatic insects and smaller spider body size. → The aquatic subsidies transport anthropogenic nitrogen to smaller riparian spiders downstream. - Smaller spiders assimilate anthropogenic nitrogen through the predation on aquatic subsides.

  9. Disentangling the phylogenetic and ecological components of spider phenotypic variation.

    Science.gov (United States)

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

  10. Development of tools for integrated monitoring and assessment of hazardous substances and their biological effects in the Baltic Sea.

    Science.gov (United States)

    Lehtonen, Kari K; Sundelin, Brita; Lang, Thomas; Strand, Jakob

    2014-02-01

    The need to develop biological effects monitoring to facilitate a reliable assessment of hazardous substances has been emphasized in the Baltic Sea Action Plan of the Helsinki Commission. An integrated chemical-biological approach is vitally important for the understanding and proper assessment of anthropogenic pressures and their effects on the Baltic Sea. Such an approach is also necessary for prudent management aiming at safeguarding the sustainable use of ecosystem goods and Services. The BEAST project (Biological Effects of Anthropogenic Chemical Stress: Tools for the Assessment of Ecosystem Health) set out to address this topic within the BONUS Programme. BEAST generated a large amount of quality-assured data on several biological effects parameters (biomarkers) in various marine species in different sub-regions of the Baltic Sea. New indicators (biological response measurement methods) and management tools (integrated indices) with regard to the integrated monitoring approach were suggested.

  11. Gauss-Kronrod-Trapezoidal Integration Scheme for Modeling Biological Tissues with Continuous Fiber Distributions

    Science.gov (United States)

    Hou, Chieh; Ateshian, Gerard A.

    2015-01-01

    Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation. PMID:26291492

  12. A Gauss-Kronrod-Trapezoidal integration scheme for modeling biological tissues with continuous fiber distributions.

    Science.gov (United States)

    Hou, Chieh; Ateshian, Gerard A

    2016-01-01

    Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element (FE) analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation.

  13. Uncovering the structure-function relationship in spider silk

    Science.gov (United States)

    Yarger, Jeffery L.; Cherry, Brian R.; van der Vaart, Arjan

    2018-03-01

    All spiders produce protein-based biopolymer fibres that we call silk. The most studied of these silks is spider dragline silk, which is very tough and relatively abundant compared with other types of spider silks. Considerable research has been devoted to understanding the relationship between the molecular structure and mechanical properties of spider dragline silks. In this Review, we overview experimental and computational studies that have provided a wealth of detail at the molecular level on the highly conserved repetitive core and terminal regions of spider dragline silk. We also discuss the role of the nanocrystalline β-sheets and amorphous regions in determining the properties of spider silk fibres, endowing them with strength and elasticity. Additionally, we outline imaging techniques and modelling studies that elucidate the importance of the hierarchical structure of silk fibres at the molecular level. These insights into structure-function relationships can guide the reverse engineering of spider silk to enable the production of superior synthetic fibres.

  14. Clarification of the Use of Biological Data and Information in the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance

    Science.gov (United States)

    The memorandum modifies the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance to provide clarity and promote consistency in the manner in which states use biological data and information in developing their 2002 submissions.

  15. Recombinant DNA production of spider silk proteins.

    Science.gov (United States)

    Tokareva, Olena; Michalczechen-Lacerda, Valquíria A; Rech, Elíbio L; Kaplan, David L

    2013-11-01

    Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  16. Programming spiders, bots, and aggregators in Java

    CERN Document Server

    Heaton, Jeff

    2006-01-01

    The content and services available on the web continue to be accessed mostly through direct human control. But this is changing. Increasingly, users rely on automated agents that save them time and effort by programmatically retrieving content, performing complex interactions, and aggregating data from diverse sources. Programming Spiders, Bots, and Aggregators in Java teaches you how to build and deploy a wide variety of these agents-from single-purpose bots to exploratory spiders to aggregators that present a unified view of information from multiple user accounts. You will quickly build on

  17. Quantifying biological integrity by taxonomic completeness: its utility in regional and global assessments.

    Science.gov (United States)

    Hawkins, Charles P

    2006-08-01

    Water resources managers and conservation biologists need reliable, quantitative, and directly comparable methods for assessing the biological integrity of the world's aquatic ecosystems. Large-scale assessments are constrained by the lack of consistency in the indicators used to assess biological integrity and our current inability to translate between indicators. In theory, assessments based on estimates of taxonomic completeness, i.e., the proportion of expected taxa that were observed (observed/expected, O/E) are directly comparable to one another and should therefore allow regionally and globally consistent summaries of the biological integrity of freshwater ecosystems. However, we know little about the true comparability of O/E assessments derived from different data sets or how well O/E assessments perform relative to other indicators in use. I compared the performance (precision, bias, and sensitivity to stressors) of O/E assessments based on five different data sets with the performance of the indicators previously applied to these data (three multimetric indices, a biotic index, and a hybrid method used by the state of Maine). Analyses were based on data collected from U.S. stream ecosystems in North Carolina, the Mid-Atlantic Highlands, Maine, and Ohio. O/E assessments resulted in very similar estimates of mean regional conditions compared with most other indicators once these indicators' values were standardized relative to reference-site means. However, other indicators tended to be biased estimators of O/E, a consequence of differences in their response to natural environmental gradients and sensitivity to stressors. These results imply that, in some cases, it may be possible to compare assessments derived from different indicators by standardizing their values (a statistical approach to data harmonization). In situations where it is difficult to standardize or otherwise harmonize two or more indicators, O/E values can easily be derived from existing

  18. GenFlow: generic flow for integration, management and analysis of molecular biology data

    Directory of Open Access Journals (Sweden)

    Marcio Katsumi Oikawa

    2004-01-01

    Full Text Available A large number of DNA sequencing projects all over the world have yielded a fantastic amount of data, whose analysis is, currently, a big challenge for computational biology. The limiting step in this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires automated analytical tools to optimize operations and efficiently generate knowledge. This paper presents an information flow model , called GenFlow, that can tackle this analytical task.

  19. Data Integration for Health and Stress Monitoring: Biological Metabolites, Wearables Data, and Self-Reporting

    Science.gov (United States)

    Dunn, Jocelyn T.

    Integrative and unobtrusive approaches to monitoring health and stress can assist in preventative medicine and disease management, and provide capabilities for complex work environments, such as military deployments and long-duration human space exploration missions. With many data streams that could potentially provide critical information about the health, behavior, and psychosocial states of individuals or small groups, the central question of this research is how to reliably measure health and stress states over time. This integrative approach to health and stress monitoring has implemented biological metabolite profiling, wearables data analysis, and survey assessment for comparing biological, behavioral, and psychological perspectives. Health monitoring technologies aim to provide objective data about health status. Providing objective information can help mitigate biases or blind spots in an individual's perception. Consider an individual who is unwilling to openly admit to psychosocial distress and unhealthy habits, or an individual who has habituated to long-term stressors and is unable to recognize a chronic state of high stress. Both honesty and self-awareness are required for accurate self-reporting. Digital health technologies, such as wearable devices, provide objective data for health monitoring. Compared to surveys, wearables are less influenced by participant openness, and compared to biological samples, wearables require less equipment and less labor for analysis. However, inherent to every data stream are limitations due to uncertainty and sensitivity. This research has been conducted in collaboration with Hawaii Space Exploration Analog and Simulation (HI-SEAS), which is a Mars analog research site on the slopes on Mauna Loa volcano in Hawaii. During 8-month and 12-month HI-SEAS missions in the 2014-2016 timeframe, twelve individuals provided hair and urine samples for metabolite profiling, utilized consumer-grade wearables to monitor sleep and

  20. Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder

    Directory of Open Access Journals (Sweden)

    Atsushi Takata

    2018-01-01

    Full Text Available Recent studies have established important roles of de novo mutations (DNMs in autism spectrum disorders (ASDs. Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the “de novo paradigm” of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244 and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs.

  1. Visual fields and eye morphology support color vision in a color-changing crab-spider.

    Science.gov (United States)

    Insausti, Teresita C; Defrize, Jérémy; Lazzari, Claudio R; Casas, Jérôme

    2012-03-01

    Vision plays a major role in many spiders, being involved in prey hunting, orientation or substrate choice, among others. In Misumena vatia, which experiences morphological color changes, vision has been reported to be involved in substrate color matching. Electrophysiological evidence reveals that at least two types of photoreceptors are present in this species, but these data are not backed up by morphological evidence. This work analyzes the functional structure of the eyes of this spider and relates it to its color-changing abilities. A broad superposition of the visual field of the different eyes was observed, even between binocular regions of principal and secondary eyes. The frontal space is simultaneously analyzed by four eyes. This superposition supports the integration of the visual information provided by the different eye types. The mobile retina of the principal eyes of this spider is organized in three layers of three different types of rhabdoms. The third and deepest layer is composed by just one large rhabdom surrounded by dark screening pigments that limit the light entry. The three pairs of secondary eyes have all a single layer of rhabdoms. Our findings provide strong support for an involvement of the visual system in color matching in this spider. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. The PRIMA Test Facility: SPIDER and MITICA test-beds for ITER neutral beam injectors

    Science.gov (United States)

    Toigo, V.; Piovan, R.; Dal Bello, S.; Gaio, E.; Luchetta, A.; Pasqualotto, R.; Zaccaria, P.; Bigi, M.; Chitarin, G.; Marcuzzi, D.; Pomaro, N.; Serianni, G.; Agostinetti, P.; Agostini, M.; Antoni, V.; Aprile, D.; Baltador, C.; Barbisan, M.; Battistella, M.; Boldrin, M.; Brombin, M.; Dalla Palma, M.; De Lorenzi, A.; Delogu, R.; De Muri, M.; Fellin, F.; Ferro, A.; Fiorentin, A.; Gambetta, G.; Gnesotto, F.; Grando, L.; Jain, P.; Maistrello, A.; Manduchi, G.; Marconato, N.; Moresco, M.; Ocello, E.; Pavei, M.; Peruzzo, S.; Pilan, N.; Pimazzoni, A.; Recchia, M.; Rizzolo, A.; Rostagni, G.; Sartori, E.; Siragusa, M.; Sonato, P.; Sottocornola, A.; Spada, E.; Spagnolo, S.; Spolaore, M.; Taliercio, C.; Valente, M.; Veltri, P.; Zamengo, A.; Zaniol, B.; Zanotto, L.; Zaupa, M.; Boilson, D.; Graceffa, J.; Svensson, L.; Schunke, B.; Decamps, H.; Urbani, M.; Kushwah, M.; Chareyre, J.; Singh, M.; Bonicelli, T.; Agarici, G.; Garbuglia, A.; Masiello, A.; Paolucci, F.; Simon, M.; Bailly-Maitre, L.; Bragulat, E.; Gomez, G.; Gutierrez, D.; Mico, G.; Moreno, J.-F.; Pilard, V.; Kashiwagi, M.; Hanada, M.; Tobari, H.; Watanabe, K.; Maejima, T.; Kojima, A.; Umeda, N.; Yamanaka, H.; Chakraborty, A.; Baruah, U.; Rotti, C.; Patel, H.; Nagaraju, M. V.; Singh, N. P.; Patel, A.; Dhola, H.; Raval, B.; Fantz, U.; Heinemann, B.; Kraus, W.; Hanke, S.; Hauer, V.; Ochoa, S.; Blatchford, P.; Chuilon, B.; Xue, Y.; De Esch, H. P. L.; Hemsworth, R.; Croci, G.; Gorini, G.; Rebai, M.; Muraro, A.; Tardocchi, M.; Cavenago, M.; D'Arienzo, M.; Sandri, S.; Tonti, A.

    2017-08-01

    The ITER Neutral Beam Test Facility (NBTF), called PRIMA (Padova Research on ITER Megavolt Accelerator), is hosted in Padova, Italy and includes two experiments: MITICA, the full-scale prototype of the ITER heating neutral beam injector, and SPIDER, the full-size radio frequency negative-ions source. The NBTF realization and the exploitation of SPIDER and MITICA have been recognized as necessary to make the future operation of the ITER heating neutral beam injectors efficient and reliable, fundamental to the achievement of thermonuclear-relevant plasma parameters in ITER. This paper reports on design and R&D carried out to construct PRIMA, SPIDER and MITICA, and highlights the huge progress made in just a few years, from the signature of the agreement for the NBTF realization in 2011, up to now—when the buildings and relevant infrastructures have been completed, SPIDER is entering the integrated commissioning phase and the procurements of several MITICA components are at a well advanced stage.

  3. A Neural Systems-Based Neurobiology and Neuropsychiatry Course: Integrating Biology, Psychodynamics, and Psychology in the Psychiatric Curriculum

    Science.gov (United States)

    Lacy, Timothy; Hughes, John D.

    2006-01-01

    Objective: Psychotherapy and biological psychiatry remain divided in psychiatry residency curricula. Behavioral neurobiology and neuropsychiatry provide a systems-level framework that allows teachers to integrate biology, psychodynamics, and psychology. Method: The authors detail the underlying assumptions and outline of a neural systems-based…

  4. The eunuch phenomenon: adaptive evolution of genital emasculation in sexually dimorphic spiders.

    Science.gov (United States)

    Kuntner, Matjaž; Agnarsson, Ingi; Li, Daiqin

    2015-02-01

    emasculation, as well as lesser genital damage and sexual cannibalism, to be significantly associated with SSD. These behavioural and morphological traits thus likely co-evolve in spiders. Emasculation can be seen as an extreme form of genital mutilation, or even a terminal investment strategy linked to the evolution of monogyny. However, as different emasculation cases in araneoid spiders are neither homologous nor biologically identical, and may or may not serve as paternity protection, the direct link to monogyny is not clear cut. Understanding better the phylogenetic patterns of emasculation and its constituent morphologies and behaviours, a clearer picture of the intricate interplay of natural and sexual selection may arise. With the here improved evolutionary resolution of spider eunuch behaviour, we can more specifically tie the evidence from adaptive hypotheses to independent cases, and propose promising avenues for further research of spider eunuchs, and of the evolution of monogyny. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

  5. Testing for non-target effects of spinosad on twospotted spider mites and their predator Phytoseiulus persimilis under greenhouse conditions.

    Science.gov (United States)

    Holt, Kiffnie M; Opit, George P; Nechols, James R; Margolies, David C

    2006-01-01

    The compatibility of the selective insecticide spinosad (Conserve SC), at rates recommended for thrips control in greenhouses, with release of the predatory mite Phytoseiulus persimilis Athias-Henriot (Acari: Phytoseiidae) to control spider mites, was investigated in a crop of ivy geranium Pelargonium peltatum, cultivar 'Amethyst 96.' Plants were inoculated with twospotted spider mites, Tetranychus urticae Koch (Acari: Tetranychidae), 2 weeks before treatments were applied. There were three treatment variables, each at two levels: predators (released or not), spray application (water or Conserve SC at 2 ml/3.79 l), and timing of spray (1 day before or after predators were released). Twospotted spider mite populations then were sampled twice each week over a three-week period. The application or timing of spinosad had no effect on the ability of the predator to reduce the population of spider mites. Spider mite populations in the no-predator treatment continued to expand over the course of the experiment, while those in the predator-release treatment declined. We conclude that P. persimilis can be used in conjunction with spinosad on ivy geraniums without causing obvious detrimental effects to this predator or leading to a reduction in biological control.

  6. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

    Science.gov (United States)

    D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

    2017-01-01

    Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

  7. Hybrid integrated biological-solid-state system powered with adenosine triphosphate.

    Science.gov (United States)

    Roseman, Jared M; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K; Shepard, Kenneth L

    2015-12-07

    There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na(+)/K(+) adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 10(6) mm(-2)) are able to sustain a short-circuit current of 32.6 pA mm(-2) and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm(-2) from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

  8. Hybrid integrated biological-solid-state system powered with adenosine triphosphate

    Science.gov (United States)

    Roseman, Jared M.; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K.; Shepard, Kenneth L.

    2015-12-01

    There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na+/K+ adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 106 mm-2) are able to sustain a short-circuit current of 32.6 pA mm-2 and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm-2 from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

  9. Scavenging by spiders (Araneae) and its relationship to pest management of the brown recluse spider.

    Science.gov (United States)

    Vetter, Richard S

    2011-06-01

    Experiments reported in Sandidge (2003; Nature 426: 30) indicated that the brown recluse spider, Loxosceles reclusa Gertsch & Mulaik, preferred to scavenge dead prey over live prey and that the spiders were not detrimentally affected when fed insecticide-killed crickets. Extrapolations made in subsequent media coverage disseminating the results of this research made counter-intuitive statements that pesticide treatment in houses would increase brown recluse populations in homes. This information was presented as if the scavenging behavior was specialized in the brown recluse; however, it was more likely that this behavior has not been well studied in other species. To provide a comparison, the current laboratory study examined the likelihood of non-Loxosceles spiders to scavenge dead prey. Of 100 non-Loxosceles spiders that were tested (from 11 families, 24 genera, and at least 29 species from a variety of spider hunting guilds), 99 scavenged dead crickets when offered in petri dishes. Some of the spiders were webspinners in which real-world scavenging of dead prey is virtually impossible, yet they scavenge when given the opportunity. Therefore, scavenging is a flexible opportunistic predatory behavior that is spread across a variety of taxa and is not a unique behavior in brown recluses. These findings are discussed in relation to pest management practices.

  10. SignalSpider: Probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles

    KAUST Repository

    Wong, Kachun

    2014-09-05

    Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo. Different combinations of DNA-binding protein occupancies may result in a gene being expressed in different tissues or at different developmental stages. To fully understand the functions of genes, it is essential to develop probabilistic models on multiple ChIP-Seq profiles to decipher the combinatorial regulatory mechanisms by multiple transcription factors. Results: In this work, we describe a probabilistic model (SignalSpider) to decipher the combinatorial binding events of multiple transcription factors. Comparing with similar existing methods, we found SignalSpider performs better in clustering promoter and enhancer regions. Notably, SignalSpider can learn higher-order combinatorial patterns from multiple ChIP-Seq profiles. We have applied SignalSpider on the normalized ChIP-Seq profiles from the ENCODE consortium and learned model instances. We observed different higher-order enrichment and depletion patterns across sets of proteins. Those clustering patterns are supported by Gene Ontology (GO) enrichment, evolutionary conservation and chromatin interaction enrichment, offering biological insights for further focused studies. We also proposed a specific enrichment map visualization method to reveal the genome-wide transcription factor combinatorial patterns from the models built, which extend our existing fine-scale knowledge on gene regulation to a genome-wide level. Availability and implementation: The matrix-algebra-optimized executables and source codes are available at the authors\\' websites: http://www.cs.toronto.edu/∼wkc/SignalSpider. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.

  11. Synthetic spider silk sustainability verification by techno-economic and life cycle analysis

    Science.gov (United States)

    Edlund, Alan

    Major ampullate spider silk represents a promising biomaterial with diverse commercial potential ranging from textiles to medical devices due to the excellent physical and thermal properties from the protein structure. Recent advancements in synthetic biology have facilitated the development of recombinant spider silk proteins from Escherichia coli (E. coli), alfalfa, and goats. This study specifically investigates the economic feasibility and environmental impact of synthetic spider silk manufacturing. Pilot scale data was used to validate an engineering process model that includes all of the required sub-processing steps for synthetic fiber manufacture: production, harvesting, purification, drying, and spinning. Modeling was constructed modularly to support assessment of alternative protein production methods (alfalfa and goats) as well as alternative down-stream processing technologies. The techno-economic analysis indicates a minimum sale price from pioneer and optimized E. coli plants at 761 kg-1 and 23 kg-1 with greenhouse gas emissions of 572 kg CO2-eq. kg-1 and 55 kg CO2-eq. kg-1, respectively. Spider silk sale price estimates from goat pioneer and optimized results are 730 kg-1 and 54 kg-1, respectively, with pioneer and optimized alfalfa plants are 207 kg-1 and 9.22 kg-1 respectively. Elevated costs and emissions from the pioneer plant can be directly tied to the high material consumption and low protein yield. Decreased production costs associated with the optimized plants include improved protein yield, process optimization, and an Nth plant assumption. Discussion focuses on the commercial potential of spider silk, the production performance requirements for commercialization, and impact of alternative technologies on the sustainability of the system.

  12. “Turn-on” fluorescence probe integrated polymer nanoparticles for sensing biological thiol molecules

    Science.gov (United States)

    Ang, Chung Yen; Tan, Si Yu; Lu, Yunpeng; Bai, Linyi; Li, Menghuan; Li, Peizhou; Zhang, Quan; Selvan, Subramanian Tamil; Zhao, Yanli

    2014-11-01

    A ``turn-on'' thiol-responsive fluorescence probe was synthesized and integrated into polymeric nanoparticles for sensing intracellular thiols. There is a photo-induced electron transfer process in the off state of the probe, and this process is terminated upon the reaction with thiol compounds. Configuration interaction singles (CIS) calculation was performed to confirm the mechanism of this process. A series of sensing studies were carried out, showing that the probe-integrated nanoparticles were highly selective towards biological thiol compounds over non-thiolated amino acids. Kinetic studies were also performed to investigate the relative reaction rate between the probe and the thiolated amino acids. Subsequently, the Gibbs free energy of the reactions was explored by means of the electrochemical method. Finally, the detection system was employed for sensing intracellular thiols in cancer cells, and the sensing selectivity could be further enhanced with the use of a cancer cell-targeting ligand in the nanoparticles. This development paves a path for the sensing and detection of biological thiols, serving as a potential diagnostic tool in the future.

  13. PathText: a text mining integrator for biological pathway visualizations

    Science.gov (United States)

    Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

    2010-01-01

    Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

  14. Treatment of high strength distillery wastewater (cherry stillage) by integrated aerobic biological oxidation and ozonation.

    Science.gov (United States)

    Beltrán, F J; Alvarez, P M; Rodríguez, E M; García-Araya, J F; Rivas, J

    2001-01-01

    The performance of integrated aerobic digestion and ozonation for the treatment of high strength distillery wastewater (i.e., cherry stillage) is reported. Experiments were conducted in laboratory batch systems operating in draw and fill mode. For the biological step, activated sludge from a municipal wastewater treatment facility was used as inoculum, showing a high degree of activity to distillery wastewater. Thus, BOD and COD overall conversions of 95% and 82% were achieved, respectively. However, polyphenol content and absorbance at 254 nm (A(254)) could not be reduced more than 35% and 15%, respectively, by means of single biological oxidation. By considering COD as substrate, the aerobic digestion process followed a Contois' model kinetics, from which the maximum specific growth rate of microorganisms (mu(max)) and the inhibition factor, beta, were then evaluated at different conditions of temperature and pH. In the combined process, the effect of a post-ozonation stage was studied. The main goals achieved by the ozonation step were the removal of polyphenols and A(254). Therefore, ozonation was shown to be an appropriate technology to aid aerobic biological oxidation in the treatment of cherry stillage.

  15. Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

    Science.gov (United States)

    Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

    2013-10-12

    Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

  16. Pollution control in pulp and paper industrial effluents using integrated chemical-biological treatment sequences.

    Science.gov (United States)

    El-Bestawy, Ebtesam; El-Sokkary, Ibrahim; Hussein, Hany; Keela, Alaa Farouk Abu

    2008-11-01

    The main objective of the present study was to improve the quality of pulp and paper industrial wastewater of two local mills RAKTA and El-Ahlia, Alexandria, Egypt, and to bring their pollutant contents to safe discharge levels. Quality improvement was carried out using integrated chemical and biological treatment approaches after their optimization. Chemical treatment (alum, lime, and ferric chloride) was followed by oxidation using hydrogen peroxide and finally biological treatment using activated sludge (90 min for RAKTA and 60 min for El-Ahlia effluents). Chemical coagulation produced low-quality effluents, while pH adjustment during coagulation treatment did not enhance the quality of the effluents. Maximum removal of the tested pollutants was achieved using the integrated treatment and the pollutants recorded residual concentrations (RCs) of 34.67, 17.33, 0.13, and 0.43 mg/l and 15.0, 11.0, 0.0, and 0.13 mg/l for chemical oxygen demand (COD), biochemical oxygen demand (BOD5), tannin and lignin, and silica in RAKTA and El-Ahlia effluents, respectively, all of which were below their maximum permissible limits (MPLs) for the safe discharge into water courses. Specific oxygen uptake rate (SOUR) and sludge volume index (SVI) values reflect good conditions and healthy activated sludge. Based on the previous results, optimized conditions were applied as bench scale on the raw effluents of RAKTA and El-Ahlia via the batch chemical and the biological treatment sequences proposed. For RAKTA effluents, the sequence was as follows: (1) coagulation with 375 mg/l FeCl3, (2) oxidation with 50 mg/l hydrogen peroxide, and (3) biological treatment using activated sludge with 2,000 mg/l initial concentration and 90 min hydraulic retention time (HRT), while for El-Ahlia raw effluents, the sequence was (1) coagulation with 250 mg/l FeCl3, (2) oxidation with 45 mg/l hydrogen peroxide, and (3) biological treatment using activated sludge with 2,000 mg/l initial concentration and 60

  17. A semantic web framework to integrate cancer omics data with biological knowledge.

    Science.gov (United States)

    Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

    2012-01-25

    The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

  18. Meteorological Integration for the Biological Warning and Incident Characterization (BWIC) System: General Guidance for BWIC Cities

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, William J.; Wang, Weiguo; Rutz, Frederick C.; Chapman, Elaine G.; Rishel, Jeremy P.; Xie, YuLong; Seiple, Timothy E.; Allwine, K Jerry

    2007-02-16

    The U.S. Department of Homeland Security (DHS) is responsible for developing systems to detect the release of aerosolized bioagents in urban environments. The system that accomplishes this, known as BioWatch, is a robust first-generation monitoring system. In conjunction with the BioWatch detection network, DHS has also developed a software tool for cities to use to assist in their response when a bioagent is detected. This tool, the Biological Warning and Incident Characterization (BWIC) System, will eventually be deployed to all BioWatch cities to aid in the interpretation of the public health significance of indicators from the BioWatch networks. BWIC consists of a set of integrated modules, including meteorological models, that estimate the effect of a biological agent on a city’s population once it has been detected. For the meteorological models in BWIC to successfully calculate the distribution of biological material, they must have as input accurate meteorological data, and wind fields in particular. The purpose of this document is to provide guidance for cities to use in identifying sources of good-quality local meteorological data that BWIC needs to function properly. This process of finding sources of local meteorological data, evaluating the data quality and gaps in coverage, and getting the data into BWIC, referred to as meteorological integration, is described. The good news for many cities is that meteorological measurement networks are becoming increasingly common. Most of these networks allow their data to be distributed in real time via the internet. Thus, cities will often only need to evaluate the quality of available measurements and perhaps add a modest number of stations where coverage is poor.

  19. Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

    Science.gov (United States)

    Nottale, Laurent; Auffray, Charles

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

  20. Similar patterns of frequency-dependent selection on animal personalities emerge in three species of social spiders.

    Science.gov (United States)

    Lichtenstein, J L L; Pruitt, J N

    2015-06-01

    Frequency-dependent selection is thought to be a major contributor to the maintenance of phenotypic variation. We tested for frequency-dependent selection on contrasting behavioural strategies, termed here 'personalities', in three species of social spiders, each thought to represent an independent evolutionary origin of sociality. The evolution of sociality in the spider genus Anelosimus is consistently met with the emergence of two temporally stable discrete personality types: an 'aggressive' or 'docile' form. We assessed how the foraging success of each phenotype changes as a function of its representation within a colony. We did this by creating experimental colonies of various compositions (six aggressives, three aggressives and three dociles, one aggressive and five dociles, six dociles), maintaining them in a common garden for 3 weeks, and tracking the mass gained by individuals of either phenotype. We found that both the docile and aggressive phenotypes experienced their greatest mass gain in mixed colonies of mostly docile individuals. However, the performance of both phenotypes decreased as the frequency of the aggressive phenotype increased. Nearly identical patterns of phenotype-specific frequency dependence were recovered in all three species. Naturally occurring colonies of these spiders exhibit mixtures dominated by the docile phenotype, suggesting that these spiders may have evolved mechanisms to maintain the compositions that maximize the success of the colony without compromising the expected reproductive output of either phenotype. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  1. Spider and burnable poison rod combinations

    International Nuclear Information System (INIS)

    Walton, L.A.

    1980-01-01

    A description is given of an improved design of burnable poison rods and their associated spiders used in the fuel assemblies of pressurized water power reactor cores which allows the rods to be installed and removed more quickly, simply and gently than in previously described systems. (U.K.)

  2. Silk Spinning in Silkworms and Spiders.

    Science.gov (United States)

    Andersson, Marlene; Johansson, Jan; Rising, Anna

    2016-08-09

    Spiders and silkworms spin silks that outcompete the toughness of all natural and manmade fibers. Herein, we compare and contrast the spinning of silk in silkworms and spiders, with the aim of identifying features that are important for fiber formation. Although spiders and silkworms are very distantly related, some features of spinning silk seem to be universal. Both spiders and silkworms produce large silk proteins that are highly repetitive and extremely soluble at high pH, likely due to the globular terminal domains that flank an intermediate repetitive region. The silk proteins are produced and stored at a very high concentration in glands, and then transported along a narrowing tube in which they change conformation in response primarily to a pH gradient generated by carbonic anhydrase and proton pumps, as well as to ions and shear forces. The silk proteins thereby convert from random coil and alpha helical soluble conformations to beta sheet fibers. We suggest that factors that need to be optimized for successful production of artificial silk proteins capable of forming tough fibers include protein solubility, pH sensitivity, and preservation of natively folded proteins throughout the purification and initial spinning processes.

  3. The aerodynamic signature of running spiders.

    Directory of Open Access Journals (Sweden)

    Jérôme Casas

    Full Text Available Many predators display two foraging modes, an ambush strategy and a cruising mode. These foraging strategies have been classically studied in energetic, biomechanical and ecological terms, without considering the role of signals produced by predators and perceived by prey. Wolf spiders are a typical example; they hunt in leaf litter either using an ambush strategy or by moving at high speed, taking over unwary prey. Air flow upstream of running spiders is a source of information for escaping prey, such as crickets and cockroaches. However, air displacement by running arthropods has not been previously examined. Here we show, using digital particle image velocimetry, that running spiders are highly conspicuous aerodynamically, due to substantial air displacement detectable up to several centimetres in front of them. This study explains the bimodal distribution of spider's foraging modes in terms of sensory ecology and is consistent with the escape distances and speeds of cricket prey. These findings may be relevant to the large and diverse array of arthropod prey-predator interactions in leaf litter.

  4. SPiDer: Smart Pill Dispenser

    OpenAIRE

    Moreno Vázquez, Jonatan

    2013-01-01

    Aquest projecte proposa el sistema SPiDer el qual te l'objectiu d'assistir a la gent gran en el procés de medicar-se evitant els problemes associats amb la baixa adherència existent actualment amb els calendaris farmacològics receptats pels doctors.

  5. Peptidomic and transcriptomic profiling of four distinct spider venoms.

    Directory of Open Access Journals (Sweden)

    Vera Oldrati

    Full Text Available Venom based research is exploited to find novel candidates for the development of innovative pharmacological tools, drug candidates and new ingredients for cosmetic and agrochemical industries. Moreover, venomics, as a well-established approach in systems biology, helps to elucidate the genetic mechanisms of the production of such a great molecular biodiversity. Today the advances made in the proteomics, transcriptomics and bioinformatics fields, favor venomics, allowing the in depth study of complex matrices and the elucidation even of minor compounds present in minute biological samples. The present study illustrates a rapid and efficient method developed for the elucidation of venom composition based on NextGen mRNA sequencing of venom glands and LC-MS/MS venom proteome profiling. The analysis of the comprehensive data obtained was focused on cysteine rich peptide toxins from four spider species originating from phylogenetically distant families for comparison purposes. The studied species were Heteropoda davidbowie (Sparassidae, Poecilotheria formosa (Theraphosidae, Viridasius fasciatus (Viridasiidae and Latrodectus mactans (Theridiidae. This led to a high resolution profiling of 284 characterized cysteine rich peptides, 111 of which belong to the Inhibitor Cysteine Knot (ICK structural motif. The analysis of H. davidbowie venom revealed a high richness in term of venom diversity: 95 peptide sequences were identified; out of these, 32 peptides presented the ICK structural motif and could be classified in six distinct families. The profiling of P. formosa venom highlighted the presence of 126 peptide sequences, with 52 ICK toxins belonging to three structural distinct families. V. fasciatus venom was shown to contain 49 peptide sequences, out of which 22 presented the ICK structural motif and were attributed to five families. The venom of L. mactans, until now studied for its large neurotoxins (Latrotoxins, revealed the presence of 14

  6. Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

    Directory of Open Access Journals (Sweden)

    Ghisalberti Giorgio

    2010-12-01

    different biological databases and integrated in the GFINDer data warehouse. By doing so, we identified in these data a variety of different types of errors and inconsistencies; this enables us to ensure good quality of the data in the GFINDer data warehouse. We reported all identified data errors and inconsistencies to the curators of the original databases from where the data were retrieved, who mainly corrected them in subsequent updating of the original database. This contributed to improve the quality of the data available, in the original databases, to the whole scientific community.

  7. Integration of Plant Defense Traits with Biological Control of Arthropod Pests: Challenges and Opportunities.

    Science.gov (United States)

    Peterson, Julie A; Ode, Paul J; Oliveira-Hofman, Camila; Harwood, James D

    2016-01-01

    Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control. Plant defense traits can influence both the numerical and functional responses of natural enemies; these interactions can be semiochemically, plant toxin-, plant nutrient-, and/or physically mediated. Case studies involving predators, parasitoids, and pathogens of crop pests will be presented and discussed. These diverse groups of natural enemies may respond differently to crop plant traits based on their own unique biology and the ecological niches they fill. Genetically modified crop plants that have been engineered to express transgenic products affecting herbivorous pests are an additional consideration. For the most part, transgenic plant incorporated protectant (PIP) traits are compatible with biological control due to their selective toxicity to targeted pests and relatively low non-target impacts, although transgenic crops may have indirect effects on higher trophic levels and arthropod communities mediated by lower host or prey number and/or quality. Host plant resistance and biological control are two of the key pillars of integrated pest management; their potential interactions, whether they are synergistic, complementary, or disruptive, are key in understanding and achieving sustainable and effective pest management.

  8. Integration of plant defense traits with biological control of arthropod pests: challenges and opportunities

    Directory of Open Access Journals (Sweden)

    Julie A Peterson

    2016-11-01

    Full Text Available Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control. Plant defense traits can influence both the numerical and functional responses of natural enemies; these interactions can be semiochemically-, plant toxin-, plant nutrient-, and/or physically-mediated. Case studies involving predators, parasitoids, and pathogens of crop pests will be presented and discussed. These diverse groups of natural enemies may respond differently to crop plant traits based on their own unique biology and the ecological niches they fill. Genetically modified crop plants that have been engineered to express transgenic products affecting herbivorous pests are an additional consideration. For the most part, transgenic plant incorporated protectant (PIP traits are compatible with biological control due to their selective toxicity to targeted pests and relatively low non-target impacts, although transgenic crops may have indirect effects on higher trophic levels and arthropod communities mediated by lower host or prey number and/or quality. Host plant resistance and biological control are two of the key pillars of integrated pest management; their potential interactions, whether they are synergistic, complementary, or disruptive, are key in understanding and achieving sustainable and effective pest management.

  9. Status of the CNESM diagnostic for SPIDER

    International Nuclear Information System (INIS)

    Muraro, A.; Croci, G.; Albani, G.; Cazzaniga, C.; Claps, G.; Cavenago, M.; Grosso, G.; Palma, M. Dalla; Fincato, M.; Murtas, F.; Pasqualotto, R.; Cippo, E. Perelli; Rebai, M.; Tollin, M.; Tardocchi, M.; Gorini, G.

    2015-01-01

    Highlights: • We have finished the design of the detector box of the CNESM diagnostic for SPIDER. • We have constructed the GEM detector of the CNESM detector for SPIDER. • We have tested the detector under fast neutron irradiation. - Abstract: The ITER neutral beam test facility under construction in Padova will host two experimental devices: SPIDER, a 100 kV negative H/D RF source, and MITICA, a full scale, 1 MeV deuterium beam injector. A detection system called close-contact neutron emission surface mapping (CNESM) is under development with the aim to resolve the horizontal beam intensity profile in MITICA and one of the eight beamlet groups in SPIDER, with a spatial resolution of 1.5 and 2.5 cm respectively. This is achieved by the evaluation of the map of the neutron emission due to interaction of the deuterium beam with the deuterons implanted in the beam dump surface. CNESM uses nGEM detectors, i.e. GEM detectors equipped with a cathode that also serves as neutron–proton converter foil. The diagnostic will be placed right behind the SPIDER and MITICA beam dump, i.e. in an UHV environment, but the nGEM detectors need to operate at atmospheric pressure: in order to maintain the detector at atmospheric pressure, a vacuum sealed box, that will be mounted inside the vacuum, has been designed. The box design was driven by the need to minimize the neutron attenuation and the distance between the beam dump surface and the detector active area. This paper presents the status of the CNESM diagnostic describing the design of the detector, the design of the sealed box and reporting the results obtained with the first full-size prototype under fast neutron irradiation.

  10. Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

    Science.gov (United States)

    He, Yongqun

    2014-07-01

    While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

  11. The use of aquatic macrophytes in monitoring and in assessment of biological integrity

    Science.gov (United States)

    Stewart, P.M.; Scribailo, R.W.; Simon, T.P.; Gerhardt, A.

    1999-01-01

    Aquatic plant species, populations, and communities should be used as indicators of the aquatic environment, allowing detection of ecosystem response to different stressors. Plant tissues bioaccumulate and concentrate toxin levels higher than what is present in the sediments; and this appears to be related to organic matter content, acidification, and buffering capacity. The majority of toxicity studies, most of these with heavy metals, have been done with several Lemna species and Vallisneria americana. Organic chemicals reviewed include pesticides and herbicides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other industrial contaminants. The use of aquatic plant communities as bioindicators of environmental quality was evaluated for specific characteristics and indices that may assess biological integrity. Indices such as the floristic quality index (FQI) and coefficient of conservatism (C) are pioneering efforts to describe the quality of natural areas and protect native biodiversity. Our case study in the Grand Calumet Lagoons found that 'least-impacted' sites had the greatest aquatic plant species richness, highest FQI and C values, and highest relative abundance. Lastly, we introduce the concepts necessary for the development of a plant index of biotic integrity. Development of reference conditions is essential to understanding aquatic plant community structure, function, individual health, condition, and abundance. Information on guild development and tolerance definition are also integral to the development of a multi-metric index.

  12. A novel neurotoxin from venom of the spider, Brachypelma albopilosum.

    Directory of Open Access Journals (Sweden)

    Yunhua Zhong

    Full Text Available Spiders have evolved highly selective toxins for insects. There are many insecticidal neurotoxins in spider venoms. Although a large amount of work has been done to focus on neurotoxicity of spider components, little information, which is related with effects of spider toxins on tumor cell proliferation and cytotoxicity, is available for Brachypelma albopilosum venom. In this work, a novel spider neurotoxin (brachyin was identified and characterized from venoms of the spider, Brachypelma albopilosum. Brachyin is composed of 41 amino acid residues with the sequence of CLGENVPCDKDRPNCCSRYECLEPTGYGWWYASYYCYKKRS. There are six cysteines in this sequence, which form three disulfided bridges. The serine residue at the C-terminus is amidated. Brachyin showed strong lethal effects on American cockroaches (Periplaneta americana and Tenebrio molitor (common mealbeetle. This neurotoxin also showed significant analgesic effects in mice models including abdominal writhing induced by acetic acid and formalin-induced paw licking tests. It was interesting that brachyin exerted marked inhibition on tumor cell proliferation.

  13. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells.

    Science.gov (United States)

    Angelici, Bartolomeo; Mailand, Erik; Haefliger, Benjamin; Benenson, Yaakov

    2016-08-30

    One of the goals of synthetic biology is to develop programmable artificial gene networks that can transduce multiple endogenous molecular cues to precisely control cell behavior. Realizing this vision requires interfacing natural molecular inputs with synthetic components that generate functional molecular outputs. Interfacing synthetic circuits with endogenous mammalian transcription factors has been particularly difficult. Here, we describe a systematic approach that enables integration and transduction of multiple mammalian transcription factor inputs by a synthetic network. The approach is facilitated by a proportional amplifier sensor based on synergistic positive autoregulation. The circuits efficiently transduce endogenous transcription factor levels into RNAi, transcriptional transactivation, and site-specific recombination. They also enable AND logic between pairs of arbitrary transcription factors. The results establish a framework for developing synthetic gene networks that interface with cellular processes through transcriptional regulators. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology.

    Science.gov (United States)

    Aricescu, A Radu; Owens, Raymond J

    2013-06-01

    Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. CoreFlow: A computational platform for integration, analysis and modeling of complex biological data

    DEFF Research Database (Denmark)

    Pasculescu, Adrian; Schoof, Erwin; Creixell, Pau

    2014-01-01

    between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion......A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which...... provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts...

  16. Neurological and biological foundations of children's social and emotional development: an integrated literature review.

    Science.gov (United States)

    Nelson, Helen Jean; Kendall, Garth Edward; Shields, Linda

    2014-08-01

    This article provides an integrated review of the expert literature on developmental processes that combine social, biological, and neurological pathways, and the mechanisms through which these pathways may influence school success and health. It begins with a historical overview of the current understanding of how attachment relationships and social environments influence brain development and plasticity and are, therefore, central to the physical and mental health of individuals and populations. It then expands on the effect of plasticity in relation to behavior and learning at school. This article concludes with a discussion of the role the school nurse may play in supporting health and learning by recognizing signs of relational stress and by advocating for prevention strategies. © The Author(s) 2013.

  17. Integrating population genetics and conservation biology in the era of genomics.

    Science.gov (United States)

    Ouborg, N Joop

    2010-02-23

    As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

  18. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

    Science.gov (United States)

    Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

    2017-10-01

    Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Numerical implementation of multiple peeling theory and its application to spider web anchorages.

    Science.gov (United States)

    Brely, Lucas; Bosia, Federico; Pugno, Nicola M

    2015-02-06

    Adhesion of spider web anchorages has been studied in recent years, including the specific functionalities achieved through different architectures. To better understand the delamination mechanisms of these and other biological or artificial fibrillar adhesives, and how their adhesion can be optimized, we develop a novel numerical model to simulate the multiple peeling of structures with arbitrary branching and adhesion angles, including complex architectures. The numerical model is based on a recently developed multiple peeling theory, which extends the energy-based single peeling theory of Kendall, and can be applied to arbitrarily complex structures. In particular, we numerically show that a multiple peeling problem can be treated as the superposition of single peeling configurations even for complex structures. Finally, we apply the developed numerical approach to study spider web anchorages, showing how their function is achieved through optimal geometrical configurations.

  20. Sparse canonical methods for biological data integration: application to a cross-platform study

    Directory of Open Access Journals (Sweden)

    Robert-Granié Christèle

    2009-01-01

    Full Text Available Abstract Background In the context of systems biology, few sparse approaches have been proposed so far to integrate several data sets. It is however an important and fundamental issue that will be widely encountered in post genomic studies, when simultaneously analyzing transcriptomics, proteomics and metabolomics data using different platforms, so as to understand the mutual interactions between the different data sets. In this high dimensional setting, variable selection is crucial to give interpretable results. We focus on a sparse Partial Least Squares approach (sPLS to handle two-block data sets, where the relationship between the two types of variables is known to be symmetric. Sparse PLS has been developed either for a regression or a canonical correlation framework and includes a built-in procedure to select variables while integrating data. To illustrate the canonical mode approach, we analyzed the NCI60 data sets, where two different platforms (cDNA and Affymetrix chips were used to study the transcriptome of sixty cancer cell lines. Results We compare the results obtained with two other sparse or related canonical correlation approaches: CCA with Elastic Net penalization (CCA-EN and Co-Inertia Analysis (CIA. The latter does not include a built-in procedure for variable selection and requires a two-step analysis. We stress the lack of statistical criteria to evaluate canonical correlation methods, which makes biological interpretation absolutely necessary to compare the different gene selections. We also propose comprehensive graphical representations of both samples and variables to facilitate the interpretation of the results. Conclusion sPLS and CCA-EN selected highly relevant genes and complementary findings from the two data sets, which enabled a detailed understanding of the molecular characteristics of several groups of cell lines. These two approaches were found to bring similar results, although they highlighted the same

  1. Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit.

    Science.gov (United States)

    Perry, Nicolas; Nelson, Edward M; Timp, Gregory

    2016-12-16

    The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

  2. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  3. The integral biologically effective dose to predict brain stem toxicity of hypofractionated stereotactic radiotherapy

    International Nuclear Information System (INIS)

    Clark, Brenda G.; Souhami, Luis; Pla, Conrado; Al-Amro, Abdullah S.; Bahary, Jean-Paul; Villemure, Jean-Guy; Caron, Jean-Louis; Olivier, Andre; Podgorsak, Ervin B.

    1998-01-01

    Purpose: The aim of this work was to develop a parameter for use during fractionated stereotactic radiotherapy treatment planning to aid in the determination of the appropriate treatment volume and fractionation regimen that will minimize risk of late damage to normal tissue. Materials and Methods: We have used the linear quadratic model to assess the biologically effective dose at the periphery of stereotactic radiotherapy treatment volumes that impinge on the brain stem. This paper reports a retrospective study of 77 patients with malignant and benign intracranial lesions, treated between 1987 and 1995, with the dynamic rotation technique in 6 fractions over a period of 2 weeks, to a total dose of 42 Gy prescribed at the 90% isodose surface. From differential dose-volume histograms, we evaluated biologically effective dose-volume histograms and obtained an integral biologically-effective dose (IBED) in each case. Results: Of the 77 patients in the study, 36 had target volumes positioned so that the brain stem received more than 1% of the prescribed dose, and 4 of these, all treated for meningioma, developed serious late damage involving the brain stem. Other than type of lesion, the only significant variable was the volume of brain stem exposed. An analysis of the IBEDs received by these 36 patients shows evidence of a threshold value for late damage to the brain stem consistent with similar thresholds that have been determined for external beam radiotherapy. Conclusions: We have introduced a new parameter, the IBED, that may be used to represent the fractional effective dose to structures such as the brain stem that are partially irradiated with stereotactic dose distributions. The IBED is easily calculated prior to treatment and may be used to determine appropriate treatment volumes and fractionation regimens minimizing possible toxicity to normal tissue

  4. Attention and amygdala activity: an fMRI study with spider pictures in spider phobia.

    Science.gov (United States)

    Alpers, Georg W; Gerdes, Antje B M; Lagarie, Bernadette; Tabbert, Katharina; Vaitl, Dieter; Stark, Rudolf

    2009-06-01

    Facilitated detection of threatening visual cues is thought to be adaptive. In theory, detection of threat cues should activate the amygdala independently from allocation of attention. However, previous studies using emotional facial expressions as well as phobic cues yielded contradictory results. We used fMRI to examine whether the allocation of attention to components of superimposed spider and bird displays modulates amygdala activation. Nineteen spider-phobic women were instructed to identify either a moving or a stationary animal in briefly presented double-exposure displays. Amygdala activation followed a dose-response relationship: Compared to congruent neutral displays (two birds), amygdala activation was most pronounced in response to congruent phobic displays (two spiders) and less but still significant in response to mixed displays (spider and bird) when attention was focused on the phobic component. When attention was focused on the neutral component, mixed displays did not result in significant amygdala activation. This was confirmed in a significant parametric graduation of the amygdala activation in the order of congruent phobic displays, mixed displays with attention focus on the spider, mixed displays with focus on the bird and congruent neutral displays. These results challenge the notion that amygdala activation in response to briefly presented phobic cues is independent from attention.

  5. What you fear will appear: detection of schematic spiders in spider fear.

    Science.gov (United States)

    Peira, Nathalie; Golkar, Armita; Larsson, Maria; Wiens, Stefan

    2010-01-01

    Various experimental tasks suggest that fear guides attention. However, because these tasks often lack ecological validity, it is unclear to what extent results from these tasks can be generalized to real-life situations. In change detection tasks, a brief interruption of the visual input (i.e., a blank interval or a scene cut) often results in undetected changes in the scene. This setup resembles real-life viewing behavior and is used here to increase ecological validity of the attentional task without compromising control over the stimuli presented. Spider-fearful and nonfearful women detected schematic spiders and flowers that were added to one of two identical background pictures that alternated with a brief blank in between them (i.e., flicker paradigm). Results showed that spider-fearful women detected spiders (but not flowers) faster than did nonfearful women. Because spiders and flowers had similar low-level features, these findings suggest that fear guides attention on the basis of object features rather than simple low-level features.

  6. Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

    International Nuclear Information System (INIS)

    Suryaman, Dhanus; Hasegawa, Kiyoshi

    2010-01-01

    We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L -1 , each: 25 mg L -1 ). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h -1 , whereas by the combined photocatalytic-biological treatment was 10.5 mg h -1 . After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO 2 particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

  7. Biological and photocatalytic treatment integrated with separation and reuse of titanium dioxide on the removal of chlorophenols in tap water

    Energy Technology Data Exchange (ETDEWEB)

    Suryaman, Dhanus, E-mail: dhanussuryaman@yahoo.com [Agency for the Assessment and Application of Technology, M.H. Thamrin No. 8, Jakarta 10340 (Indonesia); Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan); Hasegawa, Kiyoshi [Department of Chemical and Biochemical Engineering, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)

    2010-11-15

    We investigated biological, photocatalytic, and combination of biological and photocatalytic treatments in order to remove a mixture of 2-chlorophenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, and pentachlorophenol in tap water (total: 100 mg L{sup -1}, each: 25 mg L{sup -1}). The removal of chlorinated phenols was conducted with a flow biological treatment and a circulative flow photocatalytic treatment under black light and sunlight irradiations integrated with titanium dioxide separation and reuse. The combined biological-photocatalytic treatment significantly shortened the degradation and mineralization time of both the biological treatment and the photocatalytic treatment. The removed chlorophenols per hour by the combined biological-photocatalytic treatment was 25.8 mg h{sup -1}, whereas by the combined photocatalytic-biological treatment was 10.5 mg h{sup -1}. After a large portion of biodegradable 2-chlorophenol and 2,4-dichlorophenol, and around half amount of slightly biodegradable 2,4,5-trichlorophenol were removed by the biological treatment, the remained three chlorophenols, biorecalcitrant pentachlorophenol, and biodegradation products were completely removed by the subsequent photocatalytic treatment. Since titanium dioxide particles in tap water spontaneously sedimented on standing after the photocatalytic treatment, the combined treatment can be operated by integrating with the titanium dioxide separation and reuse. The TiO{sub 2} particles were recovered and reused at least three times without significantly decreasing the removal efficiency.

  8. On the ecology of the cursorial spider Odo bruchi (Araneae: Zoridae in a grassland natural reserve from central Argentina

    Directory of Open Access Journals (Sweden)

    Gabriel Pompozzi

    2014-03-01

    Full Text Available The “Ernesto Tornquist” Provincial Park (ETPP is located inside the Ventania system (Argentina and was created to protect one of the last relicts of pampean grasslands. Even though many studies have looked at the vertebrate faunal diversity, biology, and conservation in this Park, few studies have been dedicated to arthropods. Among these, spiders have been used as ecological indicators to evaluate nature conservation status, nevertheless, basic information on their distribution and ecology is necessary for their use as indicator taxa in this region. Thus the goal of this study was to present the phenology and demography of the spider Odo bruchi, a cursorial spider present in the ETPP. For this, spiders were sampled bimonthly using pitfall traps between September 2009-2010 (first year, and March 2011-2012 (second year. A total of 10 traps were placed every 10m along a transect of 100m parallel to the longest axis of a grassland slope with native vegetation. Traps were filled with 1 500mL of ethylene glycol, that were examined and refilled every 60 day period. We collected a total of 799 specimens in two years. Juveniles were the most abundant reaching 47.8% of the total, while males corresponded to 27.8% and females 24.4%. We found significant differences in the mean abundance of O. bruchi: the abundance during spring-summer (Nov-Dec-Jan-Feb was significantly higher than the other periods of the two years period. Moreover, we found an even abundance distribution throughout the year in the entire study. This work represents one of the first contributions to the ecology of this spider family in the area. Also, our results comprise relevant information to encourage future studies on this spider species as a bio-indicator of the conservation status of pampean grasslands.

  9. Learning to avoid spiders: fear predicts performance, not competence.

    Science.gov (United States)

    Luo, Xijia; Becker, Eni S; Rinck, Mike

    2018-01-05

    We used an immersive virtual environment to examine avoidance learning in spider-fearful participants. In 3 experiments, participants were asked to repeatedly lift one of 3 virtual boxes, under which either a toy car or a spider appeared and then approached the participant. Participants were not told that the probability of encountering a spider differed across boxes. When the difference was large (Exps. 1 and 2), spider-fearfuls learned to avoid spiders by lifting the few-spiders-box more often and the many-spiders-box less often than non-fearful controls did. However, they hardly managed to do so when the probability differences were small (Exp. 3), and they did not escape from threat more quickly (Exp. 2). In contrast to the observed performance differences, spider-fearfuls and non-fearfuls showed equal competence, that is comparable post-experimental knowledge about the probability to encounter spiders under the 3 boxes. The limitations and implications of the present study are discussed.

  10. Sex-specific kleptoparasitic foraging in ant-eating spiders

    DEFF Research Database (Denmark)

    Martisová, Martina; Bilde, T.; Pekar, Stano

    2009-01-01

    . To investigate this hypothesis, we studied the effect of sex and life history stage on the frequency of kleptoparasitism in ant-eating spiders of the genus Zodarion in the field. These spiders use a special capture technique involving a quick attack on an ant that is left unguarded by spiders for several minutes......, providing ample opportunities for kleptoparasitism. We found that adult females consistently hunted actively, while adult males ceased active prey capture and instead engaged in kleptoparasitism. Juvenile spiders were active hunters irrespective of sex. Consistent with an ontogenetic shift in foraging...

  11. Second-order nonlinear optical microscopy of spider silk

    Science.gov (United States)

    Zhao, Yue; Hien, Khuat Thi Thu; Mizutani, Goro; Rutt, Harvey N.

    2017-06-01

    Asymmetric β-sheet protein structures in spider silk should induce nonlinear optical interaction such as second harmonic generation (SHG) which is experimentally observed for a radial line and dragline spider silk using an imaging femtosecond laser SHG microscope. By comparing different spider silks, we found that the SHG signal correlates with the existence of the protein β-sheets. Measurements of the polarization dependence of SHG from the dragline indicated that the β-sheet has a nonlinear response depending on the direction of the incident electric field. We propose a model of what orientation the β-sheet takes in spider silk.

  12. Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

    Science.gov (United States)

    Vallat, Brinda; Webb, Benjamin; Westbrook, John D; Sali, Andrej; Berman, Helen M

    2018-04-09

    Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Development of a flexible microfluidic system integrating magnetic micro-actuators for trapping biological species

    International Nuclear Information System (INIS)

    Fulcrand, R; Jugieu, D; Escriba, C; Bancaud, A; Bourrier, D; Boukabache, A; Gué, A M

    2009-01-01

    A flexible microfluidic system embedding microelectromagnets has been designed, modeled and fabricated by using a photosensitive resin as structural material. The fabrication process involves the integration of micro-coils in a multilayer SU-8 microfluidic system by combining standard electroplating and dry films lamination. This technique offers numerous advantages in terms of integration, biocompatibility and chemical resistance. Various designs of micro-coils, including spiral, square or serpentine wires, have been simulated and experimentally tested. It has been established that thermal dissipation in micro-coils depends strongly on the number of turns and current density but remains compatible with biological applications. Real-time experimentations show that these micro-actuators are efficient in trapping magnetic micro-beads without any external field source or a permanent magnet and highlight that the size of microfluidic channels has been adequately designed for optimal trapping. Moreover, we trap magnetic beads in less than 2 s and release them instantaneously into the micro-channel. The actuation solely relies on electric fields, which are easier to control than standard magneto-fluidic modules

  14. Development of a flexible microfluidic system integrating magnetic micro-actuators for trapping biological species

    Science.gov (United States)

    Fulcrand, R.; Jugieu, D.; Escriba, C.; Bancaud, A.; Bourrier, D.; Boukabache, A.; Gué, A. M.

    2009-10-01

    A flexible microfluidic system embedding microelectromagnets has been designed, modeled and fabricated by using a photosensitive resin as structural material. The fabrication process involves the integration of micro-coils in a multilayer SU-8 microfluidic system by combining standard electroplating and dry films lamination. This technique offers numerous advantages in terms of integration, biocompatibility and chemical resistance. Various designs of micro-coils, including spiral, square or serpentine wires, have been simulated and experimentally tested. It has been established that thermal dissipation in micro-coils depends strongly on the number of turns and current density but remains compatible with biological applications. Real-time experimentations show that these micro-actuators are efficient in trapping magnetic micro-beads without any external field source or a permanent magnet and highlight that the size of microfluidic channels has been adequately designed for optimal trapping. Moreover, we trap magnetic beads in less than 2 s and release them instantaneously into the micro-channel. The actuation solely relies on electric fields, which are easier to control than standard magneto-fluidic modules.

  15. Integration of systems biology with organs-on-chips to humanize therapeutic development

    Science.gov (United States)

    Edington, Collin D.; Cirit, Murat; Chen, Wen Li Kelly; Clark, Amanda M.; Wells, Alan; Trumper, David L.; Griffith, Linda G.

    2017-02-01

    "Mice are not little people" - a refrain becoming louder as the gaps between animal models and human disease become more apparent. At the same time, three emerging approaches are headed toward integration: powerful systems biology analysis of cell-cell and intracellular signaling networks in patient-derived samples; 3D tissue engineered models of human organ systems, often made from stem cells; and micro-fluidic and meso-fluidic devices that enable living systems to be sustained, perturbed and analyzed for weeks in culture. Integration of these rapidly moving fields has the potential to revolutionize development of therapeutics for complex, chronic diseases, including those that have weak genetic bases and substantial contributions from gene-environment interactions. Technical challenges in modeling complex diseases with "organs on chips" approaches include the need for relatively large tissue masses and organ-organ cross talk to capture systemic effects, such that current microfluidic formats often fail to capture the required scale and complexity for interconnected systems. These constraints drive development of new strategies for designing in vitro models, including perfusing organ models, as well as "mesofluidic" pumping and circulation in platforms connecting several organ systems, to achieve the appropriate physiological relevance.

  16. A Candidate Vegetation Index of Biological Integrity Based on Species Dominance and Habitat Fidelity

    Science.gov (United States)

    Gara, Brian D; Stapanian, Martin A.

    2015-01-01

    Indices of biological integrity of wetlands based on vascular plants (VIBIs) have been developed in many areas of the USA and are used in some states to make critical management decisions. An underlying concept of all VIBIs is that they respond negatively to disturbance. The Ohio VIBI (OVIBI) is calculated from 10 metrics, which are different for each wetland vegetation class. We present a candidate vegetation index of biotic integrity based on floristic quality (VIBI-FQ) that requires only two metrics to calculate an overall score regardless of vegetation class. These metrics focus equally on the critical ecosystem elements of diversity and dominance as related to a species’ degree of fidelity to habitat requirements. The indices were highly correlated but varied among vegetation classes. Both indices responded negatively with a published index of wetland disturbance in 261 Ohio wetlands. Unlike VIBI-FQ, however, errors in classifying wetland vegetation may lead to errors in calculating OVIBI scores. This is especially critical when assessing the ecological condition of rapidly developing ecosystems typically associated with wetland restoration and creation projects. Compared to OVIBI, the VIBI-FQ requires less field work, is much simpler to calculate and interpret, and can potentially be applied to all habitat types. This candidate index, which has been “standardized” across habitats, would make it easier to prioritize funding because it would score the “best” and “worst” of all habitats appropriately and allow for objective comparison across different vegetation classes.

  17. Area-wide integration of lepidopteran F1 sterility and augmentative biological control

    International Nuclear Information System (INIS)

    Carpenter, James E.

    2000-01-01

    Area-wide pest management (APM) and integrated pest management (IPM) originated from two different efforts to combine two or more control techniques into programmes in which each method could synergise the effectiveness of others and thus create a level of pest control that was greater than that of a single technique (Perkins 1982). Since then, the concept of APM has evolved to include many aspects of IPM and often is now referred to as area-wide IPM. Still, the element of total population management is central to this approach of insect pest management. In support of APM, Knipling (1998) stated that of the insect pests that were of major concern to agriculture before the newer classes of insecticides were available, most are still pests today, the major exceptions being the screw-worm fly and the boll weevil in the southeastern US cotton growing region. Knipling also noted that both of these pest species were subjected to area-wide suppression programmes. In response to the USDA IPM Initiative (USDA 1993, 1994) which seeks to achieve the national goal of having 75% of the crop acres under IPM by the year 2000, the Agricultural Research Service developed an Area-wide IPM Programme. This programme combines environmentally-sound pest control techniques with the advantages of APM and develops partnerships with other federal, state, local and private sector entities. Technologies such as the integration of lepidopteran F 1 sterility and augmentative biological control may be considered for future programmes

  18. Removal of Furfural From Wastewater Using Integrated Catalytic Ozonation and Biological Approaches

    Directory of Open Access Journals (Sweden)

    Mostafa Leili

    2014-12-01

    Full Text Available Furfural with a chemical formula of C5H4O2 is a toxic compound which has several health problems for both humans and environment. It has a few exposure routes for entering the human body such as oral, dermal or nasal. In the present study, the efficacies of an integrated catalytic ozonation process (COP and novel cyclic biological reactor (CBR were explored for the removal of furfural from aqueous solutions. Activated carbon was purchased from Merck Company. It had a Brunauer, Emmett, and Teller (BET specific surface area of 1100 m2/g, with an average micropore volume and size of 0.385 cm3/g and 595 µm, respectively. The results indicated that 30% pretreatment with COP could increase furfural and chemical oxygen demand (COD removal efficiency with CBR 5.56% and 27.01%, respectively. With 70% pretreatment by COP, 98.57% furfural and 95.34% COD removal efficiencies happen in CBR. Generally, batch and continuous experiments showed that the integrated COP/CBR could be efficient in eliminating furfural from wastewater and thus may be a promising technique for treating furfural-containing wastewater.

  19. Decision-Making Under Risk: Integrating Perspectives From Biology, Economics, and Psychology.

    Science.gov (United States)

    Mishra, Sandeep

    2014-08-01

    Decision-making under risk has been variably characterized and examined in many different disciplines. However, interdisciplinary integration has not been forthcoming. Classic theories of decision-making have not been amply revised in light of greater empirical data on actual patterns of decision-making behavior. Furthermore, the meta-theoretical framework of evolution by natural selection has been largely ignored in theories of decision-making under risk in the human behavioral sciences. In this review, I critically examine four of the most influential theories of decision-making from economics, psychology, and biology: expected utility theory, prospect theory, risk-sensitivity theory, and heuristic approaches. I focus especially on risk-sensitivity theory, which offers a framework for understanding decision-making under risk that explicitly involves evolutionary considerations. I also review robust empirical evidence for individual differences and environmental/situational factors that predict actual risky decision-making that any general theory must account for. Finally, I offer steps toward integrating various theoretical perspectives and empirical findings on risky decision-making. © 2014 by the Society for Personality and Social Psychology, Inc.

  20. Abundance, Genetic Diversity and Persistence of Metarhizium Spp. Fungi from Soil of Strawberry Crops and Their Potential as Biological Control Agents against the Two-Spotted Spider Mite Tetranychus urticae

    DEFF Research Database (Denmark)

    Castro, Thiago Rodriguesde

    The growing demand for strawberries has imposed challenges, especially regarding the control of pests. Many farmers report problems with reduced chemical control efficiency, probably due to selection of resistant populations of insects and mites. An alternative is the use of biological control...... agent were performed, but this bulk of knowledge is in remarkable contrast to the lack of research on the fundamental ecology of Metarhizium in agroecosystems. This thesis aimed to evaluate the establishment, persistence and dispersal of these entomopathogenic fungi in strawberry crop soil...... in Inconfidentes, Minas Gerais, Brazil; and to study the diversity and abundance of species of Metarhizium isolated from organic and conventional strawberry crop soils, and from the field margins in Brazil and Denmark. The effectiveness of new species of Metarhizium recently found in Brazil, was evaluated against...

  1. GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

    Science.gov (United States)

    Tran, P. B.; Berrios, D. C.; Gurram, M. M.; Hashim, J. C. M.; Raghunandan, S.; Lin, S. Y.; Le, T. Q.; Heher, D. M.; Thai, H. T.; Welch, J. D.; hide

    2016-01-01

    The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system

  2. Integration of gene expression and methylation to unravel biological networks in glioblastoma patients.

    Science.gov (United States)

    Gadaleta, Francesco; Bessonov, Kyrylo; Van Steen, Kristel

    2017-02-01

    The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. Second, network theory is used to highlight important communities of genes. When applying our approach, Regression2Net to gene expression and methylation profiles for individuals with glioblastoma multiforme, we identified, respectively, 284 and 447 potentially interesting genes in relation to glioblastoma pathology. These genes showed at least one connection in the integrated networks ANDnet and XORnet derived from aforementioned EEnet and EMnet networks. Although the edges in ANDnet occur in both EEnet and EMnet, the edges in XORnet occur in EMnet but not in EEnet. In-depth biological analysis of connected genes in ANDnet and XORnet revealed genes that are related to energy metabolism, cell cycle control (AATF), immune system response, and several cancer types. Importantly, we observed significant overrepresentation of cancer-related pathways including glioma, especially in the XORnet network, suggesting a nonignorable role of methylation in glioblastoma multiforma. In the ANDnet, we furthermore identified potential glioma suppressor genes ACCN3 and ACCN4 linked to the NBPF1 neuroblastoma breakpoint family, as well as numerous ABC transporter genes (ABCA1, ABCB1) suggesting drug resistance of glioblastoma tumors. © 2016 WILEY PERIODICALS, INC.

  3. The Tobacco mosaic virus Movement Protein Associates with but Does Not Integrate into Biological Membranes

    Science.gov (United States)

    Peiró, Ana; Martínez-Gil, Luis; Tamborero, Silvia; Pallás, Vicente

    2014-01-01

    ABSTRACT Plant positive-strand RNA viruses require association with plant cell endomembranes for viral translation and replication, as well as for intra- and intercellular movement of the viral progeny. The membrane association and RNA binding of the Tobacco mosaic virus (TMV) movement protein (MP) are vital for orchestrating the macromolecular network required for virus movement. A previously proposed topological model suggests that TMV MP is an integral membrane protein with two putative α-helical transmembrane (TM) segments. Here we tested this model using an experimental system that measured the efficiency with which natural polypeptide segments were inserted into the ER membrane under conditions approximating the in vivo situation, as well as in planta. Our results demonstrated that the two hydrophobic regions (HRs) of TMV MP do not span biological membranes. We further found that mutations to alter the hydrophobicity of the first HR modified membrane association and precluded virus movement. We propose a topological model in which the TMV MP HRs intimately associate with the cellular membranes, allowing maximum exposure of the hydrophilic domains of the MP to the cytoplasmic cellular components. IMPORTANCE To facilitate plant viral infection and spread, viruses encode one or more movement proteins (MPs) that interact with ER membranes. The present work investigated the membrane association of the 30K MP of Tobacco mosaic virus (TMV), and the results challenge the previous topological model, which predicted that the TMV MP behaves as an integral membrane protein. The current data provide greatly needed clarification of the topological model and provide substantial evidence that TMV MP is membrane associated only at the cytoplasmic face of the membrane and that neither of its domains is integrated into the membrane or translocated into the lumen. Understanding the topology of MPs in the ER is vital for understanding the role of the ER in plant virus transport

  4. Nanostructure and molecular mechanics of spider dragline silk protein assemblies

    Science.gov (United States)

    Keten, Sinan; Buehler, Markus J.

    2010-01-01

    Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

  5. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Science.gov (United States)

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  6. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Directory of Open Access Journals (Sweden)

    Andra Waagmeester

    2016-06-01

    Full Text Available The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  7. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    Science.gov (United States)

    Waagmeester, Andra; Pico, Alexander R.

    2016-01-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

  8. Araneae Sloveniae: a national spider species checklist.

    Science.gov (United States)

    Kostanjšek, Rok; Kuntner, Matjaž

    2015-01-01

    The research of the spider fauna of Slovenia dates back to the very beginning of binomial nomenclature, and has gone through more and less prolific phases with authors concentrating on taxonomy, faunistics, ecology and zoogeographic reviews. Although the body of published works is remarkable for a small nation, the faunistic data has remained too scattered for a thorough understanding of regional biotic diversity, for comparative and ecological research, and for informed conservation purposes. A national checklist is long overdue. Here, a critical review of all published records in any language is provided. The species list currently comprises 738 species, is published online at http://www.bioportal.si/katalog/araneae.php under the title Araneae Sloveniae, and will be updated in due course. This tool will fill the void in cataloguing regional spider faunas and will facilitate further araneological research in central and southern Europe.

  9. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  10. Araneae Sloveniae: a national spider species checklist

    Directory of Open Access Journals (Sweden)

    Rok Kostanjšek

    2015-01-01

    Full Text Available The research of the spider fauna of Slovenia dates back to the very beginning of binomial nomenclature, and has gone through more and less prolific phases with authors concentrating on taxonomy, faunistics, ecology and zoogeographic reviews. Although the body of published works is remarkable for a small nation, the faunistic data has remained too scattered for a thorough understanding of regional biotic diversity, for comparative and ecological research, and for informed conservation purposes. A national checklist is long overdue. Here, a critical review of all published records in any language is provided. The species list currently comprises 738 species, is published online at http://www.bioportal.si/katalog/araneae.php under the title Araneae Sloveniae, and will be updated in due course. This tool will fill the void in cataloguing regional spider faunas and will facilitate further araneological research in central and southern Europe.

  11. Harnessing the Power of Integrated Mitochondrial Biology and Physiology: A Special Report on the NHLBI Mitochondria in Heart Diseases Initiative.

    Science.gov (United States)

    Ping, Peipei; Gustafsson, Åsa B; Bers, Don M; Blatter, Lothar A; Cai, Hua; Jahangir, Arshad; Kelly, Daniel; Muoio, Deborah; O'Rourke, Brian; Rabinovitch, Peter; Trayanova, Natalia; Van Eyk, Jennifer; Weiss, James N; Wong, Renee; Schwartz Longacre, Lisa

    2015-07-17

    Mitochondrial biology is the sum of diverse phenomena from molecular profiles to physiological functions. A mechanistic understanding of mitochondria in disease development, and hence the future prospect of clinical translations, relies on a systems-level integration of expertise from multiple fields of investigation. Upon the successful conclusion of a recent National Institutes of Health, National Heart, Lung, and Blood Institute initiative on integrative mitochondrial biology in cardiovascular diseases, we reflect on the accomplishments made possible by this unique interdisciplinary collaboration effort and exciting new fronts on the study of these remarkable organelles. © 2015 American Heart Association, Inc.

  12. A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

    Directory of Open Access Journals (Sweden)

    Thomas eEissing

    2011-02-01

    Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

  13. Nanofibre production in spiders without electric charge.

    Science.gov (United States)

    Joel, Anna-Christin; Baumgartner, Werner

    2017-06-15

    Technical nanofibre production is linked to high voltage, because nanofibres are typically produced by electrospinning. In contrast, spiders have evolved a way to produce nanofibres without high voltage. These spiders are called cribellate spiders and produce nanofibres within their capture thread production. It is suggested that their nanofibres become frictionally charged when brushed over a continuous area on the calamistrum, a comb-like structure at the metatarsus of the fourth leg. Although there are indications that electrostatic charges are involved in the formation of the thread structure, final proof is missing. We proposed three requirements to validate this hypothesis: (1) the removal of any charge during or after thread production has an influence on the structure of the thread; (2) the characteristic structure of the thread can be regenerated by charging; and (3) the thread is attracted to or repelled from differently charged objects. None of these three requirements were proven true. Furthermore, mathematical calculations reveal that even at low charges, the calculated structural assembly of the thread does not match the observed reality. Electrostatic forces are therefore not involved in the production of cribellate capture threads. © 2017. Published by The Company of Biologists Ltd.

  14. Progress on development of SPIDER diagnostics

    Science.gov (United States)

    Pasqualotto, R.; Agostini, M.; Barbisan, M.; Bernardi, M.; Brombin, M.; Cavazzana, R.; Croci, G.; Palma, M. Dalla; Delogu, R. S.; Gorini, G.; Lotto, L.; Muraro, A.; Peruzzo, S.; Pimazzoni, A.; Pomaro, N.; Rizzolo, A.; Serianni, G.; Spolaore, M.; Tardocchi, M.; Zaniol, B.; Zaupa, M.

    2017-08-01

    SPIDER experiment, the full size prototype of the beam source for the ITER heating neutral beam injector, has to demonstrate extraction and acceleration to 100 kV of a large negative ion hydrogen or deuterium beam with co-extracted electron fraction e-/D- SPIDER plant systems are being installed, the different diagnostic systems are in the procurement phase. Their final design is described here with a focus on some key solutions and most original and cost effective implementations. Thermocouples used to measure the power load distribution in the source and over the beam dump front surface will be efficiently fixed with proven technique and acquired through commercial and custom electronics. Spectroscopy needs to use well collimated lines of sight and will employ novel design spectrometers with higher efficiency and resolution and filtered detectors with custom built amplifiers. The electrostatic probes will be operated through electronics specifically developed to cope with the challenging environment of the RF source. The instrumented calorimeter STRIKE will use new CFC tiles, still under development. Two linear cameras, one built in house, have been tested as suitable for optical beam tomography. Some diagnostic components are off the shelf, others are custom developed: some of these are being prototyped or are under test before final production and installation, which will be completed before start of SPIDER operation.

  15. 'Integrative Physiology 2.0': Integration of systems biology into physiology and its application to cardiovascular homeostasis

    NARCIS (Netherlands)

    D.W.D. Kuster (Diederik); D. Merkus (Daphne); J. van der Velden (Jolanda); A.J.M. Verhoeven (Adrie); D.J.G.M. Duncker (Dirk)

    2011-01-01

    textabstractSince the completion of the Human Genome Project and the advent of the large scaled unbiased '-omics' techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of

  16. Fungal biological control agents for integrated management of Culicoides spp. (Diptera: Ceratopogonidae of livestock

    Directory of Open Access Journals (Sweden)

    B. W. Narladkar

    2015-02-01

    Full Text Available Aim: Entomopathogenic fungi Metarhizium anisopliae and Beauveria bassiana had wide host range against insects and hence these are being exploited as fungal bio-pesticide on a large scale. Both fungi are proved pesticides against many crop pests and farmers are well acquainted with their use on the field. Thus, research was aimed to explore the potency of these fungal spores against larval and adult Culicoides midges, a pest of livestock. Materials and Methods: In-vitro testing of both fungal biological control agents was undertaken in Petri dishes against field collected Culicoides larvae, while in plastic beakers against field collected blood-engorged female Culicoides midges. In-vivo testing was undertaken by spraying requisite concentration of fungal spores on the drainage channel against larvae and resting sites of adult Culicoides midges in the cattle shed. Lethal concentration 50 (LC50 values and regression equations were drawn by following probit analysis using SPSS statistical computerized program. Results: The results of this study revealed LC50 values of 2692 mg and 3837 mg (108 cfu/g for B. bassiana and M. anisopliae, respectively, against Culicoides spp. larvae. Death of Culicoides larvae due to B. bassiana showed greenish coloration in the middle of the body with head and tail showed intense blackish changes, while infection of M. anisopliae resulted in death of Culicoides larvae with greenish and blackish coloration of body along with total destruction, followed by desquamation of intestinal channel. The death of adult Culicoides midges were caused by both the fungi and after death growth of fungus were very well observed on the dead cadavers proving the efficacy of the fungus. Conclusion: Preliminary trials with both funguses (M. anisopliae, B. bassiana showed encouraging results against larvae and adults of Culicoides spp. Hence, it was ascertained that, these two fungal molecules can form a part of biological control and

  17. Uncharted waters: Bivalves of midway atoll and integrating mathematics into biology education

    Science.gov (United States)

    McCully, Kristin M.

    To protect and conserve the Earth's biodiversity and ecosystem services, it is important not only to understand and conserve species and ecosystems, but also to instill an understanding and appreciation for biodiversity and ecosystem services in the next generations of both scientists and citizens. Thus, this dissertation combines research into the ecology and identity of large bivalves at Midway Atoll in the Northwestern Hawaiian Islands (NWHI) with research on pedagogical strategies for integrating mathematics into undergraduate biology education. The NWHI is one of the few remaining large, mainly intact, predator-dominated coral reef ecosystems and one of the world's largest marine protected areas. Previous bivalve studies focused on the black-lipped pearl oyster, Pinctada margaritifera, which was heavily harvested in the late 1920s, has not recovered, and is now a candidate species for restoration. First, I combined remote sensing, geographic information systems, SCUBA, and mathematical modeling to quantify the abundance, spatial distributions, and filtration capacity of large epifaunal bivalves at Midway Atoll. These bivalves are most abundant on the forereef outside the atoll, but densities are much lower than reported on other reefs, and Midway's bivalves are unlikely to affect plankton abundance and productivity inside the lagoon. Second, I used molecular techniques and phylogenetic reconstructions to identify pearl oysters (Pinctada) from Midway Atoll as P. maculata , a species not previously reported in Hawaii. As a small morphologically cryptic species, P. maculata may be a native species that has not been collected previously, a native species that has been identified incorrectly as the morphologically similar P. radiata, or it may be a recent introduction or natural range extension from the western Pacific. Finally, I review science education literature integrating mathematics into undergraduate biology curricula, and then present and evaluate a

  18. Structure–Activity Relationship Study of Spider Polyamine Toxins as Inhibitors of Ionotropic Glutamate Receptors

    DEFF Research Database (Denmark)

    Xiong, Xiaofeng; Poulsen, Mette H; Hussein, Rama A

    2014-01-01

    The spider polyamine toxins Joro spider toxin-3 (JSTX-3) and Nephila polyamine toxins-1 and -8 (NPTX-1 and NPTX-8) are isolated from the venom of the orb-weaver spider Nephila clavata (Joro spider). They share a high degree of structural resemblance, their aromatic head groups being the only...

  19. Species conservation profiles of endemic spiders (Araneae) from Madeira and Selvagens archipelagos, Portugal

    Science.gov (United States)

    Crespo, Luís C; Silva, Isamberto; Borges, Paulo AV; Boieiro, Mário

    2017-01-01

    Abstract Background The North Atlantic archipelagos of Madeira and Selvagens present a unique biological diversity including, presently, 56 endemic spider species. Several recent projects provide valuable information on their distribution across most islands and habitats. To date, the only endemic spider assessed according to the IUCN Red List criteria is Hogna ingens. The objective of this paper is to assess all remaining endemic species and advise on possible future conservation actions critical for the survival of endangered species. New information Seven species were found to have a continuing decline in either range or population size. Their decline can be mostly attributed to habitat destruction or degradation, invasive plant species that reduce quality of habitat, forest fires at high mountain regions and possible competition for resources from invasive congeners. The tetragnathid M. barreti is considered as possibly extinct due to the suspected impact of a competing species. Although most endemic spiders from the Madeira and Selvagens archipelagos have relatively low extinction risk due to the good condition and protection of the laurisilva forests where many live, there are a number of species requiring urgent attention and protection measures. These include all cave and mountain-restricted species as well as those threatened by competing congeners or invasive plants. Extending current protected areas, restoring original habitats of threatened species and the control of invasive taxa should remain a priority for species survival. PMID:29104441

  20. Species conservation profiles of endemic spiders (Araneae) from Madeira and Selvagens archipelagos, Portugal.

    Science.gov (United States)

    Cardoso, Pedro; Crespo, Luís C; Silva, Isamberto; Borges, Paulo Av; Boieiro, Mário

    2017-01-01

    The North Atlantic archipelagos of Madeira and Selvagens present a unique biological diversity including, presently, 56 endemic spider species. Several recent projects provide valuable information on their distribution across most islands and habitats. To date, the only endemic spider assessed according to the IUCN Red List criteria is Hogna ingens. The objective of this paper is to assess all remaining endemic species and advise on possible future conservation actions critical for the survival of endangered species. Seven species were found to have a continuing decline in either range or population size. Their decline can be mostly attributed to habitat destruction or degradation, invasive plant species that reduce quality of habitat, forest fires at high mountain regions and possible competition for resources from invasive congeners. The tetragnathid M. barreti is considered as possibly extinct due to the suspected impact of a competing species. Although most endemic spiders from the Madeira and Selvagens archipelagos have relatively low extinction risk due to the good condition and protection of the laurisilva forests where many live, there are a number of species requiring urgent attention and protection measures. These include all cave and mountain-restricted species as well as those threatened by competing congeners or invasive plants. Extending current protected areas, restoring original habitats of threatened species and the control of invasive taxa should remain a priority for species survival.

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

    Science.gov (United States)

    Carlson, David E; Hedin, Marshal

    2017-01-01

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

  2. Who is afraid of a black Spider(-Man)?

    OpenAIRE

    Ora C. McWilliams

    2013-01-01

    An Internet post asking about Spider-Man's race in a film turned into an Internet campaign about an actor that led fans to interact with each other as well as with the actor, which in turn led to the attention of media producers, which resulted in a change in Spider-Man's race in a print comic book.

  3. Who is afraid of a black Spider(-Man?

    Directory of Open Access Journals (Sweden)

    Ora C. McWilliams

    2013-06-01

    Full Text Available An Internet post asking about Spider-Man's race in a film turned into an Internet campaign about an actor that led fans to interact with each other as well as with the actor, which in turn led to the attention of media producers, which resulted in a change in Spider-Man's race in a print comic book.

  4. Spider diversity in relation to habitat heterogeneity and an altitudinal ...

    African Journals Online (AJOL)

    Using pitfall traps, wandering spiders (Arachnida: Araneae) were sampled in a nested design from three different localities in the mountainous arid ecosystem of South Sinai at low, middle, and high altitudes. Habitat type and altitude were clearly different among the three localities. Spider diversity per trap varied spatially ...

  5. Time-dependent motor properties of multipedal molecular spiders.

    Science.gov (United States)

    Samii, Laleh; Blab, Gerhard A; Bromley, Elizabeth H C; Linke, Heiner; Curmi, Paul M G; Zuckermann, Martin J; Forde, Nancy R

    2011-09-01

    Molecular spiders are synthetic biomolecular walkers that use the asymmetry resulting from cleavage of their tracks to bias the direction of their stepping motion. Using Monte Carlo simulations that implement the Gillespie algorithm, we investigate the dependence of the biased motion of molecular spiders, along with binding time and processivity, on tunable experimental parameters, such as number of legs, span between the legs, and unbinding rate of a leg from a substrate site. We find that an increase in the number of legs increases the spiders' processivity and binding time but not their mean velocity. However, we can increase the mean velocity of spiders with simultaneous tuning of the span and the unbinding rate of a spider leg from a substrate site. To study the efficiency of molecular spiders, we introduce a time-dependent expression for the thermodynamic efficiency of a molecular motor, allowing us to account for the behavior of spider populations as a function of time. Based on this definition, we find that spiders exhibit transient motor function over time scales of many hours and have a maximum efficiency on the order of 1%, weak compared to other types of molecular motors.

  6. Evidence for competition between carnivorous plants and spiders.

    Science.gov (United States)

    Jennings, David E; Krupa, James J; Raffel, Thomas R; Rohr, Jason R

    2010-10-07

    Several studies have demonstrated that competition between disparate taxa can be important in determining community structure, yet surprisingly, to our knowledge, no quantitative studies have been conducted on competition between carnivorous plants and animals. To examine potential competition between these taxa, we studied dietary and microhabitat overlap between pink sundews (Drosera capillaris) and wolf spiders (Lycosidae) in the field, and conducted a laboratory experiment examining the effects of wolf spiders on sundew fitness. In the field, we found that sundews and spiders had a high dietary overlap with each other and with the available arthropod prey. Associations between sundews and spiders depended on spatial scale: both sundews and spiders were found more frequently in quadrats with more abundant prey, but within quadrats, spiders constructed larger webs and located them further away from sundews as the total sundew trapping area increased, presumably to reduce competition. Spiders also constructed larger webs when fewer prey were available. In the laboratory, our experiment revealed that spiders can significantly reduce sundew fitness. Our findings suggest that members of the plant and animal kingdoms can and do compete.

  7. Are temperate canopy spiders tree-species specific?

    Science.gov (United States)

    Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

    2014-01-01

    Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.

  8. Camel spider (Solifugae) use of prairie dog colonies

    Science.gov (United States)

    Solifugids (camel spiders) are widespread throughout arid regions of western North America and are thought to be important in structuring desert arthropod communities. Despite the ubiquity of camel spiders, little is known about their ecology. Black-tailed prairie dogs (Cynomys ludovicianus) are als...

  9. Spider mite control and resistance management: does a genome help?

    NARCIS (Netherlands)

    Van Leeuwen, T.; Dermauw, W.; Grbic, M.; Tirry, L.; Feyereisen, R.

    2012-01-01

    The complete genome of the two-spotted spider mite, Tetranychus urticae, has been reported. This is the first sequenced genome of a highly polyphagous and resistant agricultural pest. The question as to what the genome offers the community working on spider mite control is addressed.

  10. Three newly recorded Linyphiid spiders (Araneae: Linyphiidae from Korea

    Directory of Open Access Journals (Sweden)

    Sue Yeon Lee

    2018-03-01

    Full Text Available Three Linyphiid spiders, Caviphantes pseudosaxetorum Wunderlich, 1979, Erigone edentata Saito and Ono, 2001, and Savignia kawachiensis Oi, 1960, are reported for the first time from Korea with taxonomic illustrations and redescription. In this study, the genus Caviphantes Oi, 1960 is also newly recorded to Korean spider fauna.

  11. Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

    Science.gov (United States)

    Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

  12. Integrative Assessment of Evolutionary Theory Acceptance and Knowledge Levels of Biology Undergraduate Students from a Brazilian University

    Science.gov (United States)

    Tavares, Gustavo Medina; Bobrowski, Vera Lucia

    2018-01-01

    The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students'…

  13. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    Science.gov (United States)

    Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

    2013-01-01

    In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

  14. Effects of powdery mildew fungicide programs on twospotted spider mite (Acari: Tetranychidae), hop aphid (Hemiptera: Aphididae), and their natural enemies in hop yards.

    Science.gov (United States)

    Gent, D H; James, D G; Wright, L C; Brooks, D J; Barbour, J D; Dreves, A J; Fisher, G C; Walton, V M

    2009-02-01

    Twospotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and hop aphid, Phorodon humuli (Schrank) (Hemiptera: Aphididae), are the most important arthropod pests of hop (Humulus lupulus L.) in the Northern Hemisphere. A potential barrier for greater adoption of conservation biological control strategies for spider mites and hop aphid is the extensive use of fungicides for management of hop powdery mildew, Podosphaera macularis (Wallr.:Fr.) U. Braun & S. Takamatsu. Field studies conducted in experimental plots in Oregon and Washington in 2005 and 2006 quantified the effects of powdery mildew fungicide programs (i.e., sulfur, paraffinic oil, and synthetic fungicides) on arthropod pests and natural enemies on hop. Fungicide treatment significantly affected spider mite populations in all four studies. Multiple applications of sulfur fungicides applied before burr development resulted in 1.4-3.3-fold greater spider mite populations during summer. Near the cessation of the sulfur applications, or after a lag of 20-30 d, spider mite populations increased significantly faster on sulfur treated plants compared with water-treated plants in three of four experiments. The effect of paraffinic oil on spider mites was varied, leading to exacerbation of spider mites in Oregon and Washington in 2005, suppression of mites in Oregon in 2006, and no significant effect compared with water in Washington in 2006. Significant relative treatment effects for cone damage due to spider mite feeding were detected in Oregon in 2005 in plots treated with sulfur and paraffinic oil compared with water and synthetic fungicides. Mean populations of hop aphids were similar among treatments in Oregon, although sulfur treatment suppressed hop aphid populations in Washington in 2005 and 2006. Populations of individual predacious insect species and cumulative abundance of macropredators were not consistently suppressed or stimulated by treatments in all trials. However, predatory mite

  15. An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates.

    Science.gov (United States)

    Hawley, Robert G; Chen, Yuzhong; Riz, Irene; Zeng, Chen

    2012-05-04

    In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

  16. Optimization of integrated chemical-biological degradation of a reactive azo dye using response surface methodology

    Energy Technology Data Exchange (ETDEWEB)

    Sudarjanto, Gatut [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia); Keller-Lehmann, Beatrice [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia); Keller, Jurg [Advanced Wastewater Management Centre, The University of Queensland, Qld 4072 (Australia)]. E-mail: j.keller@awmc.uq.edu.au

    2006-11-02

    The integrated chemical-biological degradation combining advanced oxidation by UV/H{sub 2}O{sub 2} followed by aerobic biodegradation was used to degrade C.I. Reactive Azo Red 195A, commonly used in the textile industry in Australia. An experimental design based on the response surface method was applied to evaluate the interactive effects of influencing factors (UV irradiation time, initial hydrogen peroxide dosage and recirculation ratio of the system) on decolourisation efficiency and optimizing the operating conditions of the treatment process. The effects were determined by the measurement of dye concentration and soluble chemical oxygen demand (S-COD). The results showed that the dye and S-COD removal were affected by all factors individually and interactively. Maximal colour degradation performance was predicted, and experimentally validated, with no recirculation, 30 min UV irradiation and 500 mg H{sub 2}O{sub 2}/L. The model predictions for colour removal, based on a three-factor/five-level Box-Wilson central composite design and the response surface method analysis, were found to be very close to additional experimental results obtained under near optimal conditions. This demonstrates the benefits of this approach in achieving good predictions while minimising the number of experiments required.

  17. Optimization of integrated chemical-biological degradation of a reactive azo dye using response surface methodology

    International Nuclear Information System (INIS)

    Sudarjanto, Gatut; Keller-Lehmann, Beatrice; Keller, Jurg

    2006-01-01

    The integrated chemical-biological degradation combining advanced oxidation by UV/H 2 O 2 followed by aerobic biodegradation was used to degrade C.I. Reactive Azo Red 195A, commonly used in the textile industry in Australia. An experimental design based on the response surface method was applied to evaluate the interactive effects of influencing factors (UV irradiation time, initial hydrogen peroxide dosage and recirculation ratio of the system) on decolourisation efficiency and optimizing the operating conditions of the treatment process. The effects were determined by the measurement of dye concentration and soluble chemical oxygen demand (S-COD). The results showed that the dye and S-COD removal were affected by all factors individually and interactively. Maximal colour degradation performance was predicted, and experimentally validated, with no recirculation, 30 min UV irradiation and 500 mg H 2 O 2 /L. The model predictions for colour removal, based on a three-factor/five-level Box-Wilson central composite design and the response surface method analysis, were found to be very close to additional experimental results obtained under near optimal conditions. This demonstrates the benefits of this approach in achieving good predictions while minimising the number of experiments required

  18. Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

    Science.gov (United States)

    Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

    2013-01-01

    The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

  19. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

    Science.gov (United States)

    Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

    2004-01-01

    Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

  20. Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

    Science.gov (United States)

    Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

  1. A contribution key for the first recorded spider (Arachnidae: Aranae fauna from Sheringal, Khyber Pakhtunkhwa, Pakistan

    Directory of Open Access Journals (Sweden)

    Farzana Khan Perveen

    2016-03-01

    Full Text Available The spiders (Arthropoda: Arachnida have a hard cephalothorax and soft abdomen. They are environmental indicators and play an important role in biological control of pests and vectors. The present study was conducted to prepare the key for the first recorded spider fauna during June 2013-July 2014 in 6 quadrates of Sheringal, i.e., Daramdala, Doki, Guryaal, Samang, Shahoor and Sia-Sheringal, Dir Upper (DU, Khyber Pakhtunkhwa (KP, Pakistan. During the present research, 10 species belong to 7 families, and 10 genera were recorded. The family Sparassidae was the largest among collected families (nSparassidae=19, its body was larger than others, abdomen was narrow at posterior, cephalothorax region was broad and brown, chelicearae were forwarded, legs were strong, body have hairs grey to brown and they were harmless and speedy. Gnphosidae family was the smallest among collected families (nGnphosidae=3, their eyes were heterogeneous, their inner margin of chelicerae were with a wide serrated lamina, posterior row of eyes were much longer than anterior, with lateral rounded maxillae. While the family Hersiliidae was the unique in collected families (nHersiliidae=6, as they are known as two-tail spiders, they have enlarged spinnerets, their male grow up to 8 mm and female up to 10 mm, they have 2 tails and are mimic with host plants. It was concluded that the majority of the collected species belong to the family Sparassidae. It is recommended that further research may be conducted on arboreal and aquatic species of spiders in Sheringal, KP, Pakistan.

  2. The embryonic development of the central American wandering spider Cupiennius salei

    Directory of Open Access Journals (Sweden)

    Hilbrant Maarten

    2011-06-01

    Full Text Available Abstract Background The spider Cupiennius salei (Keyserling 1877 has become an important study organism in evolutionary and developmental biology. However, the available staging system for its embryonic development is difficult to apply to modern studies, with strong bias towards the earliest developmental stages. Furthermore, important embryonic events are poorly understood. We address these problems, providing a new description of the embryonic development of C. salei. The paper also discusses various observations that will improve our understanding of spider development. Results Conspicuous developmental events were used to define numbered stages 1 to 21. Stages 1 to 9 follow the existing staging system for the spider Achaearanea tepidariorum, and stages 10 to 21 provide a high-resolution description of later development. Live-embryo imaging shows cell movements during the earliest formation of embryonic tissue in C. salei. The imaging procedure also elucidates the encircling border between the cell-dense embryo hemisphere and the hemisphere with much lower cell density (a structure termed 'equator' in earlier studies. This border results from subsurface migration of primordial mesendodermal cells from their invagination site at the blastopore. Furthermore, our detailed successive sequence shows: 1 early differentiation of the precheliceral neuroectoderm; 2 the morphogenetic process of inversion and 3 initial invaginations of the opisthosomal epithelium for the respiratory system. Conclusions Our improved staging system of development in C. salei development should be of considerable value to future comparative studies of animal development. A dense germ disc is not evident during development in C. salei, but we show that the gastrulation process is similar to that in spider species that do have a dense germ disc. In the opisthosoma, the order of appearance of precursor epithelial invaginations provides evidence for the non-homology of the

  3. SPIDER: CMB Polarimetry from the Edge of Space

    Energy Technology Data Exchange (ETDEWEB)

    Gualtieri, R.; et al.

    2017-11-28

    SPIDER is a balloon-borne instrument designed to map the polarization of the millimeter-wave sky at large angular scales. SPIDER targets the B-mode signature of primordial gravitational waves in the cosmic microwave background (CMB), with a focus on mapping a large sky area with high fidelity at multiple frequencies. SPIDER's first longduration balloon (LDB) flight in January 2015 deployed a total of 2400 antenna-coupled Transition Edge Sensors (TESs) at 90 GHz and 150 GHz. In this work we review the design and in-flight performance of the SPIDER instrument, with a particular focus on the measured performance of the detectors and instrument in a space-like loading and radiation environment. SPIDER's second flight in December 2018 will incorporate payload upgrades and new receivers to map the sky at 285 GHz, providing valuable information for cleaning polarized dust emission from CMB maps.

  4. Nutrient regulation in a predator, the wolf spider Pardosa prativaga

    DEFF Research Database (Denmark)

    Jensen, Kim; Mayntz, David; Toft, Søren

    2011-01-01

    Nutrient balancing is well known in herbivores and omnivores, but has only recently been demonstrated in predators. To test how a predator might regulate nutrients when the prey varies in nutrient composition, we restricted juvenile Pardosa prativaga wolf spiders to diets of one of six fruit fly......, Drosophila melanogaster, prey types varying in lipid:protein composition during their second instar. We collected all fly remnants to estimate food and nutrient intake over each meal. The spiders adjusted their capture rate and nutrient extraction in response to prey mass and nutrient composition...... irrespective of energy intake. Intake was initially regulated to a constant lipid plus protein mass, but later spiders fed on prey with high proportions of protein increased consumption relative to spiders fed on other prey types. This pattern indicates that the spiders were prepared to overconsume vast...

  5. Spiders of Kerala Agricultural University Campus, Thrissur, Kerala, India

    Directory of Open Access Journals (Sweden)

    C. K. Adarsh

    2015-12-01

    Full Text Available A total of 86 species of spiders belonging to 56 genera of 20 families have been recorded from the Kerala Agricultural University (KAU campus, Thrissur, Kerala, southern India.  This represents 5.1% of the total spiders’ species and 33.33% of the total families of spiders recorded in India.  The dominant spider family at KAU campus is Araneidae with 18 species of nine genera. Salticidae is represented by 14 species of 13 genera.  Out of 252 endemic spiders of India, 16 have been reported from KAU campus.  Guild structure analysis shows spiders belonging to seven types of feeding guilds present in KAU campus.  Orb-web builders are the dominant feeding guild accounting for 34%, followed by stalkers (22%, ground runners (20%, ambushers (8%, scattered line weavers (8%, foliage runners (7% and sheet-web builders (1%. 

  6. Nanomechanical strength mechanisms of hierarchical biological materials and tissues.

    Science.gov (United States)

    Buehler, Markus J; Ackbarow, Theodor

    2008-12-01

    Biological protein materials (BPMs), intriguing hierarchical structures formed by assembly of chemical building blocks, are crucial for critical functions of life. The structural details of BPMs are fascinating: They represent a combination of universally found motifs such as alpha-helices or beta-sheets with highly adapted protein structures such as cytoskeletal networks or spider silk nanocomposites. BPMs combine properties like strength and robustness, self-healing ability, adaptability, changeability, evolvability and others into multi-functional materials at a level unmatched in synthetic materials. The ability to achieve these properties depends critically on the particular traits of these materials, first and foremost their hierarchical architecture and seamless integration of material and structure, from nano to macro. Here, we provide a brief review of this field and outline new research directions, along with a review of recent research results in the development of structure-property relationships of biological protein materials exemplified in a study of vimentin intermediate filaments.

  7. High population density of black-handed spider monkeys (Ateles geoffroyi) in Costa Rican lowland wet forest.

    Science.gov (United States)

    Weghorst, Jennifer A

    2007-04-01

    The main objective of this study was to estimate the population density and demographic structure of spider monkeys living in wet forest in the vicinity of Sirena Biological Station, Corcovado National Park, Costa Rica. Results of a 14-month line-transect survey showed that spider monkeys of Sirena have one of the highest population densities ever recorded for this genus. Density estimates varied, however, depending on the method chosen to estimate transect width. Data from behavioral monitoring were available to compare density estimates derived from the survey, providing a check of the survey's accuracy. A combination of factors has most probably contributed to the high density of Ateles, including habitat protection within a national park and high diversity of trees of the fig family, Moraceae. Although natural densities of spider monkeys at Sirena are substantially higher than those recorded at most other sites and in previous studies at this site, mean subgroup size and age ratios were similar to those determined in previous studies. Sex ratios were similar to those of other sites with high productivity. Although high densities of preferred fruit trees in the wet, productive forests of Sirena may support a dense population of spider monkeys, other demographic traits recorded at Sirena fall well within the range of values recorded elsewhere for the species.

  8. Biospheric Life Support - integrating biological regeneration into protection of humans in space.

    Science.gov (United States)

    Rocha, Mauricio; Iha, Koshun

    2016-07-01

    A biosphere stands for a set of biomes (regional biological communities) interacting in a materially closed (though energetically open) ecological system (CES). Earth's biosphere, the thin layer of life on the planet's surface, can be seen as a natural CES- where life "consumables" are regenerated/restored via biological, geological and chemical processes. In Life Sciences, artificial CESs- local ecosystems extracts with varying scales and degrees of closure, are considered convenient/representatives objects of study. For outer space, these concepts have been applied to the issue of life support- a significant consideration as long as distance from Earth increases. In the nineties, growing on the Russian expertise on biological life support, backed by a multidisciplinary science team, the famous Biosphere 2 appeared. That private project innovated, by assembling a set of Earth biomes samples- plus an organic ag one, inside a closed Mars base-like structure, next to 1.5 ha under glass, in Arizona, US. The crew of 8 inside completed their two years contract, though facing setbacks- the system failed, e.g., to produce enough food/air supplies. But their "failures"- if this word can be fairly applied to science endeavors, were as meaningful as their achievements for the future of life support systems (LSS) research. By this period, the Russians had accumulated experience in extended orbital stays, achieving biological outcomes inside their stations- e.g. complete wheat cycles. After reaching the Moon, the US administration decided to change national priorities, putting the space program as part of a "détente" policy, to relieve international tensions. Alongside the US space shuttle program, the Russians were invited to join the new International Space Station (ISS), bringing to that pragmatic project, also their physical/chemical LSS- top air/water regenerative technology at the time. Present US policy keeps the ISS operational, extending its service past its planned

  9. Rethinking the nature of fibrolamellar bone: an integrative biological revision of sauropod plexiform bone formation.

    Science.gov (United States)

    Stein, Koen; Prondvai, Edina

    2014-02-01

    palaeohistological studies, we introduce new osteohistological terms as well as revise widely used but incorrect terminology. To infer the role of woven bone in the bone formation of fast-growing tetrapods, we review some aspects of the interrelationships between the vascularity of bone tissues, basal metabolic rate, body size and growth rate. By putting our findings into the context of osteogenesis, we provide a new model for the diametrical limb bone growth of sauropods and present new implications for the evolution of fast growth in vertebrates. Since biomechanical studies of bone tissues suggest that predominant collagen fibre orientation (CFO) is controlled by endogenous, functional and perhaps phylogenetic factors, the relationship between CFO and bone growth rate as defined by Amprino's rule, which has been the basis for the biological interpretation of several osteohistological features, must be revised. Our findings draw attention to the urgent need for revising widely accepted basic concepts of palaeohistological studies, and for a more integrative approach to bone formation, biomechanics and bone microstructural features of extant and extinct vertebrates to infer life history traits of long extinct, iconic animals like dinosaurs. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

  10. Specific predictive power of automatic spider-related affective associations for controllable and uncontrollable fear responses toward spiders

    NARCIS (Netherlands)

    Huijdlng, J; de Jong, PJ; Huijding, J.

    This study examined the predictive power of automatically activated spider-related affective associations for automatic and controllable fear responses. The Extrinsic Affective Simon Task (EAST; De Houwer, 2003) was used to indirectly assess automatic spider fear-related associations. The EAST and

  11. And along Came a Spider: An Attentional Bias for the Detection of Spiders in Young Children and Adults

    Science.gov (United States)

    LoBue, Vanessa

    2010-01-01

    Spiders are among the most common targets of fears and phobias in the world. In visual search tasks, adults detect their presence more rapidly than other kinds of stimuli. Reported here is an investigation of whether young children share this attentional bias for the detection of spiders. In a series of experiments, preschoolers and adults were…

  12. Solubilization of spider silk proteins and its structural analysis using Fourier transform infrared spectroscopy

    Science.gov (United States)

    Osbin, K.; Jayan, Manuel; Bhadrakumari, S.; Predeep, P.

    2017-06-01

    This study investigates the presence of various amide bands present in different spider silk species, which provides extraordinary physical properties. Three different spider silks were collected from Western Ghats region. The collected spider silks samples belonging to the spider Heteropoda venatoria (species 1), Hersilia savignyi (species 2) and Pholcus phalangioides (species 3). Fourier transform infrared (FTIR) spectra reveals the protein peaks in the amide I, II, and III regions in all the three types of spider silk species.

  13. A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

    Science.gov (United States)

    Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

    2015-11-01

    A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Self-Assembly of Spider Silk-Fusion Proteins Comprising Enzymatic and Fluorescence Activity.

    Science.gov (United States)

    Humenik, Martin; Mohrand, Madeleine; Scheibel, Thomas

    2018-04-18

    The recombinant spider silk protein eADF4(C16) was genetically fused either with esterase 2 (EST2) or green fluorescent protein (GFP). The fusions EST-eADF4(C16) and GFP-eADF4(C16) were spectroscopically investigated and showed native structures of EST and GFP. The structural integrity was confirmed by the enzymatic activity of EST and the fluorescence of GFP. The spider silk moiety retained its intrinsically unstructured conformation in solution and the self-assembly into either nanofibrils or nanoparticles could be controlled by the concentration of phosphate. Particles, however, showed significantly lower activity of the EST and GFP domains likely caused by a steric hindrance. However, upon self-assembly of EST-eADF4(C16) and GFP-eADF4(C16) into fibrils the protein activities were retained. In general, the fusion of globular enzymes with the spider silk domain allows the generation of fibrous biomaterials with catalytic or light emitting properties.

  15. CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.

    Science.gov (United States)

    Pasculescu, Adrian; Schoof, Erwin M; Creixell, Pau; Zheng, Yong; Olhovsky, Marina; Tian, Ruijun; So, Jonathan; Vanderlaan, Rachel D; Pawson, Tony; Linding, Rune; Colwill, Karen

    2014-04-04

    A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts into project-specific pipelines, tracks interdependencies between related tasks, and enables the generation of summary reports as well as publication-quality images. As a result, the gap between experimental and computational components of a typical large-scale biology project is reduced, decreasing the time between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion, and modeling of multiple/selected reaction monitoring (MRM/SRM) results. CoreFlow was purposely designed as an environment for programmers to rapidly perform data analysis. These analyses are assembled into project-specific workflows that are readily shared with biologists to guide the next stages of experimentation. Its simple yet powerful interface provides a structure where scripts can be written and tested virtually simultaneously to shorten the life cycle of code development for a particular task. The scripts are exposed at every step so that a user can quickly see the relationships between the data, the assumptions that have been made, and the manipulations that have been performed. Since the scripts use commonly available programming languages, they can easily be

  16. Integration of an innovative biological treatment with physical or chemical disinfection for wastewater reuse

    International Nuclear Information System (INIS)

    De Sanctis, Marco; Del Moro, Guido; Levantesi, Caterina; Luprano, Maria Laura; Di Iaconi, Claudio

    2016-01-01

    In the present paper, the effectiveness of a Sequencing Batch Biofilter Granular Reactor (SBBGR) and its integration with different disinfection strategies (UV irradiation, peracetic acid) for producing an effluent suitable for agricultural use was evaluated. The plant treated raw domestic sewage, and its performances were evaluated in terms of the removal efficiency of a wide group of physical, chemical and microbiological parameters. The SBBGR resulted really efficient in removing suspended solids, COD and nitrogen with an average effluent concentration of 5, 32 and 10 mg/L, respectively. Lower removal efficiency was observed for phosphorus with an average concentration in the effluent of 3 mg/L. Plant effluent was also characterized by an average electrical conductivity and sodium adsorption ratio of 680 μS/cm and 2.9, respectively. Therefore, according to these gross parameters, the SBBGR effluent was conformed to the national standards required in Italy for agricultural reuse. Moreover, disinfection performances of the SBBGR was higher than that of conventional municipal wastewater treatment plants and met the quality criteria suggested by WHO (Escherichia coli < 1000 CFU/100 mL) for agricultural reuse. In particular, the biological treatment by SBBGR removed 3.8 ± 0.4 log units of Giardia lamblia, 2.8 ± 0.8 log units of E. coli, 2.5 ± 0.7 log units of total coliforms, 2.0 ± 0.3 log units of Clostridium perfringens, 2.0 ± 0.4 log units of Cryptosporidium parvum and 1.7 ± 0.7 log units of Somatic coliphages. The investigated disinfection processes (UV and peracetic acid) resulted very effective for total coliforms, E. coli and somatic coliphages. In particular, a UV radiation and peracetic acid doses of 40 mJ/cm"2 and 1 mg/L respectively reduced E. coli content in the effluent below the limit for agricultural reuse in Italy (10 CFU/100 mL). Conversely, they were both ineffective on C.perfringens spores. - Highlights: • SBBGR system showed high

  17. Integration of an innovative biological treatment with physical or chemical disinfection for wastewater reuse

    Energy Technology Data Exchange (ETDEWEB)

    De Sanctis, Marco, E-mail: marco.desanctis@ba.irsa.cnr.it [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy); Del Moro, Guido [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy); Levantesi, Caterina; Luprano, Maria Laura [Water Research Institute, CNR, Via Salaria Km 29.600, 00015 Monterotondo, RM (Italy); Di Iaconi, Claudio [Water Research Institute, CNR, Via F. De Blasio 5, 70123 Bari (Italy)

    2016-02-01

    In the present paper, the effectiveness of a Sequencing Batch Biofilter Granular Reactor (SBBGR) and its integration with different disinfection strategies (UV irradiation, peracetic acid) for producing an effluent suitable for agricultural use was evaluated. The plant treated raw domestic sewage, and its performances were evaluated in terms of the removal efficiency of a wide group of physical, chemical and microbiological parameters. The SBBGR resulted really efficient in removing suspended solids, COD and nitrogen with an average effluent concentration of 5, 32 and 10 mg/L, respectively. Lower removal efficiency was observed for phosphorus with an average concentration in the effluent of 3 mg/L. Plant effluent was also characterized by an average electrical conductivity and sodium adsorption ratio of 680 μS/cm and 2.9, respectively. Therefore, according to these gross parameters, the SBBGR effluent was conformed to the national standards required in Italy for agricultural reuse. Moreover, disinfection performances of the SBBGR was higher than that of conventional municipal wastewater treatment plants and met the quality criteria suggested by WHO (Escherichia coli < 1000 CFU/100 mL) for agricultural reuse. In particular, the biological treatment by SBBGR removed 3.8 ± 0.4 log units of Giardia lamblia, 2.8 ± 0.8 log units of E. coli, 2.5 ± 0.7 log units of total coliforms, 2.0 ± 0.3 log units of Clostridium perfringens, 2.0 ± 0.4 log units of Cryptosporidium parvum and 1.7 ± 0.7 log units of Somatic coliphages. The investigated disinfection processes (UV and peracetic acid) resulted very effective for total coliforms, E. coli and somatic coliphages. In particular, a UV radiation and peracetic acid doses of 40 mJ/cm{sup 2} and 1 mg/L respectively reduced E. coli content in the effluent below the limit for agricultural reuse in Italy (10 CFU/100 mL). Conversely, they were both ineffective on C.perfringens spores. - Highlights: • SBBGR system showed high

  18. Sparse trees and shrubs confers a high biodiversity to pastures: Case study on spiders from Transylvania.

    Science.gov (United States)

    Gallé, Róbert; Urák, István; Nikolett, Gallé-Szpisjak; Hartel, Tibor

    2017-01-01

    The integration of food production and biodiversity conservation represents a key challenge for sustainability. Several studies suggest that even small structural elements in the landscape can make a substantial contribution to the overall biodiversity value of the agricultural landscapes. Pastures can have high biodiversity potential. However, their intensive and monofunctional use typically erodes its natural capital, including biodiversity. Here we address the ecological value of fine scale structural elements represented by sparsely scattered trees and shrubs for the spider communities in a moderately intensively grazed pasture in Transylvania, Eastern Europe. The pasture was grazed with sheep, cattle and buffalo (ca 1 Livestock Unit ha-1) and no chemical fertilizers were applied. Sampling sites covered the open pasture as well as the existing fine-scale heterogeneity created by scattered trees and shrub. 40 sampling locations each being represented by three 1 m2 quadrats were situated in a stratified design while assuring spatial independency of sampling locations. We identified 140 species of spiders, out of which 18 were red listed and four were new for the Romanian fauna. Spider species assemblages of open pasture, scattered trees, trees and shrubs and the forest edge were statistically distinct. Our study shows that sparsely scattered mature woody vegetation and shrubs substantially increases the ecological value of managed pastures. The structural complexity provided by scattered trees and shrubs makes possible the co-occurrence of high spider diversity with a moderately high intensity grazing possible in this wood-pasture. Our results are in line with recent empirical research showing that sparse trees and shrubs increases the biodiversity potential of pastures managed for commodity production.

  19. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    Nanosatellites offer frequent, low-cost space access as secondary payloads on launches of larger conventional satellites. We summarize the payload science and technology of the Microsatellite in-situ Space Technologies (MisST) nanosatellite for conducting automated biological experiments. The payload (two fused 10-cm cubes) includes 1) an integrated fluidics system that maintains organism viability and supports growth and 2) a fixed-focus imager with fluorescence and scattered-light imaging capabilities. The payload monitors temperature, pressure and relative humidity, and actively controls temperature. C. elegans (nematode, 50 m diameter x 1 mm long) was selected as a model organism due to previous space science experience, its completely sequenced genome, size, hardiness, and the variety of strains available. Three strains were chosen: two green GFP-tagged strains and one red tdTomato-tagged strain that label intestinal, nerve, and pharyngeal cells, respectively. The integrated fluidics system includes bioanalytical and reservoir modules. The former consists of four 150 L culture wells and a 4x5 mm imaging zone the latter includes two 8 mL fluid reservoirs for reagent and waste storage. The fluidic system is fabricated using multilayer polymer rapid prototyping: laser cutting, precision machining, die cutting, and pressure-sensitive adhesives it also includes eight solenoid-operated valves and one mini peristaltic pump. Young larval-state (L2) nematodes are loaded in C. elegans Maintenance Media (CeMM) in the bioanalytical module during pre-launch assembly. By the time orbit is established, the worms have grown to sufficient density to be imaged and are fed fresh CeMM. The strains are pumped sequentially into the imaging area, imaged, then pumped into waste. Reagent storage utilizes polymer bags under slight pressure to prevent bubble formation in wells or channels. The optical system images green and red fluorescence bands by excitation with blue (473 nm peak

  20. Computing health quality measures using Informatics for Integrating Biology and the Bedside.

    Science.gov (United States)

    Klann, Jeffrey G; Murphy, Shawn N

    2013-04-19

    The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal. Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow

  1. The Transmission Line for the SPIDER experiment

    International Nuclear Information System (INIS)

    Boldrin, Marco; De Lorenzi, Antonio; Recchia, Mauro; Toigo, Vanni; Bonicelli, Tullio; Simon, Muriel

    2011-01-01

    The 100 keV Ion Source Test facility - Source for the Production of Ions of Deuterium Extracted from RF plasma (SPIDER) - is aimed to test the full scale prototype of the Ion Source for the ITER 1 MeV Neutral Beam Injector (NBI). The SPIDER facility requires the construction of a High Voltage Deck (HVD) and of a High Voltage Transmission Line (TL) respectively to host the Ion Source Power Supplies system polarized at 100 kV and to carry the power and signal conductors to the beam accelerator. In already existing NBI systems with beam energy above 100 keV, the TL is realized with the SF 6 Gas Insulated Line technology. In the SPIDER TL case, the presence of a large inner conductor (half meter diameter), would make the pressurized TL a complex and costly component; therefore a free air insulated solution has been proposed. The paper focuses on the design of this TL, which has to host inside the complex high potential (100 kV) inner electrode a number of power and measuring conductors and has to minimize the Electro Magnetic Interferences (EMI) produced by the frequent grids breakdowns. Finite Element (FE) analyses have been performed to verify the configuration from the electrostatic point of view, to evaluate EMI screening effectiveness and to assess the impact of the relatively high thermal dissipation of power conductors located inside the high potential electrode. Moreover, an experimental test campaign has been carried out on a TL mockup to validate the TL electrostatic configuration under DC voltage. Finally, the paper reports on the status of procurement activities for the Transmission Line.

  2. Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education.

    Science.gov (United States)

    Noble, Dorottya B; Mochrie, Simon G J; O'Hern, Corey S; Pollard, Thomas D; Regan, Lynne

    2016-11-12

    In 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to solve biological problems. Here we describe the framework of the training program, report on its effectiveness, and also share the insights we gained during its development and implementation. The program features co-teaching by faculty with complementary specializations, student peer learning, and novel hands-on courses that facilitate the seamless blending of interdisciplinary research and teaching. It also incorporates enrichment activities to improve communication skills, engage students in science outreach, and foster a cohesive program cohort, all of which promote the development of transferable skills applicable in a variety of careers. The curriculum of the graduate program is integrated with the curricular requirements of several Ph.D.-granting home programs in the physical, engineering, and biological sciences. Moreover, the wide-ranging recruiting activities of the IGPPEB serve to enhance the quality and diversity of students entering graduate school at Yale. We also discuss some of the challenges we encountered in establishing and optimizing the program, and describe the institution-level changes that were catalyzed by the introduction of the new graduate program. The goal of this article is to serve as both an inspiration and as a practical "how to" manual for those who seek to establish similar programs at their own institutions. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):537-549, 2016. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

  3. Assassin bug uses aggressive mimicry to lure spider prey.

    Science.gov (United States)

    Wignall, Anne E; Taylor, Phillip W

    2011-05-07

    Assassin bugs (Stenolemus bituberus) hunt web-building spiders by invading the web and plucking the silk to generate vibrations that lure the resident spider into striking range. To test whether vibrations generated by bugs aggressively mimic the vibrations generated by insect prey, we compared the responses of spiders to bugs with how they responded to prey, courting male spiders and leaves falling into the web. We also analysed the associated vibrations. Similar spider orientation and approach behaviours were observed in response to vibrations from bugs and prey, whereas different behaviours were observed in response to vibrations from male spiders and leaves. Peak frequency and duration of vibrations generated by bugs were similar to those generated by prey and courting males. Further, vibrations from bugs had a temporal structure and amplitude that were similar to vibrations generated by leg and body movements of prey and distinctly different to vibrations from courting males or leaves, or prey beating their wings. To be an effective predator, bugs do not need to mimic the full range of prey vibrations. Instead bugs are general mimics of a subset of prey vibrations that fall within the range of vibrations classified by spiders as 'prey'.

  4. Cuticular antifungals in spiders: density- and condition dependence.

    Directory of Open Access Journals (Sweden)

    Daniel González-Tokman

    Full Text Available Animals living in groups face a high risk of disease contagion. In many arthropod species, cuticular antimicrobials constitute the first protective barrier that prevents infections. Here we report that group-living spiders produce cuticular chemicals which inhibit fungal growth. Given that cuticular antifungals may be costly to produce, we explored whether they can be modulated according to the risk of contagion (i.e. under high densities. For this purpose, we quantified cuticular antifungal activity in the subsocial crab spider Diaea ergandros in both natural nests and experimentally manipulated nests of varying density. We quantified the body-condition of spiders to test whether antifungal activity is condition dependent, as well as the effect of spider density on body-condition. We predicted cuticular antifungal activity to increase and body-condition to decrease with high spider densities, and that antifungal activity would be inversely related to body-condition. Contrary to our predictions, antifungal activity was neither density- nor condition-dependent. However, body-condition decreased with density in natural nests, but increased in experimental nests. We suggest that pathogen pressure is so important in nature that it maintains high levels of cuticular antifungal activity in spiders, impacting negatively on individual energetic condition. Future studies should identify the chemical structure of the isolated antifungal compounds in order to understand the physiological basis of a trade-off between disease prevention and energetic condition caused by group living, and its consequences in the evolution of sociality in spiders.

  5. Silk elasticity as a potential constraint on spider body size.

    Science.gov (United States)

    Rodríguez-Gironés, Miguel A; Corcobado, Guadalupe; Moya-Laraño, Jordi

    2010-10-07

    Silk is known for its strength and extensibility and has played a key role in the radiation of spiders. Individual spiders use different glands to produce silk types with unique sets of proteins. Most research has studied the properties of major ampullate and capture spiral silks and their ecological implications, while little is known about minor ampullate silk, the type used by those spider species studied to date for bridging displacements. A biomechanical model parameterised with available data shows that the minimum radius of silk filaments required for efficient bridging grows with the square root of the spider's body mass, faster than the radius of minor ampullate silk filaments actually produced by spiders. Because the morphology of spiders adapted to walking along or under silk threads is ill suited for moving on a solid surface, for these species there is a negative relationship between body mass and displacement ability. As it stands, the model suggests that spiders that use silk for their displacements are prevented from attaining a large body size if they must track their resources in space. In particular, silk elasticity would favour sexual size dimorphism because males that must use bridging lines to search for females cannot grow large. 2010 Elsevier Ltd. All rights reserved.

  6. Cuticular antifungals in spiders: density- and condition dependence.

    Science.gov (United States)

    González-Tokman, Daniel; Ruch, Jasmin; Pulpitel, Tamara; Ponton, Fleur

    2014-01-01

    Animals living in groups face a high risk of disease contagion. In many arthropod species, cuticular antimicrobials constitute the first protective barrier that prevents infections. Here we report that group-living spiders produce cuticular chemicals which inhibit fungal growth. Given that cuticular antifungals may be costly to produce, we explored whether they can be modulated according to the risk of contagion (i.e. under high densities). For this purpose, we quantified cuticular antifungal activity in the subsocial crab spider Diaea ergandros in both natural nests and experimentally manipulated nests of varying density. We quantified the body-condition of spiders to test whether antifungal activity is condition dependent, as well as the effect of spider density on body-condition. We predicted cuticular antifungal activity to increase and body-condition to decrease with high spider densities, and that antifungal activity would be inversely related to body-condition. Contrary to our predictions, antifungal activity was neither density- nor condition-dependent. However, body-condition decreased with density in natural nests, but increased in experimental nests. We suggest that pathogen pressure is so important in nature that it maintains high levels of cuticular antifungal activity in spiders, impacting negatively on individual energetic condition. Future studies should identify the chemical structure of the isolated antifungal compounds in order to understand the physiological basis of a trade-off between disease prevention and energetic condition caused by group living, and its consequences in the evolution of sociality in spiders.

  7. First report of clinical presentation of a bite by a running spider, Philodromus sp. (Araneae: Philodromidae), with recommendations for spider bite management.

    Science.gov (United States)

    Coetzee, Maureen; Dippenaar, Ansie; Frean, John; Hunt, Richard H

    2017-06-30

    This article describes the clinical progression of symptoms over a period of 5 days of a bite inflicted by a Philodromus sp. spider. Commonly known as 'running spiders', these are not considered to be harmful to humans. This report, however, is the first description of an actual bite by a member of this group of spiders showing cytotoxic envenomation. Management of the bites should be as recommended for other cytotoxic spider bites.

  8. Structure-function-property-design interplay in biopolymers: spider silk.

    Science.gov (United States)

    Tokareva, Olena; Jacobsen, Matthew; Buehler, Markus; Wong, Joyce; Kaplan, David L

    2014-04-01

    Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  9. Inhibition of the spider heartbeat by gravity and vibration

    Science.gov (United States)

    Finck, A.

    1984-01-01

    The rate and vigor of the spider heartbeat is controlled by an external pacemaker. A mechanical feature of the spider cardio-vascular system is the production of high serum pressure in the prosoma and the legs. This appears to be the source for leg extension. The lyriform organ on the patella of the leg is sensitive to vibratory and kinesthetic stimuli. This sensitivity depends upon the degree of leg extension. Thus the activity of the heart and the response characteristics of the sense receptor are related. The effect of a supra-threshold vibratory or gravitational stimulus is to produce an inhibition and a tachycardia of the spider heartbeat.

  10. Colonization of subterranean habitats by spiders in Central Europe

    Directory of Open Access Journals (Sweden)

    Vlastimil Růžička

    2013-05-01

    Full Text Available Using data from the Czech Republic, we studied the distribution of spiders in soils, crevice systems, scree and caves, i.e. subterranean habitats at depths spanning from 10 cm to 100 m. In total, we found 161 species. The number of species declines with increasing habitat depth, with a major drop in species richness at the depth of 10 meters. Thirteen species exhibit morphological adaptations to life in subterranean habitats. At depths greater than 10 meters, spider assemblages are almost exclusively composed of troglomorphic species. We propose a hypothesis of evolution of troglomorphisms at spiders during Quaternary climatic cycles.

  11. Venomous snake bites, scorpions, and spiders.

    Science.gov (United States)

    Kularatne, S A M; Senanayake, Nimal

    2014-01-01

    Neurologic dysfunction due to natural neurotoxins is an important, but neglected, public health hazard in many parts of the world, particularly in the tropics. These toxins are produced by or found among a variety of live forms that include venomous snakes, arthropods such as scorpions, spiders, centipedes, stinging insects (Hymenoptera), ticks, certain poisonous fish, shellfish, crabs, cone shells, skin secretions of dart-poison frogs, and bacterial poisons such as botulinum toxin. These toxins commonly act on neuromuscular transmission at the neuromuscular junction where acetylcholine is the neurotransmitter, but in certain situations the toxins interfere with neurotransmitters such as GABA, noradrenaline, adrenaline, dopamine, and γ-aminobutyrate. Of the toxins, α-toxins and κ-toxins (e.g., Chinese krait, Bungarus multicinctus) act on the postsynaptic membrane, blocking the receptors, whilst β-toxin (e.g., common krait, B. caeruleus) acts on the presynaptic membrane, causing impairment of acetylcholine release. Conversely, dendrotoxins of the African mamba enhance acetylcholine release. The toxins of scorpions and spiders commonly interfere with voltage-gated ion channels. Clinically, the cardinal manifestation is muscle paralysis. In severe cases respiratory paralysis could be fatal. Effective antivenoms are the mainstay of treatment of envenoming, but their lack of availability is the major concern in the regions of the globe where they are desperately needed. Interestingly, some toxins have proved to be valuable pharmaceutical agents, while some others are widely exploited to study neuromuscular physiology and pathology. © 2014 Elsevier B.V. All rights reserved.

  12. Free amino acids in spider hemolymph.

    Science.gov (United States)

    Tillinghast, Edward K; Townley, Mark A

    2008-11-01

    We examined the free amino acid composition of hemolymph from representatives of five spider families with an interest in knowing if the amino acid profile in the hemolymph of orb-web-building spiders reflects the high demands for small organic compounds in the sticky droplets of their webs. In nearly all analyses, on both orb and non-orb builders, glutamine was the most abundant free amino acid. Glycine, taurine, proline, histidine, and alanine also tended to be well-represented in orb and non-orb builders. While indications of taxon-specific differences in amino acid composition were observed, it was not apparent that two presumptive precursors (glutamine, taurine) of orb web sticky droplet compounds were uniquely enriched in araneids (orb builders). However, total amino acid concentrations were invariably highest in the araneids and especially so in overwintering juveniles, even as several of the essential amino acids declined during this winter diapause. Comparing the data from this study with those from earlier studies revealed a number of discrepancies. The possible origins of these differences are discussed.

  13. Intracellular recording from a spider vibration receptor.

    Science.gov (United States)

    Gingl, Ewald; Burger, Anna-M; Barth, Friedrich G

    2006-05-01

    The present study introduces a new preparation of a spider vibration receptor that allows intracellular recording of responses to natural mechanical or electrical stimulation of the associated mechanoreceptor cells. The spider vibration receptor is a lyriform slit sense organ made up of 21 cuticular slits located on the distal end of the metatarsus of each walking leg. The organ is stimulated when the tarsus receives substrate vibrations, which it transmits to the organ's cuticular structures, reducing the displacement to about one tenth due to geometrical reasons. Current clamp recording was used to record action potentials generated by electrical or mechanical stimuli. Square pulse stimulation identified two groups of sensory cells, the first being single-spike cells which generated only one or two action potentials and the second being multi-spike cells which produced bursts of action potentials. When the more natural mechanical sinusoidal stimulation was applied, differences in adaptation rate between the two cell types remained. In agreement with prior extracellular recordings, both cell types showed a decrease in the threshold tarsus deflection with increasing stimulus frequency. Off-responses to mechanical stimuli have also been seen in the metatarsal organ for the first time.

  14. Spectral sensitivity of a colour changing spider.

    Science.gov (United States)

    Defrize, Jérémy; Lazzari, Claudio R; Warrant, Eric J; Casas, Jérôme

    2011-04-01

    Vision plays a paramount role in some spider families such as the Salticidae, Lycosidae and Thomisidae, as it is involved in prey hunting, orientation or choice of substrate. In the thomisid Misumena vatia, for which the substrate colour affects the body colour, vision seems to mediate morphological colour changes. However, nothing is known about which component of visual signals from the substrate might be perceived, nor whether M. vatia possesses the physiological basis for colour vision. The aim of this study is thus to investigate the vision of this spider species by measuring the spectral sensitivities of the different pairs of eyes using electrophysiological methods. Extra- and intracellular electrophysiological recordings combined with selective adaptation revealed the presence of two classes of photoreceptor cells, one sensitive in the UV region of the spectrum (around 340 nm) and one sensitive in the green (around 520 nm) regions in the four pairs of eyes. We conclude that M. vatia possesses the physiological potential to perceive both chromatic and achromatic components of the environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Spiders (Araneae) Found in Bananas and Other International Cargo Submitted to North American Arachnologists for Identification.

    Science.gov (United States)

    Vetter, Richard S; Crawford, Rodney L; Buckle, Donald J

    2014-11-01

    Spiders found in international cargo brought into North America are sometimes submitted to arachnologists for identification. Often, these spiders are presumed to be of medical importance because of size or a submitter's familiarity with a toxic spider genus from the continent of origin. Starting in 2006, requests were made for spiders found in international cargo brought into North America, in addition to the specimens from similar cargo shipments already in our museum collections. This was an ad hoc study that allowed us to focus on spiders of concern to the discoverer. We identified 135 spiders found in international cargo. A key for the most common species is provided. The most frequently submitted spiders were the pantropical huntsman spider, Heteropoda venatoria (L.) (Sparassidae), and the redfaced banana spider, Cupiennius chiapanensis Medina Soriano (Ctenidae). Spiders of medical importance were rare. The most common cargo from which spiders were submitted was bananas with most specimens coming from Central America, Ecuador, or Colombia. Lack of experience with nonnative fauna caused several experienced American arachnologists to misidentify harmless ctenid spiders (C. chiapanensis, spotlegged banana spider, Cupiennius getazi Simon) as highly toxic Phoneutria spiders. These misidentifications could have led to costly, unwarranted prophylactic eradication measures, unnecessary employee health education, heightened employee anxiety and spoilage when perishable goods are left unloaded due to safety concerns. © 2014 Entomological Society of America.

  16. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    Science.gov (United States)

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. EVALUATING THE ECOLOGICAL RESILIENT DRIVEN PERFORMANCE OF A TROPICAL WASTE STABILIZATION POND SYSTEM USING ECOLOGICAL SIGNATURE OF BIOLOGICAL INTEGRITY

    OpenAIRE

    Susmita Lahiri Ganguly; Dipanwita Sarkar Paria; B. B. Jana

    2015-01-01

    Using ecological signature of biological integrity as a measure of performance, the reclamation efficiency of waste stabilization ponds was evaluated over a period of four years in a tropical sewage treatment plant – cum fish culture consisting of two anaerobic, two facultative and four maturation ponds located serially across the sewage effluent gradient. The four maturation ponds were used for batch culture of fish. Samples of surface and bottom water as well as surface sediment were collec...

  18. Evaluating the informatics for integrating biology and the bedside system for clinical research

    Directory of Open Access Journals (Sweden)

    Meystre Stéphane M

    2009-10-01

    Full Text Available Abstract Background Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort selection tool from the Informatics for Integrating Biology and the Bedside (i2b2 group: the i2b2 hive. Methods Our evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone. Results We found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre- or post-processing, modifications to the hive metadata, etc. Conclusion The i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be

  19. Mission and Sustainability of Informatics for Integrating Biology and the Bedside (i2b2).

    Science.gov (United States)

    Murphy, Shawn; Wilcox, Adam

    2014-01-01

    A visible example of a successfully disseminated research project in the healthcare space is Informatics for Integrating Biology and the Bedside, or i2b2. The project serves to provide the software that can allow a researcher to do direct, self-serve queries against the electronic healthcare data form a hospital. The goals of these queries are to find cohorts of patients that fit specific profiles, while providing for patient privacy and discretion. Sustaining this resource and keeping its direction has always been a challenge, but ever more so as the ten year National Centers for Biomedical Computing (NCBCs) sunset their funding. Building on the i2b2 structures has helped the dissemination plans for grants leveraging it because it is a disseminated national resource. While this has not directly increased the support of i2b2 internally, it has increased the ability of institutions to leverage the resource and generally leads to increased institutional support. The successful development, use, and dissemination i2b2 has been significant in clinical research and informatics. Its evolution has been from a local research data infrastructure to one disseminated more broadly than any other product of the National Centers for Biomedical Computing, and an infrastructure spawning larger investments than were originally used to create it. Throughout this, there were two main lessons about the benefits of dissemination: that people have great creativity in utilizing a resource in different ways and that broader system use can make the system more robust. One option for long-term sustainability of the central authority would be to translate the function to an industry partner. Another option currently being pursued is to create a foundation that would be a central authority for the project. Over the past 10 years, i2b2 has risen to be an important staple in the toolkit of health care researchers. There are now over 110 hospitals that use i2b2 for research. This open

  20. Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA.

    Science.gov (United States)

    Veselka, Walter; Anderson, James T; Kordek, Walter S

    2010-05-01

    Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

  1. Using two classification schemes to develop vegetation indices of biological integrity for wetlands in West Virginia, USA.

    Science.gov (United States)

    Veselka, Walter; Rentch, James S; Grafton, William N; Kordek, Walter S; Anderson, James T

    2010-11-01

    Bioassessment methods for wetlands, and other bodies of water, have been developed worldwide to measure and quantify changes in "biological integrity." These assessments are based on a classification system, meant to ensure appropriate comparisons between wetland types. Using a local site-specific disturbance gradient, we built vegetation indices of biological integrity (Veg-IBIs) based on two commonly used wetland classification systems in the USA: One based on vegetative structure and the other based on a wetland's position in a landscape and sources of water. The resulting class-specific Veg-IBIs were comprised of 1-5 metrics that varied in their sensitivity to the disturbance gradient (R2=0.14-0.65). Moreover, the sensitivity to the disturbance gradient increased as metrics from each of the two classification schemes were combined (added). Using this information to monitor natural and created wetlands will help natural resource managers track changes in biological integrity of wetlands in response to anthropogenic disturbance and allows the use of vegetative communities to set ecological performance standards for mitigation banks.

  2. Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

    Science.gov (United States)

    Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

    2013-01-01

    Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from those of both chemical and biological analogs whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone, or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. PMID:23848138

  3. DNA damage in haemocytes and midgut gland cells of Steatoda grossa (Theridiidae) spiders exposed to food contaminated with cadmium.

    Science.gov (United States)

    Stalmach, Monika; Wilczek, Grażyna; Wilczek, Piotr; Skowronek, Magdalena; Mędrzak, Monika

    2015-03-01

    The aim of this study was to assess the genotoxic effects of Cd on haemocytes and midgut gland cells of web-building spiders, Steatoda grossa (Theridiidae), exposed to the metal under laboratory conditions. Analyzes were conducted on adult females and males, fed for four weeks with cadmium-contaminated Drosophila hydei flies, grown on a medium suplemented with 0.25 mM CdCl2. The comet assay, providing a quantitative measure of DNA strand breaks, was used to evaluate the DNA damage caused by the metal. Cadmium content was measured in whole spider bodies by the AAS method. Metal body burden was significantly lower in females (0.25 µgg(-1) dry weight) than in males (3.03 µgg(-1) dry weight), suggesting that females may have more effective mechanisms controlling the uptake of metal, via the digestive tract, or its elimination from the body. Irrespectively of sex, spiders fed prey contaminated with cadmium showed significantly higher values of comet parameters: tail DNA (TDNA), tail length (TL) and olive tail moment (OTM), in comparison with the control. In midgut gland cells, the level of DNA damage was higher for males than females, while in haemocytes the genotoxic effect of cadmium was greater in females. The obtained results indicate that in spiders cadmium displays strong genotoxic effects and may cause DNA damage even at low concentrations, however the severity of damage seems to be sex- and internal organ-dependent. The comet assay can be considered a sensitive tool for measuring the deleterious effect of cadmium on DNA integrity in spiders. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Phononic band gap and mechanical anisotropy in spider silk

    Science.gov (United States)

    Papadopoulos, Periklis; Gomopoulos, Nikos; Kremer, Friedrich; Fytas, George

    2010-03-01

    Spider dragline silk is a semi-crystalline biopolymer exhibiting superior properties compared to synthetic polymers with similar chemical structure, such as polyamides. This is ascribed to the hierarchical nanostructure that is created in the spinning duct. During this process the aqueous solution of the two protein constituents of dragline silk is crystallized, while the macromolecules maintain their high orientation, leading to a high value of the Young's modulus (in the order of 10 GPa) along the fiber. We employed spontaneous Brillouin light scattering to measure the longitudinal modulus (M//,,M) along the two symmetry directions of the native fiber with increased (decreased) pre-strain created by stretching (supercontracting after hydration). A strong mechanical anisotropy is found; at about 18% strain M///M˜5. Most important, an unexpected finding is the first observation of a unidirectional hypersonic phononic band gap in biological structures. This relates to the existence of a strain-dependent correlation length of the mechanical modulus in the submicron range along the fiber axis.

  5. Using Variable Precision Rough Set for Selection and Classification of Biological Knowledge Integrated in DNA Gene Expression

    Directory of Open Access Journals (Sweden)

    Calvo-Dmgz D.

    2012-12-01

    Full Text Available DNA microarrays have contributed to the exponential growth of genomic and experimental data in the last decade. This large amount of gene expression data has been used by researchers seeking diagnosis of diseases like cancer using machine learning methods. In turn, explicit biological knowledge about gene functions has also grown tremendously over the last decade. This work integrates explicit biological knowledge, provided as gene sets, into the classication process by means of Variable Precision Rough Set Theory (VPRS. The proposed model is able to highlight which part of the provided biological knowledge has been important for classification. This paper presents a novel model for microarray data classification which is able to incorporate prior biological knowledge in the form of gene sets. Based on this knowledge, we transform the input microarray data into supergenes, and then we apply rough set theory to select the most promising supergenes and to derive a set of easy interpretable classification rules. The proposed model is evaluated over three breast cancer microarrays datasets obtaining successful results compared to classical classification techniques. The experimental results shows that there are not significat differences between our model and classical techniques but it is able to provide a biological-interpretable explanation of how it classifies new samples.

  6. Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

    Science.gov (United States)

    Tavares, Gustavo Medina; Bobrowski, Vera Lucia

    2018-03-01

    The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

  7. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    Science.gov (United States)

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  8. The functionality of biological knowledge in the workplace. Integrating school and workplace learning about reproduction

    NARCIS (Netherlands)

    Mazereeuw, M.

    2013-01-01

    This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although

  9. An integrated strategy for biological effects monitoring in Scottish coastal waters

    International Nuclear Information System (INIS)

    Park, R.A.; Dobson, J.; Richardson, L.; Hill, A.

    1999-01-01

    The paper summarises SEPA's current programme of water quality and biological effects monitoring and, using recent examples, discusses the current environmental issues affecting the condition of our coastal waters. (author)

  10. An integrated model for interaction of electromagnetic fields with biological systems

    International Nuclear Information System (INIS)

    Apollonio, F.; Liberti, M.; Cavagnaro, M.; D'Inzeo, G.; Tarricone, L.

    1999-01-01

    In this work is described a methodology for evaluation of interaction of high frequency electromagnetic field. Biological systems via connection of many macroscopic models. In particular the analysis of neuronal membrane exposed to electromagnetic fields [it

  11. Optimization of total arc degree for stereotactic radiotherapy by using integral biologically effective dose and irradiated volume

    International Nuclear Information System (INIS)

    Lim, Do Hoon; Kim, Dae Yong; Lee, Myung Za; Chun, Ha Chung

    2001-01-01

    To find the optimal values of total arc degree to protect the normal brain tissue from high dose radiation in stereotactic radiotherapy planning. With Xknife-3 planning system and 4 MV linear accelerator, the authors planned under various values of parameters. One isocenter, 12, 20, 30, 40, 50, and 60 mm of collimator diameters, 100 deg, 200 deg, 300 deg, 400 deg, 500 deg, 600 deg, of total arc degrees, and 30 deg or 45 deg of arc intervals were used. After the completion of planning, the plans were compared each other using V 50 (the volume of normal brain that is delivered high dose radiation) and integral biologically effective dose. At 30 deg of arc interval, the values of V 50 had the decreased pattern with the increase of total arc degree in any collimator diameter. At 45 deg arc interval, up to 400 deg of total arc degree, the values of V 50 decreased with the increase of total arc degree, but at 500 deg and 600 deg of total arc degrees, the values increased. At 30 deg of arc interval, integral biologically effective dose showed the decreased pattern with the increase of total arc degree in any collimator diameter. At 45 deg arc interval with less than 40 mm collimator diameter, the integral biologically effective dose decreased with the increase of total arc degree, but with 50 and 60 mm of collimator diameters, up to 400 deg of total arc degree, integral biologically effective dose decreased with the increase of total arc degree, but at 500 deg and 600 deg of total arc degrees, the values increased. In the stereotactic radiotherapy planning for brain lesions, planning with 400 deg of total arc degree is optimal. Especially, when the larger collimator more than 50 mm diameter should be used, the uses of 500 deg and 600 deg of total arc degrees make the increase of V 50 and integral biologically effective dose, Therefore stereotactic radiotherapy planning using 400 deg of total arc degree can increase the therapeutic ratio and produce the effective outcome

  12. Vision in the nocturnal wandering spider Leucorchestris arenicola (Araneae: Sparassidae)

    DEFF Research Database (Denmark)

    Nørgaard, Thomas; Nilsson, Dan-Eric; Henschel, Joh R

    2008-01-01

    At night the Namib Desert spider Leucorchestris arenicola performs long-distance homing across its sand dune habitat. By disabling all or pairs of the spiders' eight eyes we found that homing ability was severely reduced when vision was fully abolished. Vision, therefore, seems to play a key role...... in the posterior and anteriomedian eyes, and at approximately 540 nm in the anteriolateral eyes. Theoretical calculations of photon catches showed that the eyes are likely to employ a combination of spatial and temporal pooling in order to function at night. Under starlit conditions, the raw spatial and temporal...... resolution of the eyes is insufficient for detecting any visual information on structures in the landscape, and bright stars would be the only objects visible to the spiders. However, by summation in space and time, the spiders can rescue enough vision to detect coarse landscape structures. We show that L...

  13. 46 SPIDER WEBS AS INDICATORS OF COBALT AND LEAD ...

    African Journals Online (AJOL)

    Spider webs were collected from the indoor and outdoor of 120 sampling sites of 10 zones of Kano ... diet, cobalt containing ceramic is administered into ... significant human and environmental health risk. ..... Evaluation of Health Workers.

  14. Genetic diversity analysis of various red spider mite- resistant ...

    African Journals Online (AJOL)

    User

    2011-05-02

    May 2, 2011 ... 3Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Ya'an, 625014, P. R. ... Random amplified polymorphic DNA (RAPD) is a DNA ..... spider mite-resistant, bumper, high-quality and disease-.

  15. Biotechnological Trends in Spider and Scorpion Antivenom Development

    DEFF Research Database (Denmark)

    Laustsen, Andreas Hougaard; Solà, Mireia; Jappe, Emma Christine

    2016-01-01

    in using bioactive toxins from spiders and scorpions for drug discovery purposes and for solving crystal structures of membrane-embedded receptors. Additionally, the identification and isolation of a myriad of spider and scorpion toxins has allowed research within next generation antivenoms to progress...... at an increasingly faster pace. In this review, the current knowledge of spider and scorpion venoms is presented, followed by a discussion of all published biotechnological efforts within development of spider and scorpion antitoxins based on small molecules, antibodies and fragments thereof, and next generation...... immunization strategies. The increasing number of discovery and development efforts within this field may point towards an upcoming transition from serum-based antivenoms towards therapeutic solutions based on modern biotechnology....

  16. Biomimetic calcium phosphate coatings on recombinant spider silk fibres

    NARCIS (Netherlands)

    Yang, Liang; Hedhammar, My; Blom, Tobias; Leifer, Klaus; Johansson, Jan; Habibovic, Pamela; van Blitterswijk, Clemens

    2010-01-01

    Calcium phosphate ceramic coatings, applied on surfaces of metallic and polymeric biomaterials, can improve their performance in bone repair and regeneration. Spider silk is biocompatible, strong and elastic, and hence an attractive biomaterial for applications in connective tissue repair. Recently,

  17. Peculiar torsion dynamical response of spider dragline silk

    Science.gov (United States)

    Liu, Dabiao; Yu, Longteng; He, Yuming; Peng, Kai; Liu, Jie; Guan, Juan; Dunstan, D. J.

    2017-07-01

    The torsional properties of spider dragline silks from Nephila edulis and Nephila pilipes spiders are investigated by using a torsion pendulum technique. A permanent torsional deformation is observed after even small torsional strain. This behaviour is quite different from that of the other materials tested here, i.e., carbon fiber, thin metallic wires, Kevlar fiber, and human hair. The spider dragline thus displays a strong energy dissipation upon the initial excitation (around 75% for small strains and more for a larger strain), which correspondingly reduces the amplitude of subsequent oscillations around the new equilibrium position. The variation of torsional stiffness in relaxation dynamics of spider draglines for different excitations is also determined. The experimental result is interpreted in the light of the hierarchical structure of dragline silk.

  18. SPIDER: Probing the dawn of time from above the clouds

    Science.gov (United States)

    Moncelsi, Lorenzo; Spider Collaboration

    2017-11-01

    SPIDER is a balloon-borne microwave polarimeter designed to measure cosmological B-modes on degree angular scales in the presence of Galactic foregrounds. With six independent telescopes housing a total of 2000 detectors in the 90 GHz and 150 GHz frequency bands, SPIDER is the most instantaneously-sensitive CMB polarimeter deployed on the sky to date. SPIDER was successfully launched from McMurdo Station, Antarctica in January 2015 and acquired science data for 16 days. We cover the in-flight performance and present highlights from the ongoing data-analysis. After a successful recovery, the SPIDER team is planning the next flight, featuring one foreground-optimized channel at 280GHz, which will allow us constrain the primordial tensor-mode amplitude at the level of r < 0.03 (99% CL), in the presence of foregrounds.

  19. Evolution of stenophagy in spiders (Araneae): evidence based on the comparative analysis of spider diets.

    Science.gov (United States)

    Pekár, Stano; Coddington, Jonathan A; Blackledge, Todd A

    2012-03-01

    Stenophagy (narrow diet breadth) represents an extreme of trophic specialization in carnivores, but little is known about the forces driving its evolution. We used spiders, the most diversified group of terrestrial predators, to investigate whether stenophagy (1) promoted diversification; (2) was phylogenetically conserved and evolutionarily derived state; and (3) was determined either by geographical distribution and foraging guild. We used published data on the prey of almost 600 species. Six categories of stenophagy were found: myrmecophagy, araneophagy, lepidopterophagy, termitophagy, dipterophagy, and crustaceophagy. We found that the species diversity of euryphagous genera and families was similar to stenophagous genera and families. At the family level, stenophagy evolved repeatedly and independently. Within families, the basal condition was oligophagy or euryphagy. Most types of stenophagy were clearly derived: myrmecophagy in Zodariidae; lepidopterophagy in Araneidae; dipterophagy in Theridiidae. In contrast, araneophagy was confined to basal and intermediate lineages, suggesting its ancestral condition. The diet breadth of species from the tropics and subtropics was less diverse than species from the temperate zone. Diet breadth was lower in cursorial spiders compared to web-building species. Thus, the evolution of stenophagy in spiders appears to be complex and governed by phylogeny as well as by ecological determinants. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  20. Novel approaches to the integration and analysis of systems biology data

    OpenAIRE

    Ramírez, Fidel

    2011-01-01

    The opportunity to investigate whole cellular systems using experimental and computational high-throughput methods leads to the generation of unprecedented amounts of data. Processing of these data often results in large lists of genes or proteins that need to be analyzed and interpreted in the context of all other biological information that is already available. To support such analyses, repositories aggregating and merging the biological information contained in different databases are req...

  1. Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

    Science.gov (United States)

    Bruce E. Rieman; Jason B. Dunham; James L. Clayton

    2006-01-01

    Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions....

  2. Thin Film Assembly of Spider Silk-like Block Copolymers

    Science.gov (United States)

    2011-01-01

    Shipley, N. H.; Lewis, R. V. Int. J. Biol.Macromol. 1999, 24, 271. (c) Thiel, B. L.; Guess, K. B.; Viney, C. Biopolymers 1997, 41, 703. (13) Silk ...Film Assembly of Spider Silk -like Block Copolymers Sreevidhya T. Krishnaji,†,‡ Wenwen Huang,§ Olena Rabotyagova,†,‡ Eugenia Kharlampieva, ) Ikjun Choi...Received November 26, 2010 We report the self-assembly of monolayers of spider silk -like block copolymers. Langmuir isotherms were obtained for a series of

  3. Use of Graph Database for the Integration of Heterogeneous Biological Data.

    Science.gov (United States)

    Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

    2017-03-01

    Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

  4. A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.

    NARCIS (Netherlands)

    Post, L.J.G.; Roos, M.; Marshall, M.S.; van Driel, R.; Breit, T.M.

    2007-01-01

    The numerous public data resources make integrative bioinformatics experimentation increasingly important in life sciences research. However, it is severely hampered by the way the data and information are made available. The semantic web approach enhances data exchange and integration by providing

  5. Early Cretaceous greenhouse pumped higher taxa diversification in spiders.

    Science.gov (United States)

    Shao, Lili; Li, Shuqiang

    2018-05-24

    The Cretaceous experienced one of the most remarkable greenhouse periods in geological history. During this time, ecosystem reorganizations significantly impacted the diversification of many groups of organisms. The rise of angiosperms marked a major biome turnover. Notwithstanding, relatively little remains known about how the Cretaceous global ecosystem impacted the evolution of spiders, which constitute one of the most abundant groups of predators. Herein, we evaluate the transcriptomes of 91 taxa representing more than half of the spider families. We add 23 newly sequenced taxa to the existing database to obtain a robust phylogenomic assessment. Phylogenetic reconstructions using different datasets and methods obtain novel placements of some groups, especially in the Synspermiata and the group having a retrolateral tibial apophysis (RTA). Molecular analyses indicate an expansion of the RTA clade at the Early Cretaceous with a hunting predatory strategy shift. Fossil analyses show a 7-fold increase of diversification rate at the same period, but this likely owes to the first occurrences spider in amber deposits. Additional analyses of fossil abundance show an accumulation of spider lineages in the Early Cretaceous. We speculate that the establishment of a warm greenhouse climate pumped the diversification of spiders, in particular among webless forms tracking the abundance of insect prey. Our study offers a new pathway for future investigations of spider phylogeny and diversification. Copyright © 2018. Published by Elsevier Inc.

  6. Impact of prescribed burning on a heathland inhabiting spider community

    Directory of Open Access Journals (Sweden)

    Krause, Rolf Harald

    2016-04-01

    Full Text Available Heathlands can provide refuge for many stenotopic and endangered arthropods, if habitat management practices are applied. A management measure that is rarely being used today, but which has the potential to support diversity of arthropod communities, is prescribed burning. In this study we investigated the effects of prescribed burning on spider assemblages on a burned site with Calluna vulgaris in the nature reserve Lueneburg Heath, northwest Germany. We used pitfall trapping with a sampling design of 39 traps over a period of one year and 17 sampling intervals on a burned and a control site. We compared overall species richness, activity abundance patterns and community composition of the two sites, with a particular focus on stenotopic and endangered species. We collected 5116 adult spiders and 99 species altogether in a relatively small sampling area. This number of species represents nearly one third of the regional species pool of heathland spider species. Twelve species occurred exclusively on the burned site in contrast to 28 species exclusively found on the unburned site. Although we found more than twice as many spider individuals and higher mean species richness on the control site than on the burned site, the species richness of red-listed spiders was higher on the burned site. Especially the fact that we found 24 endangered species on the burned site and only 20 on the control site indicates that the applied measure of prescribed burning can foster certain endangered spider species and contribute to preserving the overall biodiversity of heathland ecosystems.

  7. Integration of Proteomics, Bioinformatics, and Systems Biology in Traumatic Brain Injury Biomarker Discovery

    Science.gov (United States)

    Guingab-Cagmat, J.D.; Cagmat, E.B.; Hayes, R.L.; Anagli, J.

    2013-01-01

    Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed. PMID:23750150

  8. Right Versus Left Colon Cancer Biology: Integrating the Consensus Molecular Subtypes.

    Science.gov (United States)

    Lee, Michael S; Menter, David G; Kopetz, Scott

    2017-03-01

    Although clinical management of colon cancer generally has not accounted for the primary tumor site, left-sided and right-sided colon cancers harbor different clinical and biologic characteristics. Right-sided colon cancers are more likely to have genome-wide hypermethylation via the CpG island methylator phenotype (CIMP), hypermutated state via microsatellite instability, and BRAF mutation. There are also differential exposures to potential carcinogenic toxins and microbiota in the right and left colon. Gene expression analyses further shed light on distinct biologic subtypes of colorectal cancers (CRCs), with 4 consensus molecular subtypes (CMSs) identified. Importantly, these subtypes are differentially distributed between right- and left-sided CRCs, with greater proportions of the "microsatellite unstable/immune" CMS1 and the "metabolic" CMS3 subtypes found in right-sided colon cancers. This review summarizes important biologic distinctions between right- and left-sided CRCs that likely impact prognosis and may predict for differential responses to biologic therapy. Given the inferior prognosis of stage III-IV right-sided CRCs and emerging data suggesting that anti-epidermal growth factor receptor antibody therapy is associated with worse survival in right-sided stage IV CRCs compared with left-sided cancers, these biologic differences between right- and left-sided CRCs provide critical context and may provide opportunities to personalize therapy. Copyright © 2017 by the National Comprehensive Cancer Network.

  9. Phobic spider fear is associated with enhanced attentional capture by spider pictures: a rapid serial presentation event-related potential study.

    Science.gov (United States)

    Van Strien, Jan W; Franken, Ingmar H A; Huijding, Jorg

    2009-03-04

    The early posterior negativity (EPN) reflects early selective visual processing of emotionally significant information. This study explored the association between fear of spiders and the EPN for spider pictures. Fifty women completed a Spider Phobia Questionnaire and watched the random rapid serial presentation of 600 neutral, 600 negatively valenced emotional, and 600 spider pictures (three pictures per second). The EPN was scored as the mean activity in the 225-300-ms time window at lateral occipital electrodes. Participants with higher scores on the phobia questionnaire showed larger (i.e. more negative) EPN amplitudes in response to spider pictures. The results suggest that the attentional capture of spider-related stimuli is an automatic response, which is modulated by the extent of spider fear.

  10. Atomistic model of the spider silk nanostructure

    Science.gov (United States)

    Keten, Sinan; Buehler, Markus J.

    2010-04-01

    Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

  11. Systems biology integration of proteomic data in rodent models of depression reveals involvement of the immune response and glutamatergic signaling.

    Science.gov (United States)

    Carboni, Lucia; Nguyen, Thanh-Phuong; Caberlotto, Laura

    2016-12-01

    The pathophysiological basis of major depression is incompletely understood. Recently, numerous proteomic studies have been performed in rodent models of depression to investigate the molecular underpinnings of depressive-like behaviours with an unbiased approach. The objective of the study is to integrate the results of these proteomic studies in depression models to shed light on the most relevant molecular pathways involved in the disease. Network analysis is performed integrating preexisting proteomic data from rodent models of depression. The IntAct mouse and the HRPD are used as reference protein-protein interaction databases. The functionality analyses of the networks are then performed by testing overrepresented GO biological process terms and pathways. Functional enrichment analyses of the networks revealed an association with molecular processes related to depression in humans, such as those involved in the immune response. Pathways impacted by clinically effective antidepressants are modulated, including glutamatergic signaling and neurotrophic responses. Moreover, dysregulations of proteins regulating energy metabolism and circadian rhythms are implicated. The comparison with protein pathways modulated in depressive patients revealed significant overlapping. This systems biology study supports the notion that animal models can contribute to the research into the biology and therapeutics of depression. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea

    Science.gov (United States)

    Bionaz, Massimo; Loor, Juan J.

    2012-01-01

    High-throughput ‘omics’ data analysis via bioinformatics is one key component of the systems biology approach. The systems approach is particularly well-suited for the study of the interactions between nutrition and physiological state with tissue metabolism and functions during key life stages of organisms such as the transition from pregnancy to lactation in mammals, ie, the peripartal period. In modern dairy cows with an unprecedented genetic potential for milk synthesis, the nature of the physiologic and metabolic adaptations during the peripartal period is multifaceted and involves key tissues such as liver, adipose, and mammary. In order to understand such adaptation, we have reviewed several works performed in our and other labs. In addition, we have used a novel bioinformatics approach, Dynamic Impact Approach (DIA), in combination with partly previously published data to help interpret longitudinal biological adaptations of bovine liver, adipose, and mammary tissue to lactation using transcriptomics datasets. Use of DIA with transcriptomic data from those tissues during normal physiological adaptations and in animals fed different levels of energy prepartum allowed visualization and integration of most-impacted metabolic pathways around the time of parturition. The DIA is a suitable tool for applying the integrative systems biology approach. The ultimate goal is to visualize the complexity of the systems at study and uncover key molecular players involved in the tissue’s adaptations to physiological state or nutrition. PMID:22807626

  13. Fort Collins Science Center- Policy Analysis and Science Assistance Branch : Integrating social, behavioral, economic and biological sciences

    Science.gov (United States)

    2010-01-01

    The Fort Collins Science Center's Policy Analysis and Science Assistance (PASA) Branch is a team of approximately 22 scientists, technicians, and graduate student researchers. PASA provides unique capabilities in the U.S. Geological Survey by leading projects that integrate social, behavioral, economic, and biological analyses in the context of human-natural resource interactions. Resource planners, managers, and policymakers in the U.S. Departments of the Interior (DOI) and Agriculture (USDA), State and local agencies, as well as international agencies use information from PASA studies to make informed natural resource management and policy decisions. PASA scientists' primary functions are to conduct both theoretical and applied social science research, provide technical assistance, and offer training to advance performance in policy relevant research areas. Management and research issues associated with human-resource interactions typically occur in a unique context, involve difficult to access populations, require knowledge of both natural/biological science in addition to social science, and require the skill to integrate multiple science disciplines. In response to these difficult contexts, PASA researchers apply traditional and state-of-the-art social science methods drawing from the fields of sociology, demography, economics, political science, communications, social-psychology, and applied industrial organization psychology. Social science methods work in concert with our rangeland/agricultural management, wildlife, ecology, and biology capabilities. The goal of PASA's research is to enhance natural resource management, agency functions, policies, and decision-making. Our research is organized into four broad areas of study.

  14. Assessing Cross-disciplinary Efficiency of Soil Amendments for Agro-biologically, Economically, and Ecologically Integrated Soil Health Management

    Science.gov (United States)

    2010-01-01

    Preventive and/or manipulative practices will be needed to maintain soil's biological, physiochemical, nutritional, and structural health in natural, managed, and disturbed ecosystems as a foundation for food security and global ecosystem sustainability. While there is a substantial body of interdisciplinary science on understanding function and structure of soil ecosystems, key gaps must be bridged in assessing integrated agro-biological, ecological, economical, and environmental efficiency of soil manipulation practices in time and space across ecosystems. This presentation discusses the application of a fertilizer use efficiency (FUE) model for assessing agronomic, economic, ecological, environmental, and nematode (pest) management efficiency of soil amendments. FUE is defined as increase in host productivity and/or decrease in plant-parasitic nematode population density in response to a given fertilizer treatment. Using the effects of nutrient amendment on Heterodera glycines population density and normalized difference vegetative index (indicator of physiological activities) of a soybean cultivar ‘CX 252’, how the FUE model recognizes variable responses and separates nutrient deficiency and toxicity from nematode parasitism as well as suitability of treatments designed to achieve desired biological and physiochemical soil health conditions is demonstrated. As part of bridging gaps between agricultural and ecological approaches to integrated understanding and management of soil health, modifications of the FUE model for analyzing the relationships amongst nematode community structure, soil parameters (eg. pH, nutrients, %OM), and plant response to soil amendment is discussed. PMID:22736840

  15. Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models.

    Science.gov (United States)

    Sukumaran, Jeet; Knowles, L Lacey

    2018-04-20

    The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. The phylogeny of fossil whip spiders.

    Science.gov (United States)

    Garwood, Russell J; Dunlop, Jason A; Knecht, Brian J; Hegna, Thomas A

    2017-04-21

    Arachnids are a highly successful group of land-dwelling arthropods. They are major contributors to modern terrestrial ecosystems, and have a deep evolutionary history. Whip spiders (Arachnida, Amblypygi), are one of the smaller arachnid orders with ca. 190 living species. Here we restudy one of the oldest fossil representatives of the group, Graeophonus anglicus Pocock, 1911 from the Late Carboniferous (Duckmantian, ca. 315 Ma) British Middle Coal Measures of the West Midlands, UK. Using X-ray microtomography, our principal aim was to resolve details of the limbs and mouthparts which would allow us to test whether this fossil belongs in the extant, relict family Paracharontidae; represented today by a single, blind species Paracharon caecus Hansen, 1921. Tomography reveals several novel and significant character states for G. anglicus; most notably in the chelicerae, pedipalps and walking legs. These allowed it to be scored into a phylogenetic analysis together with the recently described Paracharonopsis cambayensis Engel & Grimaldi, 2014 from the Eocene (ca. 52 Ma) Cambay amber, and Kronocharon prendinii Engel & Grimaldi, 2014 from Cretaceous (ca. 99 Ma) Burmese amber. We recovered relationships of the form ((Graeophonus (Paracharonopsis + Paracharon)) + (Charinus (Stygophrynus (Kronocharon (Charon (Musicodamon + Paraphrynus)))))). This tree largely reflects Peter Weygoldt's 1996 classification with its basic split into Paleoamblypygi and Euamblypygi lineages; we were able to score several of his characters for the first time in fossils. Our analysis draws into question the monophyly of the family Charontidae. Our data suggest that Graeophonus is a crown group amblypygid, and falls within a monophyletic Paleoamblypgi clade, but outside the family Paracharontidae (= Paracharonopsis + Paracharon). Our results also suggest a new placement for the Burmese amber genus Kronocharon, a node further down from its original position. Overall, we offer a

  17. Design of laser-aided diagnostics for the negative hydrogen ion source SPIDER

    International Nuclear Information System (INIS)

    Pasqualotto, R

    2012-01-01

    ITER nuclear fusion experiment requires additional heating via neutral beams by means of two injectors, delivering 16.5 MW each, up to one hour. This power level results from the neutralization of negative deuterium ions generated by an RF source and accelerated to 1 MeV. Such specifications have never been simultaneously achieved so far and therefore a test facility is being constructed at Consorzio RFX, to demonstrate the feasibility of a prototype neutral beam injector. The facility will host two experimental devices: SPIDER, a 100 kV negative hydrogen/deuterium RF source, full size prototype of the ITER source, and MITICA, a prototype of the full ITER injector. SPIDER will be devoted to optimize the extracted negative ion current density and its spatial uniformity and to minimize the co-extracted electron current. Negative hydrogen is mainly produced by conversion of hydrogen particles at the cesium coated surface of the plasma grid. The interplay of these two species is fundamental to understand and optimize the source performance. Two laser-aided diagnostics play an important role in measuring the negative hydrogen and cesium density: cavity ring down spectroscopy and laser absorption spectroscopy. Cavity ring down spectroscopy will use the photo-detachment process to measure the absolute line-of-sight integrated negative ion density in the extraction region of the source. Laser absorption spectroscopy will be employed to measure the line integrated neutral cesium density, allowing to study the cesium distribution in the source volume, during both the plasma and the vacuum phases. In this paper, the design of the laser-aided diagnostic systems on SPIDER is presented, supported by a review of results obtained in other operating experiments.

  18. Systems biology of resilience and optimal health: integrating Chinese and Western medicine perspectives

    Directory of Open Access Journals (Sweden)

    Herman van Wietmarschen

    2017-05-01

    Full Text Available Western science has been strong in measuring details of biological systems such as gene expression levels and metabolite concentrations, and has generally followed a bottom up approach with regard to explaining biological phenomena. Chinese medicine in contrast has evolved as a top down approach in which body and mind is seen as a whole, a phenomenological approach based on the organization and dynamics of symptom patterns. Western and Chinese perspectives are developing towards a ‘middle out’ approach. Chinese medicine diagnosis, we will argue, allows bridging the gap between biologists and psychologists and offers new opportunities for the development of health monitoring tools and health promotion strategies.

  19. Systems integration: an effective and innovative response to emerging biological threats.

    Science.gov (United States)

    House, Robert V

    2007-04-20

    A rapid and effective development of vaccines and other prophylactics, as well as novel therapeutics, against emerging threats requires the development and implementation of novel strategies. One such strategy is the integrator approach. This approach utilizes an integrated development team comprising expertise in program management, scientific management, clinical research, preclinical/nonclinical development, manufacturing, testing, risk management, quality assurance, and regulatory strategy and compliance. Key to the success of this approach is the successful management of subcontracted work, as well as the seamless integration of multiple systems and data inputs into a coherent development plan.

  20. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

    Science.gov (United States)

    Schmitz, L.

    2016-01-01

    Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

  1. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

    Science.gov (United States)

    Price, S A; Schmitz, L

    2016-04-05

    Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

  2. S100A4 and its role in metastasis – computational integration of data on biological networks.

    Science.gov (United States)

    Buetti-Dinh, Antoine; Pivkin, Igor V; Friedman, Ran

    2015-08-01

    Characterising signal transduction networks is fundamental to our understanding of biology. However, redundancy and different types of feedback mechanisms make it difficult to understand how variations of the network components contribute to a biological process. In silico modelling of signalling interactions therefore becomes increasingly useful for the development of successful therapeutic approaches. Unfortunately, quantitative information cannot be obtained for all of the proteins or complexes that comprise the network, which limits the usability of computational models. We developed a flexible computational framework for the analysis of biological signalling networks. We demonstrate our approach by studying the mechanism of metastasis promotion by the S100A4 protein, and suggest therapeutic strategies. The advantage of the proposed method is that only limited information (interaction type between species) is required to set up a steady-state network model. This permits a straightforward integration of experimental information where the lack of details are compensated by efficient sampling of the parameter space. We investigated regulatory properties of the S100A4 network and the role of different key components. The results show that S100A4 enhances the activity of matrix metalloproteinases (MMPs), causing higher cell dissociation. Moreover, it leads to an increased stability of the pathological state. Thus, avoiding metastasis in S100A4-expressing tumours requires multiple target inhibition. Moreover, the analysis could explain the previous failure of MMP inhibitors in clinical trials. Finally, our method is applicable to a wide range of biological questions that can be represented as directional networks.

  3. Integrated chemical and biological assessment of contaminant impacts in selected European coastal and offshore marine areas

    NARCIS (Netherlands)

    Hylland, Ketil; Robinson, Craig D.; Burgeot, Thierry; Martínez-Gómez, Concepción; Lang, Thomas; Svavarsson, Jörundur; Thain, John E.; Vethaak, A. Dick; Gubbins, Mattew J.

    This paper reports a full assessment of results from ICON, an international workshop on marine integrated contaminant monitoring, encompassing different matrices (sediment, fish, mussels, gastropods), areas (Iceland, North Sea, Baltic, Wadden Sea, Seine estuary and the western Mediterranean) and

  4. Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.

    Science.gov (United States)

    Hulme, S Elizabeth; Whitesides, George M

    2011-05-16

    This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools-biological, chemical, and physical-that are available to researchers studying the worm. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Integrating soil physical and biological properties in contrasting tillage systems in organic and conventional farming

    NARCIS (Netherlands)

    Crittenden, S.J.; Goede, de R.G.M.

    2016-01-01

    Though soil physical and soil biological properties are intrinsically linked in the soil environment they are often studied separately. This work adds value to analyses of soil biophysical quality of tillage systems under organic and conventional farming systems by correlating physical and

  6. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  7. Treatment of acid and sulphate-rich effluents in an integrated biological/chemical process

    CSIR Research Space (South Africa)

    Maree, JP

    2004-04-01

    Full Text Available .4 g SO4/(l.d). The rate of biological sulphate removal was found to be directly related to the square root of sulphate, COD and VSS concentrations respectively, and inversely proportional to sulphide concentration. The practical value of simultaneous...

  8. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

    DEFF Research Database (Denmark)

    Canelas, Andre B.; Harrison, Nicola; Fazio, Alessandro

    2010-01-01

    The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae,...

  9. Integrative Biological Chemistry Program Includes the Use of Informatics Tools, GIS and SAS Software Applications

    Science.gov (United States)

    D'Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

    2015-01-01

    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning…

  10. Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

    2012-01-01

    Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

  11. Biodiesel and Integrated STEM: Vertical Alignment of High School Biology/Biochemistry and Chemistry

    Science.gov (United States)

    Burrows, Andrea C.; Breiner, Jonathan M.; Keiner, Jennifer; Behm, Chris

    2014-01-01

    This article explores the vertical alignment of two high school classes, biology and chemistry, around the core concept of biodiesel fuel production. High school teachers and university faculty members investigated biodiesel as it relates to societal impact through a National Science Foundation Research Experience for Teachers. Using an action…

  12. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    Science.gov (United States)

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  13. Disrupted seasonal biology impacts health, food security, and ecosystems: a call for integrated research

    NARCIS (Netherlands)

    Stevenson, T.J.; Visser, M.E.; Arnold, W.; Barrett, P.; Biello, S.; Dawson, A.; Denlinger, D.L.; Dominoni, Davide; Ebling, F.J.; Elton, S.; Evans, N.; Ferguson, H.M.; Foster, R.G.; Hau, M.; Haydon, D.T.; Hazlerigg, D.G.; Heideman, P.; Hopcraft, J.G.C.; Jonsson, N.N.; Kronfeld-Schor, N.; Kumar, V.; Lincoln, G.A.; MacLeod, R.; Martin, S.A.M.; Martinez-Bakker, M.; Nelson, R.J.; Reed, T.; Robinso, J.E.; Rock, D.; Schwartz, W.J.; Steffan-Dewenter, I.; Tauber, E.; Thackeray, S.J.; Umstatter, C.; Yoshimura, T.; Helm, B.

    2015-01-01

    The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, morphology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for

  14. Integration of biological control and transgenic insect protection for mitigation of mycotoxins in corn

    Science.gov (United States)

    Biological control is known to be effective in reducing aflatoxin contamination of corn and some transgenic corn hybrids incur greatly reduced damage from corn earworm (Helicoverpa zea). We conducted seven field trials over two years to test the hypothesis that transgenic insect protection and biol...

  15. Riparian spiders as sentinels of PCB contamination across heterogeneous aquatic ecosystems

    Science.gov (United States)

    Riparian spiders are being used increasingly to track spatial patterns of contaminants in and fluxing from aquatic ecosystems. However, our understanding of the circumstances under which spiders are effective sentinels of aquatic pollution is limited. The present study tests the ...

  16. Evolution of natural history information in the 21st century – developing an integrated framework for biological and geographical data

    Science.gov (United States)

    Reusser, Deborah A.; Lee, Henry

    2011-01-01

    Threats to marine and estuarine species operate over many spatial scales, from nutrient enrichment at the watershed/estuarine scale to invasive species and climate change at regional and global scales. To help address research questions across these scales, we provide here a standardized framework for a biogeographical information system containing queriable biological data that allows extraction of information on multiple species, across a variety of spatial scales based on species distributions, natural history attributes and habitat requirements. As scientists shift from research on localized impacts on individual species to regional and global scale threats, macroecological approaches of studying multiple species over broad geographical areas are becoming increasingly important. The standardized framework described here for capturing and integrating biological and geographical data is a critical first step towards addressing these macroecological questions and we urge organizations capturing biogeoinformatics data to consider adopting this framework.

  17. An optimized workflow for the integration of biological information into radiotherapy planning: experiences with T1w DCE-MRI

    International Nuclear Information System (INIS)

    Neff, T; Kiessling, F; Brix, G; Baudendistel, K; Zechmann, C; Giesel, F L; Bendl, R

    2005-01-01

    Planning of radiotherapy is often difficult due to restrictions on morphological images. New imaging techniques enable the integration of biological information into treatment planning and help to improve the detection of vital and aggressive tumour areas. This might improve clinical outcome. However, nowadays morphological data sets are still the gold standard in the planning of radiotherapy. In this paper, we introduce an in-house software platform enabling us to combine images from different imaging modalities yielding biological and morphological information in a workflow driven approach. This is demonstrated for the combination of morphological CT, MRI, functional DCE-MRI and PET data. Data of patients with a tumour of the prostate and with a meningioma were examined with DCE-MRI by applying pharmacokinetic two-compartment models for post-processing. The results were compared with the clinical plans for radiation therapy. Generated parameter maps give additional information about tumour spread, which can be incorporated in the definition of safety margins

  18. A "weight of evidence" approach for the integration of environmental "triad" data to assess ecological risk and biological vulnerability.

    Science.gov (United States)

    Dagnino, Alessandro; Sforzini, Susanna; Dondero, Francesco; Fenoglio, Stefano; Bona, Elisa; Jensen, John; Viarengo, Aldo

    2008-07-01

    A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C).

  19. Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling