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Sample records for chemotrophic systems reveal

  1. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

    Directory of Open Access Journals (Sweden)

    William P Inskeep

    Full Text Available The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site was obtained for five high-temperature (>65 degrees C chemotrophic microbial communities sampled from geothermal springs (or pools in Yellowstone National Park (YNP that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3 Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in

  2. Reveal for Salmonella test system.

    Science.gov (United States)

    Bird, C B; Miller, R L; Miller, B M

    1999-01-01

    The Reveal for Salmonella (RSS) test system is a presumptive qualitative test that detects the presence of Salmonella organisms in foods within 21 h total testing time, allowing the user to release negative products 24 h earlier than when using other rapid test kits. Foods are enriched with a proprietary resuscitation medium called Revive and then selectively enriched with either Selenite Cystine or Rappaport-Vassiliadis selective media. The enriched culture is used to inoculate the RSS detection device, which initiates a lateral flow through a reagent zone containing anti-Salmonella antibodies conjugated to colloidal gold particles that capture antigens present in the culture. The antigen-antibody complex migrates farther and is captured by an additional anti-Salmonella antibody, causing the colloidal gold to precipitate and form a visual line, indicating a positive result. A procedural control line also will form regardless of the presence of Salmonella organisms to indicate the test is working properly. Existing AOAC Official Methods for Salmonella organisms require a 48 h enrichment before testing. Hence, a food product has to be held before release, adding extra cost to the company and the consumer. The RSS test system was evaluated by quantitative spiking studies. Although AOAC encourages inclusion of naturally contaminated foods, almost all microbiological AOAC validation studies have been performed with artificially contaminated foods for absolute control over the study. The RSS test system is designed to test many food types for Salmonella organisms and has a limit of detection of 5-10 colony-forming units (cfu)/25 g with a false-negative rate of < 1% and a false-positive rate of < 5.0%. It showed an 81% overall agreement with the traditional procedure of the U.S. Department of Agriculture's Food Safety Inspection Service. PMID:10367381

  3. Orbital tumor revealing a systemic sarcoidosis.

    Directory of Open Access Journals (Sweden)

    Samia Hannanachi Sassi

    2015-03-01

    Full Text Available Ocular involvement is seen in approximately 25% of patients with sarcoidosis. Uveitis is the most common ocular manifestation, but sarcoidosis may involve any part of the eye. Orbital manifestations of sarcoidosis are uncommon with few series in the literature. A 65-year-old woman presented with redness of the right eye and painless, unilateral eyelid swelling. Orbital scanning revealed mass infiltrating the soft tissue of the inferior right orbital quadrant. Biopsy results showed nodular, noncaseating granulomas consistent with sarcoidosis. The complete systemic workup revealed systemic manifestations of sarcoidosis at the time of examination with hilar and mediastinal lymphadenopathies noted on CT scan. The orbital surgical treatment was followed by systemic prednisone therapy with good response. Although rare, orbital sarcoidosis must be considered in the evaluation of orbital tumors in elderly patients. A search for systemic findings should be undertaken and appropriate therapy should be instituted.

  4. Orbital tumor revealing a systemic sarcoidosis.

    Science.gov (United States)

    Hannanachi Sassi, Samia; Dhouib, Rim; Kanchal, Fatma; Doghri, Raoudha; Boujelbene, Nadia; Bouguila, Hedi; Mrad, Karima

    2015-01-01

    Ocular involvement is seen in approximately 25% of patients with sarcoidosis. Uveitis is the most common ocular manifestation, but sarcoidosis may involve any part of the eye. Orbital manifestations of sarcoidosis are uncommon with few series in the literature. A 65-year-old woman presented with redness of the right eye and painless, unilateral eyelid swelling. Orbital scanning revealed mass infiltrating the soft tissue of the inferior right orbital quadrant. Biopsy results showed nodular, noncaseating granulomas consistent with sarcoidosis. The complete systemic workup revealed systemic manifestations of sarcoidosis at the time of examination with hilar and mediastinal lymphadenopathies noted on CT scan. The orbital surgical treatment was followed by systemic prednisone therapy with good response. Although rare, orbital sarcoidosis must be considered in the evaluation of orbital tumors in elderly patients. A search for systemic findings should be undertaken and appropriate therapy should be instituted. PMID:25796029

  5. Saturn Probe: Revealing Solar System Origins

    Science.gov (United States)

    Spilker, T. R.

    2015-12-01

    Comparative studies of the gas giant and ice giant planets are needed to reliably discriminate among competing theories of the origin and evolution of giant planets and the solar system, but we lack critical measurements. A Saturn atmospheric entry probe mission would fill a vital part of that gap, allowing comparative studies of Jupiter and Saturn, providing the basis for later comparisons with the ice giants Uranus and Neptune, and informing studies of extrasolar planetary systems now being characterized. The Galileo Probe mission provided the first in situ studies of Jupiter's atmosphere. Similar measurements at Saturn, Uranus and Neptune would provide an important comparative planetology context for the Galileo results. Cassini's "Proximal Orbits" in 2017 will reveal Saturn's internal structure to complement the Juno mission's similar measurements at Jupiter. A Saturn entry probe, complementing the Galileo Probe investigations at Jupiter, would complete a solid basis for improved understanding of both Jupiter and Saturn, an important stepping stone to understanding Uranus and Neptune and solar system formation and evolution. The 2012 Decadal Survey ("DS") added Saturn Probe science objectives to NASA's New Frontiers Program: highest-priority Tier 1 objectives any New Frontiers implementation must achieve, and Tier 2, high priority but lower than Tier 1. A DS mission concept study using extremely conservative assumptions concluded that a Saturn Probe project could fit within New Frontiers resource constraints, giving a PI confidence that they could pursue some Tier 2 objectives, customizing for the proper balance of science return, science team composition, procured or contributed instruments, etc. Contributed instruments could significantly enhance the payload and the science team for greater science return. They also provide international collaboration opportunities, with science benefits well demonstrated by missions such as Cassini-Huygens and Rosetta.

  6. Orbital tumor revealing a systemic sarcoidosis.

    OpenAIRE

    Samia Hannanachi Sassi; Rim Dhouib; Fatma Kanchal; Raoudha Doghri; Nadia Boujelbene; Hedi Bouguila; Karima Mrad

    2015-01-01

    Ocular involvement is seen in approximately 25% of patients with sarcoidosis. Uveitis is the most common ocular manifestation, but sarcoidosis may involve any part of the eye. Orbital manifestations of sarcoidosis are uncommon with few series in the literature. A 65-year-old woman presented with redness of the right eye and painless, unilateral eyelid swelling. Orbital scanning revealed mass infiltrating the soft tissue of the inferior right orbital quadrant. Biopsy results showed nodular, no...

  7. Sweet syndrome revealing systemic lupus erythematosus.

    LENUS (Irish Health Repository)

    Quinn, N

    2015-02-01

    Sweet Syndrome is an acute inflammatory skin eruption which is rare in children. We report a case of childhood Systemic Lupus Erythematosus (SLE) that presented with Sweet syndrome. This case is a unique presentation of a common disorder which provides a new facet for the differential diagnosis of SLE in children. It is also the first paediatric case to be reported in a Caucasian child.

  8. Revealing Bell's Nonlocality for Unstable Systems in High Energy Physics

    CERN Document Server

    Hiesmayr, Beatrix C; Curceanu, Catalina; Gabriel, Andreas; Huber, Marcus; Larsson, Jan-Ake; Moskal, Pawel

    2011-01-01

    Entanglement and its consequences - in particular the violation of Bell inequalities, which defies our concepts of realism and locality - have been proven to play key roles in Nature by many experiments for various quantum systems. Entanglement can also be found in systems not consisting of ordinary matter and light, i.e. in massive meson--antimeson systems. Bell inequalities have been discussed for these systems, but up to date no direct experimental test to conclusively exclude local realism was found. This mainly stems from the fact that one only has access to a restricted class of observables and that these systems are also decaying. In this Letter we put forward a Bell inequality for unstable systems which can be tested at accelerator facilities with current technology. Herewith, the long awaited proof that such systems at different energy scales can reveal the sophisticated "dynamical" nonlocal feature of Nature in a direct experiment gets feasible. Moreover, the role of entanglement and CP violation, a...

  9. Revealing Bell's nonlocality for unstable systems in high energy physics

    Science.gov (United States)

    Hiesmayr, Beatrix C.; Di Domenico, Antonio; Curceanu, Catalina; Gabriel, Andreas; Huber, Marcus; Larsson, Jan-Åke; Moskal, Pawel

    2012-01-01

    Entanglement and its consequences—in particular the violation of Bell inequalities, which defies our concepts of realism and locality—have been proven to play key roles in Nature by many experiments for various quantum systems. Entanglement can also be found in systems not consisting of ordinary matter and light, i.e. in massive meson-antimeson systems. Bell inequalities have been discussed for these systems, but up to date no direct experimental test to conclusively exclude local realism was found. This mainly stems from the fact that one only has access to a restricted class of observables and that these systems are also decaying. In this Letter we put forward a Bell inequality for unstable systems which can be tested at accelerator facilities with current technology. Herewith, the long awaited proof that such systems at different energy scales can reveal the sophisticated " dynamical" nonlocal feature of Nature in a direct experiment gets feasible. Moreover, the role of entanglement and mathcal{CP} violation, an asymmetry between matter and antimatter, is explored, a special feature offered only by these meson-antimeson systems.

  10. Mesoscopic organization reveals the constraints governing Caenorhabditis elegans nervous system.

    Directory of Open Access Journals (Sweden)

    Raj Kumar Pan

    Full Text Available One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental stimuli. Investigating the intermediate or mesoscopic level of organization in the nervous system is a vital step towards understanding how the integration of micro-level dynamics results in macro-level functioning. The coordination of many different co-occurring processes at this level underlies the command and control of overall network activity. In this paper, we have considered the somatic nervous system of the nematode Caenorhabditis elegans, for which the entire neuronal connectivity diagram is known. We focus on the organization of the system into modules, i.e., neuronal groups having relatively higher connection density compared to that of the overall network. We show that this mesoscopic feature cannot be explained exclusively in terms of considerations such as, optimizing for resource constraints (viz., total wiring cost and communication efficiency (i.e., network path length. Even including information about the genetic relatedness of the cells cannot account for the observed modular structure. Comparison with other complex networks designed for efficient transport (of signals or resources implies that neuronal networks form a distinct class. This suggests that the principal function of the network, viz., processing of sensory information resulting in appropriate motor response, may be playing a vital role in determining the connection topology. Using modular spectral analysis we make explicit the intimate relation between function and structure in the nervous system. This is further brought out by identifying functionally critical neurons purely on the basis of patterns of intra- and inter-modular connections. Our study reveals how the design of the nervous system reflects several constraints, including

  11. A systems biology approach reveals common metastatic pathways in osteosarcoma

    Directory of Open Access Journals (Sweden)

    Flores Ricardo J

    2012-05-01

    Full Text Available Abstract Background Osteosarcoma (OS is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process and a single-level analysis is not likely to identify its key biological determinants. In this study, we used a systems biology approach to identify common metastatic pathways that are jointly supported by both mRNA and protein expression data in two distinct human metastatic OS models. Results mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models, suggesting a very different biological nature of the cell lines. To address this issue, we used a topological significance analysis based on a “shortest-path” algorithm to identify topological nodes, which uncovered additional biological information with respect to the genomic and glycoproteomic profiles but remained hidden from the direct analyses. Pathway analysis of the significant topological nodes revealed a striking concordance between the models and identified significant common pathways, including “Cytoskeleton remodeling/TGF/WNT”, “Cytoskeleton remodeling/Cytoskeleton remodeling”, and “Cell adhesion/Chemokines and adhesion”. Of these, the “Cytoskeleton remodeling/TGF/WNT” was the top ranked common pathway from the topological analysis of the genomic and proteomic profiles in the two metastatic models. The up-regulation of proteins in the “Cytoskeleton remodeling/TGF/WNT” pathway in the Sa

  12. In vivo behavior of NTBI revealed by automated quantification system.

    Science.gov (United States)

    Ito, Satoshi; Ikuta, Katsuya; Kato, Daisuke; Lynda, Addo; Shibusa, Kotoe; Niizeki, Noriyasu; Toki, Yasumichi; Hatayama, Mayumi; Yamamoto, Masayo; Shindo, Motohiro; Iizuka, Naomi; Kohgo, Yutaka; Fujiya, Mikihiro

    2016-08-01

    Non-Tf-bound iron (NTBI), which appears in serum in iron overload, is thought to contribute to organ damage; the monitoring of serum NTBI levels may therefore be clinically useful in iron-overloaded patients. However, NTBI quantification methods remain complex, limiting their use in clinical practice. To overcome the technical difficulties often encountered, we recently developed a novel automated NTBI quantification system capable of measuring large numbers of samples. In the present study, we investigated the in vivo behavior of NTBI in human and animal serum using this newly established automated system. Average NTBI in healthy volunteers was 0.44 ± 0.076 μM (median 0.45 μM, range 0.28-0.66 μM), with no significant difference between sexes. Additionally, serum NTBI rapidly increased after iron loading, followed by a sudden disappearance. NTBI levels also decreased in inflammation. The results indicate that NTBI is a unique marker of iron metabolism, unlike other markers of iron metabolism, such as serum ferritin. Our new automated NTBI quantification method may help to reveal the clinical significance of NTBI and contribute to our understanding of iron overload. PMID:27086349

  13. Revealing electronic open quantum systems with subsystem TDDFT

    Science.gov (United States)

    Krishtal, Alisa; Pavanello, Michele

    2016-03-01

    Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

  14. Wavelet correlations to reveal multiscale coupling in geophysical systems

    CERN Document Server

    Casagrande, Erik; Miralles, Diego; Entekhabi, Dara; Molini, Annalisa

    2015-01-01

    The interactions between climate and the environment are highly complex. Due to this complexity, process-based models are often preferred to estimate the net magnitude and directionality of interactions in the Earth System. However, these models are based on simplifications of our understanding of nature, thus are unavoidably imperfect. Conversely, observation-based data of climatic and environmental variables are becoming increasingly accessible over large scales due to the progress of space-borne sensing technologies and data-assimilation techniques. Albeit uncertain, these data enable the possibility to start unraveling complex multivariable, multiscale relationships if the appropriate statistical methods are applied. Here, we investigate the potential of the wavelet cross-correlation method as a tool for identifying multiscale interactions, feedback and regime shifts in geophysical systems. The ability of wavelet cross-correlation to resolve the fast and slow components of coupled systems is tested on syn...

  15. Maturation of the limbic system revealed by MR FLAIR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Jacques F.; Vergesslich, Klara [University Children' s Hospital UKBB, Department of Paediatric Radiology, Basel (Switzerland)

    2007-04-15

    Cortical signal intensity (SI) of the limbic system in adults is known to be higher than in neocortical structures, but time-related changes in SI during childhood have not been described. To detect maturation-related SI changes within the limbic system using a fluid-attenuated inversion recovery (FLAIR) MR sequence. Twenty children (10 boys, 10 girls; age 3.5-18 years, mean 11.2 years) with no neurological abnormality and normal MR imaging examination were retrospectively selected. On two coronal FLAIR slices, ten regions of interest (ROI) with a constant area of 10 mm{sup 2} were manually placed in the archeocortex (hippocampus), periarcheocortex (parahippocampal gyrus, subcallosal area, cingulate gyrus) and in the neocortex at the level of the superior frontal gyrus on both sides. Significant SI gradients were observed with a higher intensity in the archeocortex, intermediate intensity in the periarcheocortex and low intensity in the neocortex. Significant higher SI values in hippocampal and parahippocampal structures were detected in children up to 10 years of age. These differences mainly reflected differences in cortical structure and myelination state. Archeocortical structures especially showed significant age-related intensity progression suggesting ongoing organization and/or myelination until early adolescence. (orig.)

  16. The Indian summer monsoon as revealed by NCMRWF system

    Indian Academy of Sciences (India)

    P L S Rao; U C Mohanty; P V S Raju; Gopal Iyengar

    2003-03-01

    In this study, we present the mean seasonal features of the Indian summer monsoon circulation in the National Centre for Medium Range Weather Forecasting (NCMRWF) global data assimilation and forecast system. The large-scale budgets of heat and moisture are examined in the analyzed and model atmosphere. The daily operational analyses and forecasts (day 1 through day 5) produced for the summer seasons comprising June, July and August of 1995 and 1993 have been considered for the purpose. The principal aim of the study is two-fold. Primarily, to comprehend the influence of the systematic errors over the Indian summer monsoon, secondarily, to analyze the performance of the model in capturing the interseasonal variability. The heat and moisture balances show reduction in the influx of heat and moisture in the model forecasts compared to the analyzed atmosphere over the monsoon domain. Consequently, the diabatic heating also indicates reducing trend with increase in the forecast period. In effect, the strength of Indian summer monsoon, which essentially depends on these parameters, weakens considerably in the model forecasts. Despite producing feeble monsoon circulation, the model captures interseasonal variability realistically. Although, 1995 and 1993 are fairly normal monsoon seasons, the former received more rainfall compared to the latter in certain pockets of the monsoon domain. This is clearly indicated by the analyzed and model atmosphere in terms of energetics.

  17. The VLT-FLAMES Tarantula Survey. II. R139 revealed as a massive binary system

    NARCIS (Netherlands)

    Taylor, W.D.; Evans, C.J.; Brott, I.; de Koter, A.; Vink, J.S.

    2011-01-01

    We report the discovery that R139 in 30 Doradus is a massive spectroscopic binary system.Multi-epoch optical spectroscopy of R139 was obtained as part of the VLT-FLAMES Tarantula Survey, revealing a double-lined system. The two components are of similar spectral types; the primary exhibits strong C

  18. Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems

    OpenAIRE

    Tay, Tuan Leng; Ronneberger, Olaf; Ryu, Soojin; Nitschke, Roland; Driever, Wolfgang

    2011-01-01

    Essential components of animal behaviour are modulated by dopaminergic (DA) and noradrenergic circuitry. In this study, we reveal at cellular resolution the complete set of projections ('projectome') of every single type of DA and noradrenergio neurons in the central nervous system of zebrafish larvae. The most extensive DA projections are established by posterior tubercular otp-dependent neurons, with individual somata integrating the ascending DA system, the descending diencephalospinal, as...

  19. Panarchy: Discontinuities Reveal Similarities in the Dynamic System Structure of Ecological and Social Systems

    Directory of Open Access Journals (Sweden)

    Craig R. Allen

    2009-06-01

    Full Text Available In this paper, we review the empirical evidence of discontinuous distributions in complex systems within the context of panarchy theory and discuss the significance of discontinuities for understanding emergent properties such as resilience. Over specific spatial-temporal scale ranges, complex systems can configure in a variety of regimes, each defined by a characteristic set of self-organized structures and processes. A system may remain within a regime or dramatically shift to another regime. Understanding the drivers of regime shifts has provided critical insight into system structure and resilience. Although analyses of regime shifts have tended to focus on the system level, new evidence suggests that the same system behaviors operate within scales. In essence, complex systems exhibit multiple dynamic regimes nested within the larger system, each of which operates at a particular scale. Discrete size classes observed in variables in complex systems are evidence of these multiple regimes within complex systems, and the discontinuities between size classes indicate changes in scale.

  20. Limitations of Superfluid Helium Droplets as Host System Revealed by Electronic Spectroscopy of Embedded Molecules

    OpenAIRE

    Premke, Tobias

    2016-01-01

    Superfluid helium nanodroplets serve a unique cryogenic host system ideal to prepare cold molecules and clusters. Structures as well as dynamic processes can be examined by means of high resolution spectroscopy. Dopant spectra are accompanied by helium-induced spectroscopic features which reveal information on the dopant to helium interaction. For this reason the experimental research focuses on the investigation of such helium-induced effects in order to provide new information on the micros...

  1. The VLT-FLAMES Tarantula Survey: II. R139 revealed as a massive binary system

    OpenAIRE

    Taylor, W.D.; Evans, C J; Sana, H.A.A.; N. R. Walborn; Mink, de, S.E.; Stroud, V.E.; Alvarez-Candal, A.; R. H. Barbá; Bestenlehner, J. M.; Bonanos, A. Z.; Brott, I; Crowther, P. A.; Koter, de, A.; Friedrich, K.; Gräfener, G.

    2011-01-01

    We report the discovery that R139 in 30 Doradus is a massive spectroscopic binary system. Multi-epoch optical spectroscopy of R139 was obtained as part of the VLT-FLAMES Tarantula Survey, revealing a double-lined system. The two components are of similar spectral types; the primary exhibits strong C III 4650 emission and is classified as an O6.5 Iafc supergiant, while the secondary is an O6 Iaf supergiant. The radial-velocity variations indicate a highly eccentric orbit with a period of 153.9...

  2. The VLT-FLAMES Tarantula Survey. II. R139 revealed as a massive binary system

    OpenAIRE

    Taylor, W.D.; Evans, C J; Brott, I; de Koter, A.; Vink, J. S.

    2011-01-01

    We report the discovery that R139 in 30 Doradus is a massive spectroscopic binary system.Multi-epoch optical spectroscopy of R139 was obtained as part of the VLT-FLAMES Tarantula Survey, revealing a double-lined system. The two components are of similar spectral types; the primary exhibits strong C III λ4650 emission and is classified as an O6.5 Iafc supergiant, while the secondary is an O6 Iaf supergiant. The radial-velocity variations indicate a highly eccentric orbit with a period of 153.9...

  3. Revealing Bell's nonlocality for unstable systems in high energy physics

    Energy Technology Data Exchange (ETDEWEB)

    Hiesmayr, Beatrix C.; Gabriel, Andreas; Huber, Marcus [University of Vienna, Faculty of Physics, Vienna (Austria); Di Domenico, Antonio [Sapienza Universita di Roma (Italy); INFN Sezione di Roma, Rome (Italy); Curceanu, Catalina [Laboratori Nazionali di Frascati dell' INFN, Frascati (Italy); Larsson, Jan-Aake [Linkoepings Universitet, Institionen foer Systemteknik, Linkoeping (Sweden); Moskal, Pawel [Jagiellonian University, Institute of Physics, Cracow (Poland)

    2012-01-15

    Entanglement and its consequences - in particular the violation of Bell inequalities, which defies our concepts of realism and locality - have been proven to play key roles in Nature by many experiments for various quantum systems. Entanglement can also be found in systems not consisting of ordinary matter and light, i.e. in massive meson-antimeson systems. Bell inequalities have been discussed for these systems, but up to date no direct experimental test to conclusively exclude local realism was found. This mainly stems from the fact that one only has access to a restricted class of observables and that these systems are also decaying. In this Letter we put forward a Bell inequality for unstable systems which can be tested at accelerator facilities with current technology. Herewith, the long awaited proof that such systems at different energy scales can reveal the sophisticated ''dynamical'' nonlocal feature of Nature in a direct experiment gets feasible. Moreover, the role of entanglement and CP violation, an asymmetry between matter and antimatter, is explored, a special feature offered only by these meson-antimeson systems. (orig.)

  4. Extreme Imaging: Revealing the structure of debris disks on solar systems scales with GPI

    Science.gov (United States)

    Kalas, Paul G.; Rajan, Abhijith; Wang, Jason; Millar-Blanchaer, Max; Duchene, Gaspard; Chen, Christine H.; Fitzgerald, Michael P.; Patience, Jennifer; Dong, Ruobing; Graham, James R.; Murray-Clay, Ruth; Macintosh, Bruce

    2015-12-01

    A new generation of extreme adaptive optics systems enables an unprecedented exploration of dusty debris disks on solar system scales. Here we review the new science derived from over a dozen debris disks imaged in total intensity and polarized intensity with the Gemini Planet Imager (GPI). These early results typically reveal narrow belts of material with evacuated regions roughly 50 AU in radius and with subtle asymmetries in structure. In many cases, complementary wider field images obtained with the Hubble Space Telescope uncover more extreme asymmetries in the distribution of dust on 100’s of AU scales. We will discuss the possible causes of these asymmetries, such as the dynamical upheavals that can occur via internal or external perturbations. In a few cases, a gas giant planet has also been imaged in the system, raising new questions about the possible dynamical co-evolution of exoplanets and debris disks.

  5. Reveal non-Markovianity of open quantum systems via local operations

    CERN Document Server

    Yang, Huan; Chen, Yanbei

    2011-01-01

    Non-Markovianity, as an important feature of general open quantum systems, is usually difficult to quantify with limited knowledge of how the plant that we are interested in interacts with its environment-the bath. It often happens that the reduced dynamics of the plant attached to a non-Markovian bath becomes indistinguishable from the one with a Markovian bath, if we left the entire system freely evolve. Here we show that non-Markovianity can be revealed via applying local unitary operations on the plant-they will influence the plant evolution at later times due to memory of the bath. This not only provides a new criterion for non-Markovianity, but also sheds light on protecting and recovering quantum coherence in non-Markovian systems, which will be useful for quantum-information processing.

  6. Issues in Indonesia's tsunami disaster management system revealed after the 2004 Sumatra event

    Science.gov (United States)

    Sugimoto, M.; Koyama, A.; Sun, H.; Kang, I.; Arakawa, T.; Kobayashi, J.; Nagata, M.; Nakanishi, R.; Nakano, M.; Noguchi, S.

    2014-12-01

    During the 2004 Indian Ocean Tsunami, Indonesia had the largest number of casualties around 170,000. International society has supported tsunami early warning system, disaster management and disaster education for Indonesia. The past ten years saw several tsunamis in Indonesia after the 2004 Indian Ocean tsunami. Construction of tsunami early warning system was not in time the 2006 Pangandaran tsunami in Jawa Island. On the other hand, tsunami science has been developed for this decade. Tsunami early warning system has been developed by deep ocean pressure gauges (DART system), coastal tide gauges, GPS buoys and so on. Tsunami folklore has been collected and used education and connected with tsunami deposit. However, the tsunami early warning system and other science application were not widely used at once in Indonesia. GPS buoys were stolen by fishery people. One tsunami evacuation building are not used for evacuation by local people in Aceh Sumatra Island in 2012 though locations of the buildings were selected by scientific numerical simulation. Big panic and trafic accidents occurred by M8.6 earthquake in Aceh in April 2012 and reveal lack of disaster management planning in urban planning during reconstruction (Fig.1: Trafic jam in Banda Aceh, source MSN news photo). In addition to this, the 2011 Tohoku earthquake and tsunami reveal fragilities tsunami preparedness. How should we decide to use the tsunami science? We research field situation in Aceh the after 10 years past from the 2004 Sumatra event. This presentation discusses issues of the gap between tsunami science and operations through field research in Aceh now.

  7. Revealing the functions of the transketolase enzyme isoforms in Rhodopseudomonas palustris using a systems biology approach.

    Directory of Open Access Journals (Sweden)

    Chia-Wei Hu

    Full Text Available BACKGROUND: Rhodopseudomonas palustris (R. palustris is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin-Benson-Bassham (CBB cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. METHODOLOGY/PRINCIPAL FINDINGS: By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth

  8. A multi-scale model of hepcidin promoter regulation reveals factors controlling systemic iron homeostasis.

    Directory of Open Access Journals (Sweden)

    Guillem Casanovas

    2014-01-01

    Full Text Available Systemic iron homeostasis involves a negative feedback circuit in which the expression level of the peptide hormone hepcidin depends on and controls the iron blood levels. Hepcidin expression is regulated by the BMP6/SMAD and IL6/STAT signaling cascades. Deregulation of either pathway causes iron-related diseases such as hemochromatosis or anemia of inflammation. We quantitatively analyzed how BMP6 and IL6 control hepcidin expression. Transcription factor (TF phosphorylation and reporter gene expression were measured under co-stimulation conditions, and the promoter was perturbed by mutagenesis. Using mathematical modeling, we systematically analyzed potential mechanisms of cooperative and competitive promoter regulation by the transcription factors, and experimentally validated the model predictions. Our results reveal that hepcidin cross-regulation primarily occurs by combinatorial transcription factor binding to the promoter, whereas signaling crosstalk is insignificant. We find that the presence of two BMP-responsive elements enhances the steepness of the promoter response towards the iron-sensing BMP signaling axis, which promotes iron homeostasis in vivo. IL6 co-stimulation reduces the promoter sensitivity towards the BMP signal, because the SMAD and STAT transcription factors compete for recruiting RNA polymerase to the transcription start site. This may explain why inflammatory signals disturb iron homeostasis in anemia of inflammation. Taken together, our results reveal why the iron homeostasis circuit is sensitive to perturbations implicated in disease.

  9. The VLT-FLAMES Tarantula Survey II: R139 revealed as a massive binary system

    CERN Document Server

    Taylor, W D; Sana, H; Walborn, N R; de Mink, S E; Stroud, V E; Alvarez-Candal, A; Barbá, R H; Bestenlehner, J M; Bonanos, A Z; Brott, I; Crowther, P A; de Koter, A; Friedrich, K; Gräfener, G; Hénault-Brunet, V; Herrero, A; Kaper, L; Langer, N; Lennon, D J; Apellániz, J Maíz; Markova, N; Morrell, N; Monaco, L; Vink, J S

    2011-01-01

    We report the discovery that R139 in 30 Doradus is a massive spectroscopic binary system. Multi-epoch optical spectroscopy of R139 was obtained as part of the VLT-FLAMES Tarantula Survey, revealing a double-lined system. The two components are of similar spectral types; the primary exhibits strong C III 4650 emission and is classified as an O6.5 Iafc supergiant, while the secondary is an O6 Iaf supergiant. The radial-velocity variations indicate a highly eccentric orbit with a period of 153.9 days. Photometry obtained with the Faulkes Telescope South shows no evidence for significant variability within an 18 month period. The orbital solution yields lower mass limits for the components of M1sin^3 i = 78 \\pm 8 Msun and M2sin^3 i = 66 \\pm 7 Msun. As R139 appears to be the most massive binary system known to contain two evolved Of supergiants, it will provide an excellent test for atmospheric and evolutionary models.

  10. The electromagnetic environment of Magnetic Resonance Imaging systems. Occupational exposure assessment reveals RF harmonics

    Science.gov (United States)

    Gourzoulidis, G.; Karabetsos, E.; Skamnakis, N.; Kappas, C.; Theodorou, K.; Tsougos, I.; Maris, T. G.

    2015-09-01

    Magnetic Resonance Imaging (MRI) systems played a crucial role in the postponement of the former occupational electromagnetic fields (EMF) European Directive (2004/40/EC) and in the formation of the latest exposure limits adopted in the new one (2013/35/EU). Moreover, the complex MRI environment will be finally excluded from the implementation of the new occupational limits, leading to an increased demand for Occupational Health and Safety (OHS) surveillance. The gradient function of MRI systems and the application of the RF excitation frequency result in low and high frequency exposures, respectively. This electromagnetic field exposure, in combination with the increased static magnetic field exposure, makes the MRI environment a unique case of combined EMF exposure. The electromagnetic field levels in close proximity of different MRI systems have been assessed at various frequencies. Quality Assurance (QA) & safety issues were also faced. Preliminary results show initial compliance with the forthcoming limits in each different frequency band, but also revealed peculiar RF harmonic components, of no safety concern, to the whole range detected (20-1000MHz). Further work is needed in order to clarify their origin and characteristics.

  11. Problems of positive list system revealed by survey of pesticide residue in food.

    Science.gov (United States)

    Iwasaki, Mariko; Sato, Itaru; Jin, Yihe; Saito, Norimitsu; Tsuda, Shuji

    2007-05-01

    The positive list system became effective from May 29, 2006 to improve the regulation of residual agricultural chemicals (pesticides, feed additives and veterinary drugs) in foods. In accordance with the system, we investigated pesticide residues in 50 agricultural products purchased in Morioka city from March to November 2006. Analyses were performed according to the "Multiresidue Method for Agricultural Chemicals by GC/MS", the Notice of the Ministry of Health, Labour and Welfare. Five pesticides and two non-agricultural chemicals were detected from 16 samples. Ortho-phenylphenol (OPP) was detected from 8 samples: immature pea, snap bean, kiwi, plain-boiled bamboo shoot, mango, white asparagus, lemon and domestic shiitake mushroom. Maximum residue limits (MRLs) have not been established for these products, and they exceeded the uniform level of 0.01 ppm. DDT was detected from Philippines banana (0.30 ppm) and Korean paprika (0.45 ppm). The residual level in Philippines banana was lower than the MRL, but Korean paprika exceeded its MRL. Chlorpyrifos, Thiabendazole and Imazaril were detected from citrus imported from the U.S.A., but their residue levels were lower than the respective MRLs. Aniline and 2-pyrrolidone were detected from several imported products. These two may not be regulated by the positive list system because they are not agricultural chemicals, although their derivatives are used as pesticides or veterinary drugs. Three problems have been revealed from this survey: 1) application of the uniform level to minor agricultural products, 2) residues of non-agricultural chemicals whose toxicity is uncertain, 3) metabolites of agricultural chemicals, which are also regulated by the positive list system, have not been clearly defined. PMID:17538241

  12. Model systems of protein-misfolding diseases reveal chaperone modifiers of proteotoxicity

    Science.gov (United States)

    2016-01-01

    ABSTRACT Chaperones and co-chaperones enable protein folding and degradation, safeguarding the proteome against proteotoxic stress. Chaperones display dynamic responses to exogenous and endogenous stressors and thus constitute a key component of the proteostasis network (PN), an intricately regulated network of quality control and repair pathways that cooperate to maintain cellular proteostasis. It has been hypothesized that aging leads to chronic stress on the proteome and that this could underlie many age-associated diseases such as neurodegeneration. Understanding the dynamics of chaperone function during aging and disease-related proteotoxic stress could reveal specific chaperone systems that fail to respond to protein misfolding. Through the use of suppressor and enhancer screens, key chaperones crucial for proteostasis maintenance have been identified in model organisms that express misfolded disease-related proteins. This review provides a literature-based analysis of these genetic studies and highlights prominent chaperone modifiers of proteotoxicity, which include the HSP70-HSP40 machine and small HSPs. Taken together, these studies in model systems can inform strategies for therapeutic regulation of chaperone functionality, to manage aging-related proteotoxic stress and to delay the onset of neurodegenerative diseases. PMID:27491084

  13. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

    Science.gov (United States)

    Vonk, Freek J; Casewell, Nicholas R; Henkel, Christiaan V; Heimberg, Alysha M; Jansen, Hans J; McCleary, Ryan J R; Kerkkamp, Harald M E; Vos, Rutger A; Guerreiro, Isabel; Calvete, Juan J; Wüster, Wolfgang; Woods, Anthony E; Logan, Jessica M; Harrison, Robert A; Castoe, Todd A; de Koning, A P Jason; Pollock, David D; Yandell, Mark; Calderon, Diego; Renjifo, Camila; Currier, Rachel B; Salgado, David; Pla, Davinia; Sanz, Libia; Hyder, Asad S; Ribeiro, José M C; Arntzen, Jan W; van den Thillart, Guido E E J M; Boetzer, Marten; Pirovano, Walter; Dirks, Ron P; Spaink, Herman P; Duboule, Denis; McGlinn, Edwina; Kini, R Manjunatha; Richardson, Michael K

    2013-12-17

    Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection. PMID:24297900

  14. The complement system of elasmobranches revealed by liver transcriptome analysis of a hammerhead shark, Sphyrna zygaena.

    Science.gov (United States)

    Goshima, Masayuki; Sekiguchi, Reo; Matsushita, Misao; Nonaka, Masaru

    2016-08-01

    Comprehensive studies of the complement genes in basal vertebrates have revealed that cyclostomes have apparently primitive complement systems whereas bony fish have well-developed complement systems comparable to those of mammals. Here we have performed liver transcriptome analysis of a hammerhead shark, Sphyrna zygaeana, to elucidate the early history of vertebrate complement evolution. Identified genes were; one C1qB, one C1r, one C1s, one MASP-1/-3, one MASP-2, two factor B/C2, one C3, three C4, one C5, one C6, one C7, one C8A, three C8B, one C8G, one C9, two factor I and one S protein. No MBL, ficolin, C1qA or C1qC were found. These results indicate that the lectin, classical, alternative and lytic pathways were established in the common ancestor of jawed vertebrates. In addition to the absence of MBL and ficolin, the MASP transcripts lacked the serine protease domain, suggesting that the lectin pathway was lost in the hammerhead shark lineage. PMID:26987526

  15. The Evolution of Two-Component Systems in Bacteria RevealsDifferent Strategies for Niche Adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Alm, Eric; Huang, Katherine; Arkin, Adam

    2006-09-13

    Two-component systems including histidine protein kinasesrepresent the primary signal transduction paradigm in prokaryoticorganisms. To understand how these systems adapt to allow organisms todetect niche-specific signals, we analyzed the phylogenetic distributionof nearly 5000 histidine protein kinases from 207 sequenced prokaryoticgenomes. We found that many genomes carry a large repertoire of recentlyevolved signaling genes, which may reflect selective pressure to adapt tonew environmental conditions. Both lineage-specific gene family expansionand horizontal gene transfer play major roles in the introduction of newhistidine kinases into genomes; however, there are differences in howthese two evolutionary forces act. Genes imported via horizontal transferare more likely to retain their original functionality as inferred from asimilar complement of signaling domains, while gene family expansionaccompanied by domain shuffling appears to be a major source of novelgenetic diversity. Family expansion is the dominantsource of newhistidine kinase genes in the genomes most enriched in signalingproteins, and detailed analysis reveals that divergence in domainstructure and changes in expression patterns are hallmarks of recentexpansions. Finally, while these two modes of gene acquisition arewidespread across bacterial taxa, there are clear species-specificpreferences for which mode is used.

  16. Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN system.

    Directory of Open Access Journals (Sweden)

    Axel Hausmann

    Full Text Available BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN system of BOLD (Barcode of Life Datasystems, a method that supports automated, rapid species delineation and identification. METHODOLOGY/PRINCIPAL FINDINGS: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88% in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93% were found to possess diagnostic barcode sequences at the European level while only three species pairs (3% were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads shared BINs, while specimens from the remaining species (18% were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed

  17. Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly

    Directory of Open Access Journals (Sweden)

    Amy J. Gerc

    2015-09-01

    Full Text Available The Type VI secretion system (T6SS is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassemblies of the machinery simultaneously and on multiple timescales in vivo. We report that the localization and dynamic behavior of each of the components examined is distinct, revealing a multi-stage and dynamic assembly process for the T6SS machinery. We also show that the T6SS can assemble and fire without needing a cell contact trigger, defining an aggressive strategy that broadens target range and suggesting that activation of the T6SS is tailored to survival in specific niches.

  18. Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly.

    Science.gov (United States)

    Gerc, Amy J; Diepold, Andreas; Trunk, Katharina; Porter, Michael; Rickman, Colin; Armitage, Judith P; Stanley-Wall, Nicola R; Coulthurst, Sarah J

    2015-09-29

    The Type VI secretion system (T6SS) is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassemblies of the machinery simultaneously and on multiple timescales in vivo. We report that the localization and dynamic behavior of each of the components examined is distinct, revealing a multi-stage and dynamic assembly process for the T6SS machinery. We also show that the T6SS can assemble and fire without needing a cell contact trigger, defining an aggressive strategy that broadens target range and suggesting that activation of the T6SS is tailored to survival in specific niches. PMID:26387948

  19. Traumatic left ventricular aneurysm revealed by systemic embolism. Interest of Indium 111 labelled platelets scintigraphy

    Energy Technology Data Exchange (ETDEWEB)

    Vahanian, A.; Villemant, D.; Grimberg, F.; Farah, E.; Acar, J.; Drouet, L.

    1984-01-01

    A case of traumatic left ventricular aneurysm, presenting with recurrent cerebral embolism, 36 years after a thoraco-brachial bullet wound was reported. The 58 year old man had no symptoms of angina or particular cardiovascular risk factors. The ECG showed changes of chronic anterior wall infarction, observed 10 years previously on a routine preoperative recording. There was a calcified circular para-apical shadow on chest X-Ray. The antero-apical region showed hypofixation on myocardial scintigraphy, and hypokinesia on isotopic angiography. The coronary arteries were normal. Indium 111 platelet marking revealed a focus of hyperfixation within the left ventricle. At surgery, a true calcific para-apical left ventricular aneurysm was discovered, containing a fresh thrombus. This lesion was resected. Peroperative Indium 111 platelet test confirmed that the thrombus was the site of high uptake. The surgical result was good at 6 months follow-up. This case illustrates: the value of the Indium test which would appear to be a very specific and sensitive method of detecting intraventricular thrombi. This test, which appreciates the thrombolic activy of intracardiac masses is a useful complement to other non-invasive methods such as 2D echocardiography; the special characteristics of post-trauma left ventricular aneurysms which are rare, often diagnosed late, at the time of complications such as systemic embolism, commonly pose medico-legal problems, and for which surgical treatment seems to be indicated in symptomatic patients.

  20. In situ Expression of Functional Genes Reveals Nitrogen Cycling at High Temperatures in Terrestrial Hydrothermal Systems

    Science.gov (United States)

    Loiacono, S. T.; Meyer-Dombard, D. R.

    2011-12-01

    using (reverse-transcription) polymerase chain reaction to identify the presence and expression of nifH genes, and resultant (RT-)PCR product was cloned and sequenced. Results reveal high-temperature in situ expression of nifH in select LGB features [7] which is, to the authors' knowledge, the first direct evidence of nifH transcription in the chemosynthetic zones of terrestrial hydrothermal systems. Results also indicate the presence of novel nifH sequences and allow phylogenetic comparison of nifH genes along geochemical gradients within individual hot spring features and between various thermal features in the LGB. Collectively, these results provide evidence for microbial adaptations that have led to the ability to support basic metabolic processes under "extreme" conditions. [1] Hall et al., 2008. AEM 74: 4910-4922. [2] Steunou et al., 2008. The ISME Journal 2: 364-378. [3] Hamilton et al., 2011. Microb Ecol DOI 10.1007/s00248-011-9824-9. [4] Raymond et al., 2008. EOS Trans AGU. Abstract B14A-03. [5] Havig et al., 2010. J Geophys Res-Biogeo 116: G01005. [6] Mehta & Baross, 2006. Science 314: 1783-1786. [7] Loiacono et al., 2011. Submitted FEMS Microbiol Ecol.

  1. Proteomic analysis reveals metabolic and regulatory systems involved the syntrophic and axenic lifestyle of Syntrophomonas wolfei.

    Directory of Open Access Journals (Sweden)

    Jessica Rhea Sieber

    2015-02-01

    Full Text Available Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomic approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL and GroES chaperonins, a small heat shock protein, and proteins involved in electron transfer, beta-oxidation, and ATP synthesis. Several putative energy conservation enzyme systems that utilize NADH and ferredoxin were present. The abundance of an EtfAB2 and the membrane-bound iron-sulfur oxidoreductase (Swol_0698 gene product delineated a potential conduit for electron transfer between acyl-CoA dehydrogenases and membrane redox carriers. Proteins detected only when S. wolfei was grown with M. hungatei included a zinc-dependent dehydrogenase with a GroES domain, whose gene is present in genomes in many organisms capable of syntrophy, and transcriptional regulators responsive to environmental stimuli or the physiological status of the cell. The proteomic analysis revealed an emphasis macromolecular stability and energy metabolism to S. wolfei and presence of regulatory mechanisms responsive to external stimuli and cellular physiological status.

  2. International Baccalaureate as a Litmus Test Revealing Conflicting Values and Power Relations in the Israeli Education System

    Science.gov (United States)

    Yemini, Miri; Dvir, Yuval

    2016-01-01

    This study comprises a comprehensive attempt to reveal the power relations and conflicting interests within the local-global nexus of the Israeli public education system. The perceptions of different stakeholders were explored, in regard to the implementation of the International Baccalaureate Diploma Program as an example of a globally oriented…

  3. Intravital imaging technology reveals immune system dynamics in vivo

    OpenAIRE

    Masaru Ishii

    2016-01-01

    Fluorescent ‘intravital’ imaging is a new research technique by which the interior of living tissues and organs (in living bodies, if possible) can be observed, revealing the kinetics of cell and molecular processes in real time. Recent technological innovations in optical equipment and fluorescence imaging techniques have enabled a variety of cellular phenomena in different tissues and organs to be characterized under completely native conditions. This shift from static to dynamic biology co...

  4. Magnetic resonance microscopy and spectroscopy reveal kinetics of cryoprotectant permeation in a multicompartmental biological system.

    OpenAIRE

    Hagedorn, M; Hsu, E. W.; Pilatus, U; Wildt, D E; Rall, W R; Blackband, S.J.

    1996-01-01

    Successful cryopreservation of most multicompartmental biological systems has not been achieved. One prerequisite for success is quantitative information on cryoprotectant permeation into and amongst the compartments. This report describes direct measurements of cryoprotectant permeation into a multicompartmental system using chemical shift selective magnetic resonance (MR) microscopy and MR spectroscopy. We used the developing zebrafish embryo as a model for studying these complex systems be...

  5. Multiple electron transfer systems in oxygen reducing biocathodes revealed by different conditions of aeration/agitation.

    Science.gov (United States)

    Rimboud, Mickaël; Bergel, Alain; Erable, Benjamin

    2016-08-01

    Oxygen reducing biocathodes were formed at -0.2V/SCE (+0.04V/SHE) from compost leachate. Depending on whether aeration was implemented or not, two different redox systems responsible for the electrocatalysis of oxygen reduction were evidenced. System I was observed at low potential (-0.03V/SHE) on cyclic voltammetries (CVs). It appeared during the early formation of the biocathode (few hours) and resisted the hydrodynamic conditions induced by the aeration. System II was observed at higher potential on CV (+0.46V/SHE); it required a longer lag time (up to 10days) and quiescent conditions to produce an electrochemical signal. The hydrodynamic effects produced by the forced aeration led to its extinction. From their different behaviors and examples in the literature, system I was identified as being a membrane-bound cytochrome-related molecule, while system II was identified as a soluble redox mediator excreted by the biofilm. This study highlighted the importance of controlling the local hydrodynamics to design efficient oxygen reducing biocathodes able to operate at high potential. PMID:27035588

  6. Identifying modular flows on multilayer networks reveals highly overlapping organization in social systems

    CERN Document Server

    De Domenico, Manlio; Arenas, Alex; Rosvall, Martin

    2014-01-01

    Unveiling the community structure of networks is a powerful methodology to comprehend interconnected systems across the social and natural sciences. To identify different types of functional modules in interaction data aggregated in a single network layer, researchers have developed many powerful methods. For example, flow-based methods have proven useful for identifying modular dynamics in weighted and directed networks that capture constraints on flow in the systems they represent. However, many networked systems consist of agents or components that exhibit multiple layers of interactions. Inevitably, representing this intricate network of networks as a single aggregated network leads to information loss and may obscure the actual organization. Here we propose a method based on compression of network flows that can identify modular flows in non-aggregated multilayer networks. Our numerical experiments on synthetic networks show that the method can accurately identify modules that cannot be identified in agg...

  7. Application of dynamical systems theory to global weather phenomena revealed by satellite imagery

    Science.gov (United States)

    Saltzman, Barry; Ebisuzaki, Wesley; Maasch, Kirk A.; Oglesby, Robert; Pandolfo, Lionel; Tang, Chung-Muh

    1989-01-01

    Theoretical studies of low frequency and seasonal weather variability; dynamical properties of observational and general circulation model (GCM)-generated records; effects of the hydrologic cycle and latent heat release on extratropical weather; and Earth-system science studies are summarized.

  8. Pyrosequencing Reveals a Core Community of Anodic Bacterial Biofilms in Bioelectrochemical Systems from China.

    Science.gov (United States)

    Xiao, Yong; Zheng, Yue; Wu, Song; Zhang, En-Hua; Chen, Zheng; Liang, Peng; Huang, Xia; Yang, Zhao-Hui; Ng, I-Son; Chen, Bor-Yann; Zhao, Feng

    2015-01-01

    Bioelectrochemical systems (BESs) are promising technologies for energy and product recovery coupled with wastewater treatment, and the core microbial community in electrochemically active biofilm in BESs remains controversy. In the present study, 7 anodic communities from 6 bioelectrochemical systems in 4 labs in southeast, north and south-central of China are explored by 454 pyrosequencing. A total of 251,225 effective sequences are obtained for 7 electrochemically active biofilm samples at 3% cutoff level. While Alpha-, Beta-, and Gamma-proteobacteria are the most abundant classes (averaging 16.0-17.7%), Bacteroidia and Clostridia are the two sub-dominant and commonly shared classes. Six commonly shared genera i.e., Azospira, Azospirillum, Acinetobacter, Bacteroides, Geobacter, Pseudomonas, and Rhodopseudomonas dominate the electrochemically active communities and are defined as core genera. A total of 25 OTUs with average relative abundance >0.5% were selected and designated as core OTUs, and some species relating to these OTUs have been reported electrochemically active. Furthermore, cyclic voltammetry and chronoamperometry tests show that two strains from Acinetobacter guillouiae and Stappia indica, bacteria relate to two core OTUs, are electrochemically active. Using randomly selected bioelectrochemical systems, the study has presented extremely diverse bacterial communities in anodic biofilms, though, we still can suggest some potentially microbes for investigating the electrochemical mechanisms in bioelectrochemical systems. PMID:26733958

  9. 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,...

  10. Recent plumbing system of the Krakatau volcano revealed by teleseismic earthquake distribution

    Czech Academy of Sciences Publication Activity Database

    Špičák, Aleš; Vaněk, Jiří; Hanuš, Václav

    2011-01-01

    Roč. 100, č. 6 (2011), s. 1375-1381. ISSN 1437-3254 R&D Projects: GA MŠk ME09011 Institutional research plan: CEZ:AV0Z30120515 Keywords : subduction-related volcanoes * Krakatau * earth quake distribution * volcanic plumbing system Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 2.342, year: 2011

  11. Concurrent TMS-fMRI Reveals Interactions between Dorsal and Ventral Attentional Systems

    DEFF Research Database (Denmark)

    Leitao, Joana; Thielscher, Axel; Tuennerhoff, Johannes;

    2015-01-01

    interactively in this process. This fMRI study used concurrent transcranial magnetic stimulation (TMS) as a causal perturbation approach to investigate the interactions between dorsal and ventral attentional systems and sensory processing areas. In a sustained spatial attention paradigm, human participants...

  12. The Pluto-Charon system as revealed during the mutual events

    International Nuclear Information System (INIS)

    This year is the last of a five-year interval when the Earth passes through the orbital plane of Pluto and its satellite Charon, causing alternate transits and occultations of the satellite as seen from Earth. Spectrophotometric observations of the system made both in and out of eclipse were obtained in the visual and near-infrared. The Pluto-Charon system is found to be compositionally diverse, a result unanticipated before the mutual events. Water frost was identified and is ubiquitous on Charon's surface, while Pluto has a methane veneer. The spectral activity of Pluto's methane is seen to vary with rotational phase. On Pluto, surface albedo appears to be correlated with composition. Dark regions tend to be redder and depleted in methane relative to bright regions. Dependence of geometric albedo with wavelength were calculated for both bodies, from 0.4 to 2.4 microns. The albedo model of Marcialis (1983, 1988) has emerged favorably after several severe tests. Accurate radii and system bulk density derived from the mutual events were used to construct models of phenomena unanticipated a decade ago. Recent interior models are used to show that viscous relaxation of topography is expected to be significant on Pluto but not on Charon. Horizontal topographic features on the primary probably are limited in extent to less than a few tens of kilometers. Globally, Pluto's figure is essentially hydrostatic. Astrometric observations of the system are presented, as evidence that the discovery of Charon just seven years before the initial mutual events was not fortuitous, but most probable. The astrometry will help to refine Pluto's orbit, making prediction of future stellar occultations by the system more reliable

  13. {sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

    2011-04-15

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  14. 1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    International Nuclear Information System (INIS)

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  15. RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere.

    Science.gov (United States)

    Mynampati, Kalyan Chakravarthy; Lee, Yong Jian; Wijdeveld, Arjan; Reuben, Sheela; Samavedham, Lakshminarayanan; Kjelleberg, Staffan; Swarup, Sanjay

    2015-12-01

    In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health. PMID:26386206

  16. Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly

    OpenAIRE

    Amy J. Gerc; Andreas Diepold; Katharina Trunk; Michael Porter; Colin Rickman; Judith P. Armitage; Nicola R. Stanley-Wall; Sarah J. Coulthurst

    2015-01-01

    Summary The Type VI secretion system (T6SS) is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassembli...

  17. Online Reputation and Polling Systems: Data Incest, Social Learning and Revealed Preferences

    OpenAIRE

    Krishnamurthy, Vikram; Hoiles, William

    2015-01-01

    This paper considers online reputation and polling systems where individuals make recommendations based on their private observations and recommendations of friends. Such interaction of individuals and their social influence is modelled as social learning on a directed acyclic graph. Data incest (misinformation propagation) occurs due to unintentional re-use of identical actions in the for- mation of public belief in social learning; the information gathered by each agent is mistakenly consid...

  18. The components of the Daphnia pulex immune system as revealed by complete genome sequencing

    OpenAIRE

    Blaxter Mark L; Colbourne John K; Conlon Claire; McTaggart Seanna J; Little Tom J

    2009-01-01

    Abstract Background Branchiopod crustaceans in the genus Daphnia are key model organisms for investigating interactions between genes and the environment. One major theme of research on Daphnia species has been the evolution of resistance to pathogens and parasites, but lack of knowledge of the Daphnia immune system has limited the study of immune responses. Here we provide a survey of the immune-related genome of D. pulex, derived from the newly completed genome sequence. Genes likely to be ...

  19. A short-time scale colloidal system reveals early bacterial adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Christophe Beloin

    2008-07-01

    Full Text Available The development of bacteria on abiotic surfaces has important public health and sanitary consequences. However, despite several decades of study of bacterial adhesion to inert surfaces, the biophysical mechanisms governing this process remain poorly understood, due, in particular, to the lack of methodologies covering the appropriate time scale. Using micrometric colloidal surface particles and flow cytometry analysis, we developed a rapid multiparametric approach to studying early events in adhesion of the bacterium Escherichia coli. This approach simultaneously describes the kinetics and amplitude of early steps in adhesion, changes in physicochemical surface properties within the first few seconds of adhesion, and the self-association state of attached and free-floating cells. Examination of the role of three well-characterized E. coli surface adhesion factors upon attachment to colloidal surfaces--curli fimbriae, F-conjugative pilus, and Ag43 adhesin--showed clear-cut differences in the very initial phases of surface colonization for cell-bearing surface structures, all known to promote biofilm development. Our multiparametric analysis revealed a correlation in the adhesion phase with cell-to-cell aggregation properties and demonstrated that this phenomenon amplified surface colonization once initial cell-surface attachment was achieved. Monitoring of real-time physico-chemical particle surface properties showed that surface-active molecules of bacterial origin quickly modified surface properties, providing new insight into the intricate relations connecting abiotic surface physicochemical properties and bacterial adhesion. Hence, the biophysical analytical method described here provides a new and relevant approach to quantitatively and kinetically investigating bacterial adhesion and biofilm development.

  20. Evolutionary strategies of cells and viruses in deep-sea hydrothermal systems revealed through comparative metagenomics

    Science.gov (United States)

    Anderson, R.; Sogin, M. L.; Baross, J. A.

    2013-12-01

    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems must also withstand these environmental extremes, and a high proportion of viruses in these systems are lysogenic. Comparative analysis of a cellular and viral metagenome from a diffuse flow hydrothermal vent has provided insights into the evolutionary strategies of both cells and viruses in hydrothermal systems. We detected numerous mobile elements in the viral and cellular gene pools as well as a large number of prophage in the cellular fraction. We show that the hydrothermal vent viral gene pool is relatively enriched in genes related to energy metabolism, a feature that is unique to the hydrothermal vent viral gene pool compared to viral gene pools from other environments, indicating a potential for integrated prophage to enhance host metabolic flexibility. We also detected stronger purifying selection in the viral versus cellular gene pool, indicating selection pressures that promote prolonged viral integration in the host. Our results support the hypothesis that viruses enhance host genomic plasticity and adaptability in this extreme and dynamic environment. Finally, we will discuss general implications of this work for understanding the viral impact on biogeochemical cycles and evolutionary trajectories of microbial populations in the deep subsurface biosphere.

  1. Collaborative play in young children as a complex dynamic system: revealing gender related differences.

    Science.gov (United States)

    Steenbeek, Henderien; van der Aalsvoort, Diny; van Geert, Paul

    2014-07-01

    This study was focused on the role of gender-related differences in collaborative play, by examining properties of play as a complex system, and by using micro-genetic analysis techniques. A complex dynamic systems model of dyadic play was used to make predictions with regard to duration and number of contact-episodes during play of same-sex dyads, both on the micro- (i.e., per individual session), meso- (i.e., in smoothed data), and macro time scale (i.e., the change over six consecutive play sessions). The empirical data came from a study that examined the collaborative play skills of children who experienced six twenty minute play sessions within a three week period of time. Monte Carlo permutation analyses were used to compare model predictions and empirical data. The findings point to strongly asymmetric distributions in the duration and number of contact episodes in all dyads over the six sessions, as a direct consequence of the underlying dynamics of the play system. The model prediction that girls-dyads would show longer contact episodes than boys-dyads was confirmed, but the prediction regarding the difference in number of peaks was not confirmed. In addition, the majority of the model predictions regarding changes over the course of six sessions were consistent with the data. That is, the average duration and the maximum duration of contact-episodes increases both in boys-dyads and girls-dyads, but differences occur in the strength of the increase. Contrary to expectation, the number of contact-episodes decreases both in boys-dyads and in girls-dyads. PMID:24894265

  2. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems

    Science.gov (United States)

    Hook, Vivian; Bandeira, Nuno

    2015-12-01

    Neuropeptides regulate intercellular signaling as neurotransmitters of the central and peripheral nervous systems, and as peptide hormones in the endocrine system. Diverse neuropeptides of distinct primary sequences of various lengths, often with post-translational modifications, coordinate and integrate regulation of physiological functions. Mass spectrometry-based analysis of the diverse neuropeptide structures in neuropeptidomics research is necessary to define the full complement of neuropeptide signaling molecules. Human neuropeptidomics has notable importance in defining normal and dysfunctional neuropeptide signaling in human health and disease. Neuropeptidomics has great potential for expansion in translational research opportunities for defining neuropeptide mechanisms of human diseases, providing novel neuropeptide drug targets for drug discovery, and monitoring neuropeptides as biomarkers of drug responses. In consideration of the high impact of human neuropeptidomics for health, an observed gap in this discipline is the few published articles in human neuropeptidomics compared with, for example, human proteomics and related mass spectrometry disciplines. Focus on human neuropeptidomics will advance new knowledge of the complex neuropeptide signaling networks participating in the fine control of neuroendocrine systems. This commentary review article discusses several human neuropeptidomics accomplishments that illustrate the rapidly expanding diversity of neuropeptides generated by protease processing of pro-neuropeptide precursors occurring within the secretory vesicle proteome. Of particular interest is the finding that human-specific cathepsin V participates in producing enkephalin and likely other neuropeptides, indicating unique proteolytic mechanisms for generating human neuropeptides. The field of human neuropeptidomics has great promise to solve new mechanisms in disease conditions, leading to new drug targets and therapeutic agents for human

  3. Systemic administration of 3-bromopyruvate reveals its interaction with serum proteins in a rat model

    OpenAIRE

    Kunjithapatham, Rani; Geschwind, Jean-Francois H; Rao, Pramod P.; Boronina, Tatiana N; Robert N Cole; Ganapathy-Kanniappan, Shanmugasundaram

    2013-01-01

    Background 3-bromopyruvate (3-BrPA) is a glycolytic inhibitor that affects cancer cells by targeting energy metabolism. Preclinical reports have established that a 1.75 mM dose of 3-BrPA is effective and sufficient to inhibit tumor growth when administered under a loco-regional approach (intraarterial and intratumoral). This loco-regional therapeutic dose was found to be nontoxic when given systemically as well. Yet, the mechanism underlying this lack of toxicity of 1.75 mM 3-BrPA during syst...

  4. Transcriptional Analysis Reveals Gender-Specific Changes in the Aging of the Human Immune System

    OpenAIRE

    Marttila, Saara; Jylhävä, Juulia; Nevalainen, Tapio; Nykter, Matti; Jylhä, Marja; Hervonen, Antti; Tserel, Liina; Peterson, Pärt; Hurme, Mikko

    2013-01-01

    Aging and gender have a strong influence on the functional capacity of the immune system. In general, the immune response in females is stronger than that in males, but there is scant information about the effect of aging on the gender difference in the immune response. To address this question, we performed a transcriptomic analysis of peripheral blood mononuclear cells derived from elderly individuals (nonagenarians, n = 146) and young controls (aged 19–30 years, n = 30). When compared to y...

  5. Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior

    Directory of Open Access Journals (Sweden)

    DeSimone Douglas W

    2007-10-01

    Full Text Available Abstract Background Tissue morphogenesis is a complex process whereby tissue structures self-assemble by the aggregate behaviors of independently acting cells responding to both intracellular and extracellular cues in their environment. During embryonic development, morphogenesis is particularly important for organizing cells into tissues, and although key regulatory events of this process are well studied in isolation, a number of important systems-level questions remain unanswered. This is due, in part, to a lack of integrative tools that enable the coupling of biological phenomena across spatial and temporal scales. Here, we present a new computational framework that integrates intracellular signaling information with multi-cell behaviors in the context of a spatially heterogeneous tissue environment. Results We have developed a computational simulation of mesendoderm migration in the Xenopus laevis explant model, which is a well studied biological model of tissue morphogenesis that recapitulates many features of this process during development in humans. The simulation couples, via a JAVA interface, an ordinary differential equation-based mass action kinetics model to compute intracellular Wnt/β-catenin signaling with an agent-based model of mesendoderm migration across a fibronectin extracellular matrix substrate. The emergent cell behaviors in the simulation suggest the following properties of the system: maintaining the integrity of cell-to-cell contact signals is necessary for preventing fractionation of cells as they move, contact with the Fn substrate and the existence of a Fn gradient provides an extracellular feedback loop that governs migration speed, the incorporation of polarity signals is required for cells to migrate in the same direction, and a delicate balance of integrin and cadherin interactions is needed to reproduce experimentally observed migratory behaviors. Conclusion Our computational framework couples two different

  6. Characterization of the Mycobacterial NER System Reveals Novel Functions of the uvrD1 Helicase

    OpenAIRE

    Guthlein, C.; Wanner, R M; Sander, P; Davis, E O; Bosshard, M.; Jiricny, J; Bottger, E. C.; Springer, B.

    2008-01-01

    In this study, we investigated the role of the nucleotide excision repair (NER) pathway in mycobacterial DNA repair. Mycobacterium smegmatis lacking the NER excinuclease component uvrB or the helicase uvrD1 gene and a double knockout lacking both genes were constructed, and their sensitivities to a series of DNA-damaging agents were analyzed. As anticipated, the mycobacterial NER system was shown to be involved in the processing of bulky DNA adducts and interstrand cross-links. In addition, i...

  7. Characterisation of the mycobacterial NER system reveals novel functions of uvrD1 helicase

    OpenAIRE

    Güthlein, C; Wanner, R M; Sander, P; Davis, E O; Bosshard, M.; Jiricny, J; Böttger, E C; Springer, B.

    2009-01-01

    In this study, we investigated the role of the nucleotide excision repair (NER) pathway in mycobacterial DNA repair. Mycobacterium smegmatis lacking the NER excinuclease component uvrB, the helicase uvrD1 and a double knock-out lacking both proteins were constructed and their sensitivity to a series of DNA damaging agents wa analysed. As anticipated, the mycobacterial NER system was shown to be involved in the processing of bulky DNA adducts and inter-strand cross-links. In addition, it coul...

  8. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

    Science.gov (United States)

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

  9. Index cohesive force analysis reveals that the US market became prone to systemic collapses since 2002.

    Directory of Open Access Journals (Sweden)

    Dror Y Kenett

    Full Text Available BACKGROUND: The 2007-2009 financial crisis, and its fallout, has strongly emphasized the need to define new ways and measures to study and assess the stock market dynamics. METHODOLOGY/PRINCIPAL FINDINGS: The S&P500 dynamics during 4/1999-4/2010 is investigated in terms of the index cohesive force (ICF--the balance between the stock correlations and the partial correlations after subtraction of the index contribution, and the Eigenvalue entropy of the stock correlation matrices. We found a rapid market transition at the end of 2001 from a flexible state of low ICF into a stiff (nonflexible state of high ICF that is prone to market systemic collapses. The stiff state is also marked by strong effect of the market index on the stock-stock correlations as well as bursts of high stock correlations reminiscence of epileptic brain activity. CONCLUSIONS/SIGNIFICANCE: The market dynamical states, stability and transition between economic states was studies using new quantitative measures. Doing so shed new light on the origin and nature of the current crisis. The new approach is likely to be applicable to other classes of complex systems from gene networks to the human brain.

  10. Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity.

    Directory of Open Access Journals (Sweden)

    Himadri Mukhopadhyay

    Full Text Available Receptor phosphorylation is thought to be tightly regulated because phosphorylated receptors initiate signaling cascades leading to cellular activation. The T cell antigen receptor (TCR on the surface of T cells is phosphorylated by the kinase Lck and dephosphorylated by the phosphatase CD45 on multiple immunoreceptor tyrosine-based activation motifs (ITAMs. Intriguingly, Lck sequentially phosphorylates ITAMs and ZAP-70, a cytosolic kinase, binds to phosphorylated ITAMs with differential affinities. The purpose of multiple ITAMs, their sequential phosphorylation, and the differential ZAP-70 affinities are unknown. Here, we use a systems model to show that this signaling architecture produces emergent ultrasensitivity resulting in switch-like responses at the scale of individual TCRs. Importantly, this switch-like response is an emergent property, so that removal of multiple ITAMs, sequential phosphorylation, or differential affinities abolishes the switch. We propose that highly regulated TCR phosphorylation is achieved by an emergent switch-like response and use the systems model to design novel chimeric antigen receptors for therapy.

  11. Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane.

    Science.gov (United States)

    Lee, Hsiao-Lin; Chiang, I-Chen; Liang, Suh-Yuen; Lee, Der-Yen; Chang, Geen-Dong; Wang, Kwan-Yu; Lin, Shu-Yu; Shih, Yu-Ling

    2016-05-01

    The Min system of Escherichia coli mediates placement of the division septum at the midcell. It oscillates from pole to pole to establish a concentration gradient of the division inhibition that is high at the poles but low at the midcell; the cell middle thereby becomes the most favorable site for division. Although Min oscillation is well studied from molecular and biophysical perspectives, it is still an enigma as to whether such a continuous, energy-consuming, and organized movement of the Min proteins would affect cellular processes other than the division site selection. To tackle this question, we compared the inner membrane proteome of the wild-type and Δmin strains using a quantitative approach. Forty proteins that showed differential abundance on the inner membrane of the mutant cells were identified and defined as proteins of interest (POIs). More than half of the POIs were peripheral membrane proteins, suggesting that the Min system affects mainly reversible protein association with the inner membrane. In addition, 6 out of 10 selected POIs directly interacted with at least one of the Min proteins, confirming the correlation between POIs and the Min system.Further analysis revealed a functional relationship between metabolism and the Min system. Metabolic enzymes accounted for 45% of the POIs, and there was a change of metabolites in the related reactions. We hypothesize that the Min system could alter the membrane location of proteins to modulate their enzymatic activity. Thus, the metabolic modulation in the Δmin mutant is likely an adaptive phenotype in cells of abnormal size and chromosome number due to an imbalanced abundance of proteins on the inner membrane. Taken together, the current work reports novel interactions of the Min system and reveals a global physiological impact of the Min system in addition to the division site placement. PMID:26889046

  12. Comparison of three neurotropic viruses reveals differences in viral dissemination to the central nervous system.

    Science.gov (United States)

    Luethy, Lauren N; Erickson, Andrea K; Jesudhasan, Palmy R; Ikizler, Mine; Dermody, Terence S; Pfeiffer, Julie K

    2016-01-01

    Neurotropic viruses initiate infection in peripheral tissues prior to entry into the central nervous system (CNS). However, mechanisms of dissemination are not completely understood. We used genetically marked viruses to compare dissemination of poliovirus, yellow fever virus 17D (YFV-17D), and reovirus type 3 Dearing in mice from a hind limb intramuscular inoculation site to the sciatic nerve, spinal cord, and brain. While YFV-17D likely entered the CNS via blood, poliovirus and reovirus likely entered the CNS by transport through the sciatic nerve to the spinal cord. We found that dissemination was inefficient in adult immune-competent mice for all three viruses, particularly reovirus. Dissemination of all viruses was more efficient in immune-deficient mice. Although poliovirus and reovirus both accessed the CNS by transit through the sciatic nerve, stimulation of neuronal transport by muscle damage enhanced dissemination only of poliovirus. Our results suggest that these viruses access the CNS using different pathways. PMID:26479325

  13. An integrative systems genetics approach reveals potential causal genes and pathways related to obesity

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Zhernakova, Daria V.; Westra, Harm-Jan; Cirera Salicio, Susanna; Fredholm, Merete; Franke, Lude; Kadarmideen, Haja

    2015-01-01

    BACKGROUND: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the...... porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. METHODS: Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential...... expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected...

  14. Exciton interference revealed by energy dependent exciton transfer rate for ring-structured molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Yun-An, E-mail: yunan@gznc.edu.cn [Guizhou Provincial Key Laboratory of Computational Nanomaterial Science, Guizhou Education University, Guiyang, Guizhou 550018 (China)

    2016-01-14

    The quantum interference is an intrinsic phenomenon in quantum physics for photon and massive quantum particles. In principle, the quantum interference may also occur with quasi-particles, such as the exciton. In this study, we show how the exciton quantum interference can be significant in aggregates through theoretical simulations with hierarchical equations of motion. The systems under investigation are generalized donor-bridge-acceptor model aggregates with the donor consisting of six homogeneous sites assuming the nearest neighbor coupling. For the models with single-path bridge, the exciton transfer time only shows a weak excitation energy dependence. But models with double-path bridge have a new short transfer time scale and the excitation energy dependence of the exciton transfer time assumes clear peak structure which is detectable with today’s nonlinear spectroscopy. This abnormality is attributed to the exciton quantum interference and the condition for a clear observation in experiment is also explored.

  15. Topological cluster analysis reveals the systemic organization of the Caenorhabditis elegans connectome.

    Directory of Open Access Journals (Sweden)

    Yunkyu Sohn

    2011-05-01

    Full Text Available The modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture. Here we use the modularity-based community detection method for directed, weighted networks to examine hierarchically organized modules in the complete wiring diagram (connectome of Caenorhabditis elegans (C. elegans and to investigate their topological properties. Incorporating bilateral symmetry of the network as an important cue for proper cluster assignment, we identified anatomical clusters in the C. elegans connectome, including a body-spanning cluster, which correspond to experimentally identified functional circuits. Moreover, the hierarchical organization of the five clusters explains the systemic cooperation (e.g., mechanosensation, chemosensation, and navigation that occurs among the structurally segregated biological circuits to produce higher-order complex behaviors.

  16. Functional and structural analysis of yeast trx system reveals structural elements of substrate specificity

    International Nuclear Information System (INIS)

    Thioredoxin reductases (Trr) are members of the nucleotide pyridine disulfide oxide reductase family, which includes glutathione reductase (Gr), alkyl hydroperoxide reductase F (AhpF) and lipoamide dehydrogenase (Lpd). Constituents of this family are homodimeric flavoproteins containing one redoxactive disulfide and one tightly bound flavin adenine dinucleotide (FAD) per subunit. Trr catalyzes the disulfide reduction of oxidized Thioredoxin (Trx) using nicotinamide adenine dinucleotide phosphate (NADPH) via a FAD molecule and a redox-active cysteine motif. In this context, FAD transfers the reducing equivalents from NADPH molecule to the reactive cysteines and then to the Trx. Trx, Trr and NADPH comprise the Trx system. Trx are low molecular weight proteins (∼12 KDa) which are involved in several thiol-dependent cellular reactions such as synthesis of deoxyribonucleotides, sulphur metabolism, regulation of the gene expression and oxidative stress defenses. Remarkably, Trr - Trx interactions presents high species and organelle specificities. (author)

  17. Exciton interference revealed by energy dependent exciton transfer rate for ring-structured molecular systems

    International Nuclear Information System (INIS)

    The quantum interference is an intrinsic phenomenon in quantum physics for photon and massive quantum particles. In principle, the quantum interference may also occur with quasi-particles, such as the exciton. In this study, we show how the exciton quantum interference can be significant in aggregates through theoretical simulations with hierarchical equations of motion. The systems under investigation are generalized donor-bridge-acceptor model aggregates with the donor consisting of six homogeneous sites assuming the nearest neighbor coupling. For the models with single-path bridge, the exciton transfer time only shows a weak excitation energy dependence. But models with double-path bridge have a new short transfer time scale and the excitation energy dependence of the exciton transfer time assumes clear peak structure which is detectable with today’s nonlinear spectroscopy. This abnormality is attributed to the exciton quantum interference and the condition for a clear observation in experiment is also explored

  18. Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

    Directory of Open Access Journals (Sweden)

    Gomez-Alvarez Vicente

    2012-06-01

    Full Text Available Abstract Background Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top and invert (bottom sections of a corroded wastewater pipe. Results Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP and bottom pipe (BP communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems. Conclusions The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.

  19. A magma-hydrothermal system beneath Hakone volcano, central Japan, revealed by highly resolved velocity structures

    Science.gov (United States)

    Yukutake, Yohei; Honda, Ryou; Harada, Masatake; Arai, Ryuta; Matsubara, Makoto

    2015-05-01

    High-resolution images of subsurface structures are necessary to understand the transport processes of crustal fluids from deep magma sources and their relationship to earthquake swarms in active volcanic regions. Based on a seismic tomography approach, we have developed a new model for the magma-hydrothermal system beneath Hakone volcano, central Japan, where shallow earthquake swarms and crustal deformation associated with inflation of an open-crack source are often observed. By applying travel-time data for local earthquakes to a tomographic inversion, we obtained highly resolved seismic velocity structures that show a region of low P-wave velocity (Vp), low S-wave velocity (Vs), and high Vp/Vs ratios at depths of 10-20 km beneath the volcano, corresponding to the location of the open-crack source. We suggest that the high Vp/Vs ratios represent a deep magma chamber with a high concentration of melt and/or fluids. Deep low-frequency earthquakes, located just beneath this high Vp/Vs zone, may indicate that magmatic fluids are supplied from below. Above the high Vp/Vs zone, a region of low Vp, low Vs, and low Vp/Vs ratios exists at depths of 3-10 km, suggesting the presence of crack-filled water or CO2 supplied from the inferred deep magma chamber. Many earthquake swarms occur in this low Vp/Vs zone, indicating that crustal fluids play an important role in generating the swarms. Similar relationships between magma reservoirs, overlying hydrothermal systems, and swarm activity have been reported from other volcanic areas and thus may be a ubiquitous feature beneath active volcanoes.

  20. Complex Regulation Pattern of IRF3 Activation Revealed by a Novel Dimerization Reporter System.

    Science.gov (United States)

    Wang, Zining; Ji, Jingyun; Peng, Di; Ma, Feng; Cheng, Genhong; Qin, F Xiao-Feng

    2016-05-15

    Induction of type I IFN (IFN-I) is essential for host antiviral immune responses. However, IFN-I also plays divergent roles in antibacterial immunity, persistent viral infections, autoimmune diseases, and tumorigenesis. IFN regulatory factor 3 (IRF3) is the master transcription factor that controls IFN-I production via phosphorylation-dependent dimerization in most cell types in response to viral infections and various innate stimuli by pathogen-associated molecular patterns (PAMPs). To monitor the dynamic process of IRF3 activation, we developed a novel IRF3 dimerization reporter based on bimolecular luminescence complementation (BiLC) techniques, termed the IRF3-BiLC reporter. Robust induction of luciferase activity of the IRF3-BiLC reporter was observed upon viral infection and PAMP stimulation with a broad dynamic range. Knockout of TANK-binding kinase 1, the critical upstream kinase of IRF3, as well as the mutation of serine 386, the essential phosphorylation site of IRF3, completely abolished the luciferase activity of IRF3-BiLC reporter, confirming the authenticity of IRF3 activation. Taken together, these results demonstrated that the IRF3-BiLC reporter is a highly specific, reliable, and sensitive system to measure IRF3 activity. Using this reporter system, we further observed that the temporal pattern and magnitude of IRF3 activation induced by various PAMPs are highly complex with distinct cell type-specific characteristics, and IRF3 dimerization is a direct regulatory node for IFN-α/β receptor-mediated feed-forward regulation and crosstalk with other pathways. Therefore, the IRF3-BiLC reporter has multiple potential applications, including mechanistic studies as well as the identification of novel compounds that can modulate IRF3 activation. PMID:27045107

  1. Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato.

    Science.gov (United States)

    van Muijen, Dennis; Anithakumari, A M; Maliepaard, Chris; Visser, Richard G F; van der Linden, C Gerard

    2016-09-01

    In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co-expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid- and environmental stress-inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection. PMID:27353051

  2. What can nuclear magnetic moments reveal about the microscopic nature of tunnelling systems in glasses?

    International Nuclear Information System (INIS)

    More than thirty years ago anomalies in glasses at low temperatures were successfully explained by introducing atomic tunnelling systems (TS), described by the phenomenological standard tunnelling model. However, the universal behaviour of glasses prevented the experimental investigation of the microscopic nature of these TSs. Recently, unexpected magnetic field effects of the dielectric constant and of the two pulse polarisation echo amplitude, observed in non-magnetic glasses, turned out to be a proper experimental tool to investigate the microscopics of TSs. The echo experiments, done on glycerol and deuterated glycerol, prove that the interaction of nuclear quadrupole moments with local electric field gradients as well as interacting nuclear magnetic dipoles cause the observed magnetic field effects. Interestingly, the magnitude of the echo amplitude variations in magnetic fields is governed by the motion of the TSs. We present the measured effects together with numerical calculations based on the mentioned interactions which enable us to derive details of the TS's microscopic motions in glycerol. These calculations were done without considering dissipative processes acting at finite temperatures and, therefore, are strictly valid only at T=0. An analysis of the measured echo decay at different temperatures suggests that this quantum behaviour is observed, on the time scale of our measurements, at temperatures below 5mK.

  3. Multivariate and multiscale dependence in the global climate system revealed through complex networks

    Energy Technology Data Exchange (ETDEWEB)

    Steinhaeuser, Karsten [Oak Ridge National Laboratory, Geographic Information Science and Technology Group, Computational Sciences and Engineering Division, Oak Ridge, TN (United States); University of Notre Dame, Department of Computer Science and Engineering and Interdisciplinary Center for Network Science and Applications, Notre Dame, IN (United States); Ganguly, Auroop R. [Oak Ridge National Laboratory, Geographic Information Science and Technology Group, Computational Sciences and Engineering Division, Oak Ridge, TN (United States); University of Tennessee at Knoxville, Department of Civil and Environmental Engineering, Knoxville, TN (United States); Chawla, Nitesh V. [University of Notre Dame, Department of Computer Science and Engineering and Interdisciplinary Center for Network Science and Applications, Notre Dame, IN (United States)

    2012-08-15

    A systematic characterization of multivariate dependence at multiple spatio-temporal scales is critical to understanding climate system dynamics and improving predictive ability from models and data. However, dependence structures in climate are complex due to nonlinear dynamical generating processes, long-range spatial and long-memory temporal relationships, as well as low-frequency variability. Here we utilize complex networks to explore dependence in climate data. Specifically, networks constructed from reanalysis-based atmospheric variables over oceans and partitioned with community detection methods demonstrate the potential to capture regional and global dependence structures within and among climate variables. Proximity-based dependence as well as long-range spatial relationships are examined along with their evolution over time, yielding new insights on ocean meteorology. The tools are implicitly validated by confirming conceptual understanding about aggregate correlations and teleconnections. Our results also suggest a close similarity of observed dependence patterns in relative humidity and horizontal wind speed over oceans. In addition, updraft velocity, which relates to convective activity over the oceans, exhibits short spatiotemporal decorrelation scales but long-range dependence over time. The multivariate and multi-scale dependence patterns broadly persist over multiple time windows. Our findings motivate further investigations of dependence structures among observations, reanalysis and model-simulated data to enhance process understanding, assess model reliability and improve regional climate predictions. (orig.)

  4. The components of the Daphnia pulex immune system as revealed by complete genome sequencing

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L

    2009-04-01

    Full Text Available Abstract Background Branchiopod crustaceans in the genus Daphnia are key model organisms for investigating interactions between genes and the environment. One major theme of research on Daphnia species has been the evolution of resistance to pathogens and parasites, but lack of knowledge of the Daphnia immune system has limited the study of immune responses. Here we provide a survey of the immune-related genome of D. pulex, derived from the newly completed genome sequence. Genes likely to be involved in innate immune responses were identified by comparison to homologues from other arthropods. For each candidate, the gene model was refined, and we conducted an analysis of sequence divergence from homologues from other taxa. Results and conclusion We found that some immune pathways, in particular the TOLL pathway, are fairly well conserved between insects and Daphnia, while other elements, in particular antimicrobial peptides, could not be recovered from the genome sequence. We also found considerable variation in gene family copy number when comparing Daphnia to insects and present phylogenetic analyses to shed light on the evolution of a range of conserved immune gene families.

  5. Perilipin Expression Reveals Adipogenic Potential of hADSCs inside Superporous Polymeric Cellular Delivery Systems

    Directory of Open Access Journals (Sweden)

    Sorina Dinescu

    2014-01-01

    Full Text Available Recent progress in tissue engineering and regenerative medicine envisages the use of cell-scaffold bioconstructs to best mimic the natural in vivo microenvironment. Our aim was not only to develop novel 3D porous scaffolds for regenerative applications by the association of gelatin (G, alginate (A, and polyacrylamide (PAA major assets but also to evaluate their in vitro potential to support human adipose-derived stem cells (hADSCs adipogenesis. G-A-PAA biomatrix investigated in this work is an interesting substrate combining the advantages of the three individual constituents, namely, biodegradability of G, hydrophilicity of A and PAA, superior elasticity at compression with respect to the G-A and PAA controls, and the capacity to generate porous scaffolds. hADSCs inside these novel interpenetrating polymer networks (IPNs were able to populate the entire scaffold structure and to display their characteristic spindle-like shape as a consequence of a good interaction with G component of the matrices. Additionally, hADSCs proved to display the capacity to differentiate towards mature adipocytes, to accumulate lipids inside their cytoplasm, and to express perilipin late adipogenic marker inside novel IPNs described in this study. On long term, this newly designed biomatrix aims to represent a stem cell delivery system product dedicated for modern regenerative strategies.

  6. X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture.

    Science.gov (United States)

    Rogers, Eric D; Monaenkova, Daria; Mijar, Medhavinee; Nori, Apoorva; Goldman, Daniel I; Benfey, Philip N

    2016-07-01

    Root system architecture (RSA) impacts plant fitness and crop yield by facilitating efficient nutrient and water uptake from the soil. A better understanding of the effects of soil on RSA could improve crop productivity by matching roots to their soil environment. We used x-ray computed tomography to perform a detailed three-dimensional quantification of changes in rice (Oryza sativa) RSA in response to the physical properties of a granular substrate. We characterized the RSA of eight rice cultivars in five different growth substrates and determined that RSA is the result of interactions between genotype and growth environment. We identified cultivar-specific changes in RSA in response to changing growth substrate texture. The cultivar Azucena exhibited low RSA plasticity in all growth substrates, whereas cultivar Bala root depth was a function of soil hardness. Our imaging techniques provide a framework to study RSA in different growth environments, the results of which can be used to improve root traits with agronomic potential. PMID:27208237

  7. Talc-dominated seafloor deposits reveal a new class of hydrothermal system

    Science.gov (United States)

    Hodgkinson, Matthew R. S.; Webber, Alexander P.; Roberts, Stephen; Mills, Rachel A.; Connelly, Douglas P.; Murton, Bramley J.

    2015-12-01

    The Von Damm Vent Field (VDVF) is located on the flanks of the Mid-Cayman Spreading Centre, 13 km west of the axial rift, within a gabbro and peridotite basement. Unlike any other active vent field, hydrothermal precipitates at the VDVF comprise 85-90% by volume of the magnesium silicate mineral, talc. Hydrothermal fluids vent from a 3-m high, 1-m diameter chimney and other orifices at up to 215 °C with low metal concentrations, intermediate pH (5.8) and high concentrations (667 mmol kg-1) of chloride relative to seawater. Here we show that the VDVF vent fluid is generated by interaction of seawater with a mafic and ultramafic basement which precipitates talc on mixing with seawater. The heat flux at the VDVF is measured at 487+/-101 MW, comparable to the most powerful magma-driven hydrothermal systems known, and may represent a significant mode of off-axis oceanic crustal cooling not previously recognized or accounted for in global models.

  8. Can global navigation satellite system signals reveal the ecological attributes of forests?

    Science.gov (United States)

    Liu, Jingbin; Hyyppä, Juha; Yu, Xiaowei; Jaakkola, Anttoni; Liang, Xinlian; Kaartinen, Harri; Kukko, Antero; Zhu, Lingli; Wang, Yunsheng; Hyyppä, Hannu

    2016-08-01

    Forests have important impacts on the global carbon cycle and climate, and they are also related to a wide range of industrial sectors. Currently, one of the biggest challenges in forestry research is effectively and accurately measuring and monitoring forest variables, as the exploitation potential of forest inventory products largely depends on the accuracy of estimates and on the cost of data collection. A low-cost crowdsourcing solution is needed for forest inventory to collect forest variables. Here, we propose global navigation satellite system (GNSS) signals as a novel type of observables for predicting forest attributes and show the feasibility of utilizing GNSS signals for estimating important attributes of forest plots, including mean tree height, mean diameter at breast height, basal area, stem volume and tree biomass. The prediction accuracies of the proposed technique were better in boreal forest conditions than those of the conventional techniques of 2D remote sensing. More importantly, this technique provides a novel, cost-effective way of collecting large-scale forest measurements in the crowdsourcing context. This technique can be applied by, for example, harvesters or persons hiking or working in forests because GNSS devices are widely used, and the field operation of this technique is simple and does not require professional forestry skills.

  9. Competing mechanisms for perfluoroalkyl acid accumulation in plants revealed using an Arabidopsis model system.

    Science.gov (United States)

    Müller, Claudia E; LeFevre, Gregory H; Timofte, Anca E; Hussain, Fatima A; Sattely, Elizabeth S; Luthy, Richard G

    2016-05-01

    Perfluoroalkyl acids (PFAAs) bioaccumulate in plants, presenting a human exposure route if present in irrigation water. Curiously, accumulation of PFAAs in plant tissues is greatest for both the short-chain and long-chain PFAAs, generating a U-shaped relationship with chain length. In the present study, the authors decouple competing mechanisms of PFAA accumulation using a hydroponic model plant system (Arabidopsis thaliana) exposed to a suite of 10 PFAAs to determine uptake, depuration, and translocation kinetics. Rapid saturation of root concentrations occurred for all PFAAs except perfluorobutanoate, the least-sorptive (shortest-chain) PFAA. Shoot concentrations increased continuously, indicating that PFAAs are efficiently transported and accumulate in shoots. Tissue concentrations of PFAAs during depuration rapidly declined in roots but remained constant in shoots, demonstrating irreversibility of the translocation process. Root and shoot concentration factors followed the U-shaped trend with perfluoroalkyl chain length; however, when normalized to dead-tissue sorption, this relationship linearized. The authors therefore introduce a novel term, the "sorption normalized concentration factor," to describe PFAA accumulation in plants; because of their hydrophobicity, sorption is the determining factor for long-chain PFAAs, whereas the shortest-chain PFAAs are most effectively transported in the plant. The present study provides a mechanistic explanation for previously unexplained PFAA accumulation trends in plants and suggests that shorter-chained PFAAs may bioaccumulate more readily in edible portions. Environ Toxicol Chem 2016;35:1138-1147. © 2015 SETAC. PMID:26383989

  10. Systems Biology Strategy Reveals PKC-delta is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma

    Directory of Open Access Journals (Sweden)

    Kentaro eHayashi

    2015-01-01

    Full Text Available Cancer cells are highly variable and resistant to therapeutic intervention. Recently, the use of the tumor necrosis factor related apoptosis-inducing ligand (TRAIL induced treatment is gaining momentum, due to TRAIL’s ability to specifically target cancers with limited effect on normal cells. However, several malignant cancer types still remain non-sensitive to TRAIL. Previously, we developed a dynamic computational model, based on perturbation-response approach, and predicted protein kinase C (PKC as the most effective target, with over 95% capacity to kill human fibrosarcoma (HT1080 in TRAIL stimulation (Piras, V. et al. 2011, Scientific Reports. Here, to validate the model prediction, which has significant implications for cancer treatment, we conducted experiments on two TRAIL-resistant cancer cell lines (HT1080 and HT29. Using PKC inhibitor Bisindolylmaleimide I, we first demonstrate, as predicted by our previous model, cell viability is significantly impaired with over 95% death of both cancer types. Next, to identify crucial PKC isoform from 10 known members, we analyzed their mRNA expressions in HT1080 cells and shortlisted 4 isoforms for siRNA knock-down (KD experiments. From these KDs, PKC-delta produced the most cancer cell death in conjunction with TRAIL. Overall, systems biology approach, combining model prediction with experimental validation, holds promise for TRAIL-based cancer therapy.

  11. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

    Science.gov (United States)

    Fahlgren, Noah; Feldman, Maximilian; Gehan, Malia A; Wilson, Melinda S; Shyu, Christine; Bryant, Douglas W; Hill, Steven T; McEntee, Colton J; Warnasooriya, Sankalpi N; Kumar, Indrajit; Ficor, Tracy; Turnipseed, Stephanie; Gilbert, Kerrigan B; Brutnell, Thomas P; Carrington, James C; Mockler, Todd C; Baxter, Ivan

    2015-10-01

    Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available. PMID:26099924

  12. Physiological effects of cigarette smoking in the limbic system revealed by 3 tesla magnetic resonance spectroscopy.

    Science.gov (United States)

    Mennecke, Angelika; Gossler, Andrea; Hammen, Thilo; Dörfler, Arnd; Stadlbauer, Andreas; Rösch, Julie; Kornhuber, Johannes; Bleich, Stefan; Dölken, Marc; Thürauf, Norbert

    2014-10-01

    Several studies and recent models of effects of nicotine, the main addictive and psychoactive component in tobacco, point to action of the drug on the limbic system during maintenance of addiction, either direct or indirect via projections from the ventral tegmental area. The objective of this study was to demonstrate physiological effects of cigarette smoking on the hippocampus and the grey matter of the dorsal anterior cingulate cortex in the human brain with regard to addiction and withdrawal. This aim was achieved by group comparisons of results of magnetic resonance spectroscopy between non-smokers, smokers and smokers during withdrawal. 12 smokers and 12 non-smokers were measured with single voxel proton magnetic resonance spectroscopy for total N-acetyl aspartate, glutamate and glutamine, choline-containing compounds, myo-inositol and total creatine in the right and the left hippocampus and in the right and the left dorsal anterior cingulate cortex. Smokers were examined twice, first during regular cigarette smoking and second on the third day of nicotine withdrawal. The ratios to total creatine were used for better reliability. In our study, Glx/tCr was significantly increased and tCho/tCr was significantly decreased in the left cingulate cortex in smokers compared to non-smokers (p = 0.01, both). Six out of seven smokers showed normalization of the Glx/tCr in the left cingulate cortex during withdrawal. Although these results are preliminary due to the small sample size, our results confirm the assumption that cigarette smoking interferes directly or indirectly with the glutamate circuit in the dorsal anterior cingulate cortex. PMID:24643301

  13. Revealing of complex system of starch synthetic metabolism in higher plants using rice mutants

    International Nuclear Information System (INIS)

    In this presentation, the concept and perspective of molecular mutation breeding of starch biosynthesis are discussed. Amylopectin, a major component of starch, has a distinct highly-ordered structure referred to as 'tamdem-cluster structure'. The starch synthesis system has developed during the process of evolution of plants, and key enzymes involved in the construction of amylopectin tamdem-cluster structure have differentiated into multiple isozymes with specific functions. Detailed analyses of changes in the structure of amylopectin and the physicochemical properties of starch granules in rice endosperm induced by lesion of each isoform of starch branching enzyme, starch synthase, starch debranching enzymes and others have established that the individual mutants exhibit distinct characteristics in terms of the starch structure and properties. These patterns of changes reflected by the specific functions of enzymes in starch biosynthesis enable us to expect to what extent and how the structure and properties of starch can be engineered. In fact, numerous rice mutant lines could be used in the industrial purpose in the future by the production of novel starches in endosperm. Transcriptome analysis established that changes in the transcript levels of starch synthesizing enzyme genes in rice endosperm are largely divided into two patterns. One group of genes are highly expressed in the very early stage of the endosperm development prior to the onset of the rapid starch production whereas the other group genes are greatly expressed in accord with the start of a great amount of starch accumulation in the endosperm. These results strongly suggest that the initiation process of starch biosynthesis and the accumulationen process of increases in number of starch molecules and starch granule are regulated by different mechanisms with varied sets of isozymes. Our recent studies showed that plastidial phosphorylase plays a crucial role in the initial stage of starch

  14. Revealing halogen bonding interactions with anomeric systems: an ab initio quantum chemical studies.

    Science.gov (United States)

    Lo, Rabindranath; Ganguly, Bishwajit

    2015-02-01

    A computational study has been performed using MP2 and CCSD(T) methods on a series of O⋯X (X=Br, Cl and I) halogen bonds to evaluate the strength and characteristic of such highly directional noncovalent interactions. The study has been carried out on a series of dimeric complexes formed between interhalogen compounds (such as BrF, BrCl and BrI) and oxygen containing electron donor molecule. The existence and consequences of the anomeric effect of the electron donor molecule has also been investigated through an exploration of halogen bonding interactions in this halogen bonded complexes. The ab initio quantum chemical calculations have been employed to study both the nature and directionality of the halogen molecules toward the sp(3) oxygen atom in anomeric systems. The presence of anomeric nO→σ*CN interaction involves a dominant role for the availability of the axial and equatorial lone pairs of donor O atom to participate with interhalogen compounds in the halogen-bonded complexes. The energy difference between the axial and equatorial conformers with interhalogen compounds reaches up to 4.60 kJ/mol, which however depends upon the interacting halogen atoms and its attaching atoms. The energy decomposition analysis further suggests that the total halogen bond interaction energies are mainly contributed by the attractive electrostatic and dispersion components. The role of substituents attached with the halogen atoms has also been evaluated in this study. With the increase of halogen atom size and the positive nature of σ-hole, the halogen atom interacted more with the electron donor atom and the electrostatic contribution to the total interaction energy enhances appreciably. Further, noncovalent interaction (NCI) studies have been carried out to locate the noncovalent halogen bonding interactions in real space. PMID:25522359

  15. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.

    Science.gov (United States)

    Chaiboonchoe, Amphun; Ghamsari, Lila; Dohai, Bushra; Ng, Patrick; Khraiwesh, Basel; Jaiswal, Ashish; Jijakli, Kenan; Koussa, Joseph; Nelson, David R; Cai, Hong; Yang, Xinping; Chang, Roger L; Papin, Jason; Yu, Haiyuan; Balaji, Santhanam; Salehi-Ashtiani, Kourosh

    2016-07-19

    Metabolic networks, which are mathematical representations of organismal metabolism, are reconstructed to provide computational platforms to guide metabolic engineering experiments and explore fundamental questions on metabolism. Systems level analyses, such as interrogation of phylogenetic relationships within the network, can provide further guidance on the modification of metabolic circuitries. Chlamydomonas reinhardtii, a biofuel relevant green alga that has retained key genes with plant, animal, and protist affinities, serves as an ideal model organism to investigate the interplay between gene function and phylogenetic affinities at multiple organizational levels. Here, using detailed topological and functional analyses, coupled with transcriptomics studies on a metabolic network that we have reconstructed for C. reinhardtii, we show that network connectivity has a significant concordance with the co-conservation of genes; however, a distinction between topological and functional relationships is observable within the network. Dynamic and static modes of co-conservation were defined and observed in a subset of gene-pairs across the network topologically. In contrast, genes with predicted synthetic interactions, or genes involved in coupled reactions, show significant enrichment for both shorter and longer phylogenetic distances. Based on our results, we propose that the metabolic network of C. reinhardtii is assembled with an architecture to minimize phylogenetic profile distances topologically, while it includes an expansion of such distances for functionally interacting genes. This arrangement may increase the robustness of C. reinhardtii's network in dealing with varied environmental challenges that the species may face. The defined evolutionary constraints within the network, which identify important pairings of genes in metabolism, may offer guidance on synthetic biology approaches to optimize the production of desirable metabolites. PMID:27357594

  16. Revealing the Complex System of Starch Biosynthesis in Higher Plants Using Rice Mutants and Transformants

    International Nuclear Information System (INIS)

    Starch is the end product of photosynthesis and a primary material for food and industrial uses. Starch has a variety of distinct physico-chemical properties such as gelatinization and pasting properties, and these features are strongly related to the molecular structure of amylopectin and the formation of starch granules, whose morphology depends on the plant species. The multi-dimensional, unique structure of starch is achieved by concerted reactions catalyzed by multiple isozymes of a set of enzymes that include starch synthase, starch branching enzyme and starch debranching enzyme. The action mechanism of each of these isozymes is currently being studied. This paper summarizes recent results of biochemical and genetic analyses of starch biosynthesis in rice endosperm obtained from various mutants and transformants, and dis- cusses ideas about the regulation of starch biosynthesis in plants. Starch is glucose polymer with two α-glucosidic linkages, linearly linked α-1,4-glucosidic chains are branched by α-1,4-glucosidic linkages, and it comprises linear or rarely branched amylose and highly branched amylopectin. Amylopectin has a distinct highly ordered structure called a 'tandem-cluster structure', in which most of side chains are arranged in parallel and neighboring chains form double helices when linear portions of facing chains reach the length equivalent to degree of polymerization (DP) ≥ 10. The formation of double helices in the amylopectin cluster dramatically induces its hydrophobicity and crystallinity. These specific features of amylopectin fine structure are enabled by the localization of branch positions within the restricted region of the cluster. The starch synthesis system has developed during the evolution of plants and key enzymes involved in the construction of amylopectin tandem-cluster structure have differentiated into multiple isozymes with distinct functions, whereas in glycogen synthesizing organisms, such as bacteria and animals

  17. A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

    Science.gov (United States)

    Antoneli, Fernando; Ferreira, Renata C; Briones, Marcelo R S

    2016-06-01

    Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs. PMID:27036626

  18. Identification of Bacterial Community Composition in Freshwater Aquaculture System Farming of Litopenaeus vannamei Reveals Distinct Temperature-Driven Patterns

    Directory of Open Access Journals (Sweden)

    Yuyi Tang

    2014-08-01

    Full Text Available Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL. Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT and at lower (WLT temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

  19. Unexpected Regularity in Swimming Behavior of Clausocalanus furcatus Revealed by a Telecentric 3D Computer Vision System.

    Directory of Open Access Journals (Sweden)

    Giuseppe Bianco

    Full Text Available Planktonic copepods display a large repertoire of motion behaviors in a three-dimensional environment. Two-dimensional video observations demonstrated that the small copepod Clausocalanus furcatus, one the most widely distributed calanoids at low to medium latitudes, presented a unique swimming behavior that was continuous and fast and followed notably convoluted trajectories. Furthermore, previous observations indicated that the motion of C. furcatus resembled a random process. We characterized the swimming behavior of this species in three-dimensional space using a video system equipped with telecentric lenses, which allow tracking of zooplankton without the distortion errors inherent in common lenses. Our observations revealed unexpected regularities in the behavior of C. furcatus that appear primarily in the horizontal plane and could not have been identified in previous observations based on lateral views. Our results indicate that the swimming behavior of C. furcatus is based on a limited repertoire of basic kinematic modules but exhibits greater plasticity than previously thought.

  20. Systems-Pharmacology Dissection of Traditional Chinese Medicine Compound Saffron Formula Reveals Multi-scale Treatment Strategy for Cardiovascular Diseases.

    Science.gov (United States)

    Liu, Jianling; Mu, Jiexin; Zheng, Chunli; Chen, Xuetong; Guo, Zihu; Huang, Chao; Fu, Yingxue; Tian, Guihua; Shang, Hongcai; Wang, Yonghua

    2016-01-01

    Cardiovascular diseases (CVDs) have been regarding as "the world's first killer" of human beings in recent years owing to the striking morbidity and mortality, the involved molecular mechanisms are extremely complex and remain unclear. Traditional Chinese medicine (TCM) adheres to the aim of combating complex diseases from an integrative and holistic point of view, which has shown effectiveness in CVDs therapy. However, system-level understanding of such a mechanism of multi-scale treatment strategy for CVDs is still difficult. Here, we developed a system pharmacology approach with the purpose of revealing the underlying molecular mechanisms exemplified by a famous compound saffron formula (CSF) in treating CVDs. First, by systems ADME analysis combined with drug targeting process, 103 potential active components and their corresponding 219 direct targets were retrieved and some key interactions were further experimentally validated. Based on this, the network relationships among active components, targets and diseases were further built to uncover the pharmacological actions of the drug. Finally, a "CVDs pathway" consisted of several regulatory modules was incorporated to dissect the therapeutic effects of CSF in different pathological features-relevant biological processes. All this demonstrates CSF has multi-scale curative activity in regulating CVD-related biological processes, which provides a new potential way for modern medicine in the treatment of complex diseases. PMID:26813334

  1. COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians.

    Directory of Open Access Journals (Sweden)

    Martis W Cowles

    2014-10-01

    Full Text Available Members of the COE family of transcription factors are required for central nervous system (CNS development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals.

  2. COE loss-of-function analysis reveals a genetic program underlying maintenance and regeneration of the nervous system in planarians.

    Science.gov (United States)

    Cowles, Martis W; Omuro, Kerilyn C; Stanley, Brianna N; Quintanilla, Carlo G; Zayas, Ricardo M

    2014-10-01

    Members of the COE family of transcription factors are required for central nervous system (CNS) development. However, the function of COE in the post-embryonic CNS remains largely unknown. An excellent model for investigating gene function in the adult CNS is the freshwater planarian. This animal is capable of regenerating neurons from an adult pluripotent stem cell population and regaining normal function. We previously showed that planarian coe is expressed in differentiating and mature neurons and that its function is required for proper CNS regeneration. Here, we show that coe is essential to maintain nervous system architecture and patterning in intact (uninjured) planarians. We took advantage of the robust phenotype in intact animals to investigate the genetic programs coe regulates in the CNS. We compared the transcriptional profiles of control and coe RNAi planarians using RNA sequencing and identified approximately 900 differentially expressed genes in coe knockdown animals, including 397 downregulated genes that were enriched for nervous system functional annotations. Next, we validated a subset of the downregulated transcripts by analyzing their expression in coe-deficient planarians and testing if the mRNAs could be detected in coe+ cells. These experiments revealed novel candidate targets of coe in the CNS such as ion channel, neuropeptide, and neurotransmitter genes. Finally, to determine if loss of any of the validated transcripts underscores the coe knockdown phenotype, we knocked down their expression by RNAi and uncovered a set of coe-regulated genes implicated in CNS regeneration and patterning, including orthologs of sodium channel alpha-subunit and pou4. Our study broadens the knowledge of gene expression programs regulated by COE that are required for maintenance of neural subtypes and nervous system architecture in adult animals. PMID:25356635

  3. Developmental analysis reveals labial and subradular ganglia and the primary framework of the nervous system in nudibranch gastropods.

    Science.gov (United States)

    Page, L R

    1993-11-01

    Previous ultrastructural observations on late stage larvae of dorid nudibranchs (Gastropoda, Opisthobranchia) revealed two pairs of ganglia within the base of the foot that do not have obvious counterparts in existing descriptions of other gastropod larvae [Chia and Koss (1989). Cell Tiss. Res. 256:17-26.] One of these ganglionic pairs has been implicated in the initiation of settlement preceding metamorphosis [Arkett et al. (1989). Biol. Bull. 176:155-160.] By examining neurogenesis in sequential larval stages, I have found that the pattern of connectives and commissures associated with these enigmatic ganglia is comparable to patterns found in less consolidated adult nervous systems of chitons, monoplacophorans, and archaeogastropods. These comparative data suggest that the two pairs of ganglia in dorid nudibranch larvae are homologues of labial and subradular ganglia. The labial ganglia become incorporated into the cerebral ganglia at metamorphosis. In an attempt to integrate anatomical and developmental observations with behavioral and neurophysiological results, I suggest that receptor cells of the larval labial ganglia may become postmetamorphic primary mechanoreceptors of the oral tube, which have central cell bodies within the "cerebral" ganglia and which help coordinate feeding. Results of this study also address a larger evolutionary issue by questioning the traditional model of an ancestral molluscan nervous system that consists of four longitudinal nerve cords that arise from separate sites along a circumesophageal nerve ring. This pattern results from secondary connections in nudibranchs and possibly other molluscs. The primary condition of a single axon bundle emerging from each cerebral ganglion is more similar to the developing nervous system in polychaete annelids than what has been recognized previously. PMID:8283184

  4. High-frequency monitoring reveals nutrient sources and transport processes in an agriculture-dominated lowland water system

    Directory of Open Access Journals (Sweden)

    B. van der Grift

    2015-08-01

    Full Text Available Many agriculture-dominated lowland water systems worldwide suffer from eutrophication caused by high nutrient loads. Insight in the hydrochemical functioning of embanked polder catchments is highly relevant for improving the water quality in such areas. This paper introduces new insights in nutrient sources and transport processes in a low elevated polder in the Netherlands using high-frequency monitoring technology at the outlet, where the water is pumped into a higher situated lake, combined with a low-frequency water quality monitoring program at six locations within the drainage area. Seasonal trends and short scale temporal dynamics in concentrations indicated that the NO3 concentration at the pumping station originated from N-loss from agricultural lands. The NO3 loads appear as losses with drain water discharge after intensive rainfall events during the winter months due to preferential flow through the cracked clay soil. Transfer function-noise modelling of hourly NO3 concentrations reveals that a large part of the dynamics in NO3 concentrations during the winter months can be related to rainfall. The total phosphorus (TP concentration almost doubled during operation of the pumping station which points to resuspension of particulate P from channel bed sediments induced by changes in water flow due to pumping. Rainfall events that caused peaks in NO3 concentrations did not results in TP concentration peaks. The by rainfall induced and NO3 enriched quick interflow, may also be enriched in TP but this is then buffered in the water system due to sedimentation of particulate P. Increased TP concentrations associated with run-off events is only observed during a rainfall event at the end of a freeze–thaw cycle. All these observations suggest that the P retention potential of polder water systems is highly due to the artificial pumping regime that buffers high flows. As the TP concentration is affected by operation of the pumping station

  5. Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots.

    Science.gov (United States)

    Ma, Jianhui; Dong, Wen; Zhang, Daijing; Gao, Xiaolong; Jiang, Lina; Shao, Yun; Tong, Doudou; Li, Chunxi

    2016-01-01

    Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat. PMID:27602297

  6. Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems.

    Science.gov (United States)

    Hoberg, E P; Klassen, G J

    2002-01-01

    Parasites are integral components of marine ecosystems, a general observation accepted by parasitologists, but often considered of trifling significance to the broader community of zoologists. Parasites, however, represent elegant tools to explore the origins, distribution and maintenance of biodiversity. Among these diverse assemblages, host and geographic ranges described by various helminths are structured and historically constrained by genealogical and ecological associations that can be revealed and evaluated using phylogenetic methodologies within the context of frameworks and hypotheses for co-evolution and historical biogeography. Despite over 200 years of sporadic investigations of helminth systematics, knowledge of parasite faunal diversity in chondrichthyan and osteichthyan fishes, seabirds and marine mammals remains to be distilled into a coherent and comprehensive picture that can be assessed using phylogenetic approaches. Phylogenetic studies among complex host-parasite assemblages that encompass varying temporal and geographic scales are the critical context for elucidating biodiversity and faunal structure, and for identifying historical and contemporary determinants of ecological organization and biogeographic patterns across the marine biosphere. Insights from phylogenetic inference indicate (1) the great age of marine parasite faunas; (2) a significant role for colonization in diversification across a taxonomic continuum at deep and relatively recent temporal scales; and (3) a primary role for allopatric speciation. Integration of ecological and phylogenetic knowledge from the study of parasites is synergistic, contributing substantial insights into the history and maintenance of marine systems. PMID:12396213

  7. Systems biology modeling reveals a possible mechanism of the tumor cell death upon oncogene inactivation in EGFR addicted cancers.

    Directory of Open Access Journals (Sweden)

    Jian-Ping Zhou

    Full Text Available Despite many evidences supporting the concept of "oncogene addiction" and many hypotheses rationalizing it, there is still a lack of detailed understanding to the precise molecular mechanism underlying oncogene addiction. In this account, we developed a mathematic model of epidermal growth factor receptor (EGFR associated signaling network, which involves EGFR-driving proliferation/pro-survival signaling pathways Ras/extracellular-signal-regulated kinase (ERK and phosphoinositol-3 kinase (PI3K/AKT, and pro-apoptotic signaling pathway apoptosis signal-regulating kinase 1 (ASK1/p38. In the setting of sustained EGFR activation, the simulation results show a persistent high level of proliferation/pro-survival effectors phospho-ERK and phospho-AKT, and a basal level of pro-apoptotic effector phospho-p38. The potential of p38 activation (apoptotic potential due to the elevated level of reactive oxygen species (ROS is largely suppressed by the negative crosstalk between PI3K/AKT and ASK1/p38 pathways. Upon acute EGFR inactivation, the survival signals decay rapidly, followed by a fast increase of the apoptotic signal due to the release of apoptotic potential. Overall, our systems biology modeling together with experimental validations reveals that inhibition of survival signals and concomitant release of apoptotic potential jointly contribute to the tumor cell death following the inhibition of addicted oncogene in EGFR addicted cancers.

  8. Revealing the complex nature of the strong gravitationally lensed system H-ATLAS J090311.6+003906 using ALMA

    CERN Document Server

    Dye, S; Swinbank, A M; Vlahakis, C; Nightingale, J W; Dunne, L; Eales, S A; Smail, Ian; Oteo-Gomez, I; Hunter, T; Negrello, M; Dannerbauer, H; Ivison, R J; Gavazzi, R; Cooray, A; van der Werf, P

    2015-01-01

    We have modelled Atacama Large Millimeter/sub-millimeter Array (ALMA) long baseline imaging of the strong gravitational lens system H-ATLAS J090311.6+003906 (SDP.81). We have reconstructed the distribution of continuum emission in the z=3.042 source and we have determined its kinematic properties by reconstructing CO line emission. The continuum imaging reveals a highly non-uniform distribution of dust with clumps on scales of ~200pc. In contrast, the CO line emission shows a relatively smooth velocity field which resembles disk-like dynamics. Modelling the velocity field as a rotating disk indicates an inclination angle of (40 +/- 5) degrees, implying an intrinsic asymptotic rotation velocity of 320km/s and a dynamical mass of 3.5x10^{10} M_sol within 1.5kpc. We obtain similar estimates of the total molecular gas mass of 2.7x10^{10} M_sol and 1.4x10^{10} M_sol from the dust continuum emission and CO emission respectively. Our new reconstruction of the lensed HST near-infrared emission shows two objects that ...

  9. Comprehensive Mutational Analysis of Sucrose-Metabolizing Pathways in Streptococcus mutans Reveals Novel Roles for the Sucrose Phosphotransferase System Permease

    Science.gov (United States)

    Zeng, Lin

    2013-01-01

    Sucrose is perhaps the most efficient carbohydrate for the promotion of dental caries in humans, and the primary caries pathogen Streptococcus mutans encodes multiple enzymes involved in the metabolism of this disaccharide. Here, we engineered a series of mutants lacking individual or combinations of sucrolytic pathways to understand the control of sucrose catabolism and to determine whether as-yet-undisclosed pathways for sucrose utilization were present in S. mutans. Growth phenotypes indicated that gtfBCD (encoding glucan exopolysaccharide synthases), ftf (encoding the fructan exopolysaccharide synthase), and the scrAB pathway (sugar-phosphotransferase system [PTS] permease and sucrose-6-PO4 hydrolase) constitute the majority of the sucrose-catabolizing activity; however, mutations in any one of these genes alone did not affect planktonic growth on sucrose. The multiple-sugar metabolism pathway (msm) contributed minimally to growth on sucrose. Notably, a mutant lacking gtfBC, which cannot produce water-insoluble glucan, displayed improved planktonic growth on sucrose. Meanwhile, loss of scrA led to growth stimulation on fructooligosaccharides, due in large part to increased expression of the fruAB (fructanase) operon. Using the LevQRST four-component signal transduction system as a model for carbohydrate-dependent gene expression in strains lacking extracellular sucrases, a PlevD-cat (EIIALev) reporter was activated by pulsing with sucrose. Interestingly, ScrA was required for activation of levD expression by sucrose through components of the LevQRST complex, but not for activation by the cognate LevQRST sugars fructose or mannose. Sucrose-dependent catabolite repression was also evident in strains containing an intact sucrose PTS. Collectively, these results reveal a novel regulatory circuitry for the control of sucrose catabolism, with a central role for ScrA. PMID:23222725

  10. High-frequency monitoring reveals nutrient sources and transport processes in an agriculture-dominated lowland water system

    Science.gov (United States)

    van der Grift, Bas; Broers, Hans Peter; Berendrecht, Wilbert; Rozemeijer, Joachim; Osté, Leonard; Griffioen, Jasper

    2016-05-01

    Many agriculture-dominated lowland water systems worldwide suffer from eutrophication caused by high nutrient loads. Insight in the hydrochemical functioning of embanked polder catchments is highly relevant for improving the water quality in such areas or for reducing export loads to downstream water bodies. This paper introduces new insights in nutrient sources and transport processes in a polder in the Netherlands situated below sea level using high-frequency monitoring technology at the outlet, where the water is pumped into a higher situated lake, combined with a low-frequency water quality monitoring programme at six locations within the drainage area. Seasonal trends and short-scale temporal dynamics in concentrations indicated that the NO3 concentration at the pumping station originated from N loss from agricultural lands. The NO3 loads appear as losses via tube drains after intensive rainfall events during the winter months due to preferential flow through the cracked clay soil. Transfer function-noise modelling of hourly NO3 concentrations reveals that a large part of the dynamics in NO3 concentrations during the winter months can be related to rainfall. The total phosphorus (TP) concentration and turbidity almost doubled during operation of the pumping station, which points to resuspension of particulate P from channel bed sediments induced by changes in water flow due to pumping. Rainfall events that caused peaks in NO3 concentrations did not results in TP concentration peaks. The rainfall induced and NO3 enriched quick interflow, may also be enriched in TP but retention of TP due to sedimentation of particulate P then results in the absence of rainfall induced TP concentration peaks. Increased TP concentrations associated with run-off events is only observed during a rainfall event at the end of a freeze-thaw cycle. All these observations suggest that the P retention potential of polder water systems is primarily due to the artificial pumping regime

  11. Genome-wide transcriptional profiling reveals two distinct outcomes in central Nervous system infections of rabies virus

    Directory of Open Access Journals (Sweden)

    Daiting eZhang

    2016-05-01

    Full Text Available Rabies remains a major public health concern in many developing countries. The precise neuropathogenesis of rabies is unknown, though it is hypothesized to be due to neuronal death or dysfunction. Mice that received intranasal inoculation of an attenuated rabies virus (RABV strain HEP-Flury exhibited subtle clinical signs, and eventually recovered, which is different from the fatal encephalitis caused by the virulent RABV strain CVS-11. To understand the neuropathogenesis of rabies and the mechanisms of viral clearance, we applied RNA sequencing (RNA-Seq to compare the brain transcriptomes of normal mice versus HEP-Flury or CVS-11 intranasally inoculated mice. Our results revealed that both RABV strains altered positively and negatively the expression levels of many host genes, including genes associated with innate and adaptive immunity, inflammation and cell death. It is found that HEP-Flury infection can activate the innate immunity earlier through the RIG-I/MDA-5 signaling, and the innate immunity pre-activated by HEP-Flury or Newcastle disease virus (NDV infection can effectively prevent the CVS-11 to invade central nervous system (CNS, but fails to clear the CVS-11 after its entry into the CNS. In addition, following CVS-11 infection, genes implicated in cell adhesion, blood vessel morphogenesis and coagulation were mainly up-regulated, while the genes involved in synaptic transmission and ion transport were significantly down-regulated. On the other hand, several genes involved in the MHC class II-mediated antigen presentation pathway were activated to a greater extent after the HEP-Flury infection as compared with the CVS-11 infection suggesting that the collaboration of CD4+ T cells and MHC class II-mediated antigen presentation is critical for the clearance of attenuated RABV from the CNS. The differentially regulated genes reported here are likely to include potential therapeutic targets for expanding the postexposure treatment window

  12. The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V. (UMKC); (OKLU)

    2012-03-26

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

  13. Genome-Wide Transcriptional Profiling Reveals Two Distinct Outcomes in Central Nervous System Infections of Rabies Virus

    Science.gov (United States)

    Zhang, Daiting; He, Feilong; Bi, Shuilian; Guo, Huixia; Zhang, Baoshi; Wu, Fan; Liang, Jiaqi; Yang, Youtian; Tian, Qin; Ju, Chunmei; Fan, Huiying; Chen, Jinding; Guo, Xiaofeng; Luo, Yongwen

    2016-01-01

    Rabies remains a major public health concern in many developing countries. The precise neuropathogenesis of rabies is unknown, though it is hypothesized to be due to neuronal death or dysfunction. Mice that received intranasal inoculation of an attenuated rabies virus (RABV) strain HEP-Flury exhibited subtle clinical signs, and eventually recovered, which is different from the fatal encephalitis caused by the virulent RABV strain CVS-11. To understand the neuropathogenesis of rabies and the mechanisms of viral clearance, we applied RNA sequencing (RNA-Seq) to compare the brain transcriptomes of normal mice vs. HEP-Flury or CVS-11 intranasally inoculated mice. Our results revealed that both RABV strains altered positively and negatively the expression levels of many host genes, including genes associated with innate and adaptive immunity, inflammation and cell death. It is found that HEP-Flury infection can activate the innate immunity earlier through the RIG-I/MDA-5 signaling, and the innate immunity pre-activated by HEP-Flury or Newcastle disease virus (NDV) infection can effectively prevent the CVS-11 to invade central nervous system (CNS), but fails to clear the CVS-11 after its entry into the CNS. In addition, following CVS-11 infection, genes implicated in cell adhesion, blood vessel morphogenesis and coagulation were mainly up-regulated, while the genes involved in synaptic transmission and ion transport were significantly down-regulated. On the other hand, several genes involved in the MHC class II-mediated antigen presentation pathway were activated to a greater extent after the HEP-Flury infection as compared with the CVS-11 infection suggesting that the collaboration of CD4+ T cells and MHC class II-mediated antigen presentation is critical for the clearance of attenuated RABV from the CNS. The differentially regulated genes reported here are likely to include potential therapeutic targets for expanding the post-exposure treatment window for RABV

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

    Directory of Open Access Journals (Sweden)

    Carlos A Rossetti

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

  15. Cholinergic neurons and terminal fields revealed by immunohistochemistry for the vesicular acetylcholine transporter. II. The peripheral nervous system.

    Science.gov (United States)

    Schäfer, M K; Eiden, L E; Weihe, E

    1998-05-01

    immunoreactivity was particularly useful for identification of parasympathetic intrinsic ganglia, and their terminal fields, in heart, uterus, and other peripheral organs receiving parasympathetic innervation. Extensive vesicular acetylcholine transporter-positive terminal fields were apparent in both atrial and ventricular tissues of the heart targeting cardiomyocytes as well as cardiac microvessels. Pericardiac brown adipose tissue was also supplied by vesicular acetylcholine transporter-positive varicose fibres. The enteric ganglia of the myenteric and submucous plexus, their synaptic junctions with circular and longitudinal smooth muscle, and terminal fields of the lamina propria of the stomach and intestine and of the local microvasculature were intensely vesicular acetylcholine transporter positive. Vesicular acetylcholine transporter-positive innervation was delivered to the exocrine and endocrine pancreas originating from vesicular acetylcholine transporter-positive intrapancreatic ganglia. Vesicular acetylcholine transporter immunoreactivity in urogenital organs revealed the patterns of terminal cholinergic fields arising from the sacral parasympathetic innervation of these structures. Components of the cholinergic nervous system in the periphery whose existence has been controversial have been confirmed, and the existence of new components of the cholinergic nervous system has been documented, with vesicular acetylcholine transporter immunohistochemistry. Visualization of vesicular acetylcholine transporter will allow documentation of changes in synaptic patency during development, in disease, and during changes in neurotransmission accompanying injury and dystrophy, in the peripheral nervous system. PMID:9539210

  16. Geochemistry driven trends in microbial diversity and function across a temperature transect of a shallow water hydrothermal system off Milos (Greece)

    Science.gov (United States)

    Bühring, Solveig I.; Amend, Jan P.; Gómez Sáez, Gonzalo V.; Häusler, Stefan; Hinrichs, Kai-Uwe; Pichler, Thomas; Pop Ristova, Petra; Price, Roy E.; Santi, Ioulia; Sollich, Miriam

    2014-05-01

    The shallow water hydrothermal vents off Milos Island, Greece, discharge hot, slightly acidic, reduced fluids into colder, slightly alkaline, oxygenated seawater. Gradients in temperature, pH, and geochemistry are established as the two fluids mix, leading to the formation of various microbial microniches. In contrast to deep-sea hydrothermal systems, the availability of sun light allows for a combination of photo- and chemotrophic carbon fixation. Despite the comparably easy accessibility of shallow water hydrothermal systems, little is known about their microbial diversity and functioning. We present data from a shallow hydrothermal system off Milos Island, one of the most hydrothermally active regions in the Mediterranean Sea. The physico-chemical changes from ambient seafloor to hydrothermal area were investigated and documented by in situ microsensor profiling of temperature, pH, total reduced sulfur and dissolved oxygen alongside porewater geochemistry. The spatial microbial diversity was determined using a combination of gene- and lipid-based approaches, whereas microbial functioning was assessed by stable isotope probing experiments targeting lipid biomarkers. In situ microprofiles indicated an extreme environment with steep gradients, offering a variety of microniches for metabolically diverse microbial communities. We sampled a transect along a hydrothermal patch, following an increase in sediment surface temperature from background to 90°C, including five sampling points up to 20 cm sediment depth. Investigation of the bacterial diversity using ARISA revealed differences in the community structure along the geochemical gradients, with the least similarity between the ambient and highly hydrothermally impacted sites. Furthermore, using multivariate statistical analyses it was shown that variations in the community structure could be attributed to differences in the sediment geochemistry and especially the sulfide content, and only indirectly to shifts in

  17. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  18. Revealed Attention

    OpenAIRE

    Masatlioglu, Yusufcan; NAKAJIMA, Daisuke; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide wellestablished evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed behav...

  19. Revealed Attention

    OpenAIRE

    Yusufcan Masatlioglu; Daisuke Nakajima; Ozbay, Erkut Y

    2012-01-01

    The standard revealed preference argument relies on an implicit assumption that a decision maker considers all feasible alternatives. The marketing and psychology literatures, however, provide well-established evidence that consumers do not consider all brands in a given market before making a purchase (Limited Attention). In this paper, we illustrate how one can deduce both the decision maker's preference and the alternatives to which she pays attention and inattention from the observed beha...

  20. Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.

    Directory of Open Access Journals (Sweden)

    Wen Xie

    Full Text Available BACKGROUND: Bemisia tabaci (Gennadius is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. METHODOLOGY AND PRINCIPAL FINDINGS: Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45% unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10-5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. CONCLUSIONS: This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the

  1. Metagenomics and in situ analyses reveal Propionivibrio spp. to be abundant GAO in biological wastewater treatment systems

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Albertsen, Mads; Stokholm-Bjerregaard, Mikkel;

    to be present at equal levels. Metagenomics was employed to elucidate the identity and recover genomes from the abundant community members. Phylogenetic analyses revealed closely related “Ca. Accumulibacter” and Propionivibrio genera were co-dominant and were both targeted by the PAOmix probes. In situ staining...

  2. Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism.

    Science.gov (United States)

    Tripathy, Swetaleena; Padhi, Soumesh Kumar; Mohanty, Sriprakash; Samanta, Mrinal; Maiti, Nikhil Kumar

    2016-07-01

    Alkaline sulfur hot springs notable for their specialized and complex ecosystem powered by geothermal energy are abundantly rich in different chemotrophic and phototrophic thermophilic microorganisms. Survival and adaptation of these organisms in the extreme environment is specifically related to energy metabolism. To gain a better understanding of survival mechanism of the organisms in these ecosystems, we determined the different gene encoding enzymes associated with anaerobic pathways of energy metabolism by applying the metatranscriptomics approach. The analysis of the microbial population of hot sulfur spring revealed the presence of both aerobic and anaerobic organisms indicating dual mode of lifestyle of the community members. Proteobacteria (28.1 %) was the most dominant community. A total of 988 reads were associated with energy metabolism, out of which 33.7 % of the reads were assigned to nitrogen, sulfur, and methane metabolism based on KEGG classification. The major lineages of hot spring communities were linked with the anaerobic pathways. Different gene encoding enzymes (hao, nir, nar, cysH, cysI, acs) showed the involvement of microbial members in nitrification, denitrification, dissimilatory sulfate reduction, and methane generation. This study enhances our understanding of important gene encoding enzymes involved in energy metabolism, required for the survival and adaptation of microbial communities in the hot spring. PMID:27290724

  3. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

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

  4. Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems

    OpenAIRE

    Adams, Alyssa M.; Zenil, Hector; Davies, Paul CW; Walker, Sara I

    2016-01-01

    One of the most remarkable features of the > 3.5 billion year history of life on Earth is the apparent trend of innovation and open-ended growth of complexity. Similar trends are apparent in artificial and technological systems. However, a general framework for understanding open-ended evolution as it might occur in biological or technological systems has not yet been achieved. Here, we cast the problem within the broader context of dynamical systems theory to uncover and characterize mechani...

  5. Two Eyes on the Prize: Revealing the Complete Architectures of Planetary Systems through Transit Timing with Kepler and Spitzer

    Science.gov (United States)

    Fabrycky, Daniel; Stevenson, Kevin; Ballard, Sarah; Agol, Eric; Holman, Matthew; Bean, Jacob; Ragozzine, Darin

    2013-11-01

    The transit timing variation (TTV) technique has recently become a crucial method for determining the complete architectures (i.e., planet masses, orbital eccentricities, inclinations, and resonant properties) of extrasolar planetary systems. This technique has blossomed because of the Kepler mission's discovery of systems with multiple transiting planets and individual planets exhibiting very large TTVs. All of Kepler's results in this area so far have been for relatively short-period planets, but Kepler has also discovered dynamically-interacting systems with planets that have longer periods, similar to those of the Solar System. However, the ill-timed failure of the Kepler telescope has left us with an incomplete picture of these systems due to a lack of the required time baseline. Fortunately, Spitzer is positioned to leverage the unique potential that these planets offer, by extending the time baseline of transit observations. We propose to observe transits of seven Kepler-discovered planets in four particularly compelling systems to precisely determine their transit times. Combining the legacy Kepler transit times with the new times from Spitzer will give us the baseline that is needed to confirm and characterize these dynamically interacting systems of planets. This information will allow us to assess the complete architectures of these systems -- we will discover planets that do not transit and determine the masses and orbital properties of all the planets. For 6 planets in these systems, the TTVs will allow us to measure the planetary masses to better than 20%, which will approximately double the number of cool giant planets with known masses and radii. Several of the systems have mean-motion resonances between the planets, and characterizing these interactions yields information on the formation and migration of giant planets. The required precision and duration of these observations render Spitzer the only remaining instrument capable of such study.

  6. Cloning and characterization of the Bg/II restriction-modification system reveals a possible evolutionary footprint.

    Science.gov (United States)

    Anton, B P; Heiter, D F; Benner, J S; Hess, E J; Greenough, L; Moran, L S; Slatko, B E; Brooks, J E

    1997-03-10

    Bg/II, a type II restriction-modification (R-M) system from Bacillus globigii, recognizes the sequence 5'-AGATCT-3'. The system has been cloned into E. coli in multiple steps: first the methyltransferase (MTase) gene, bglIIM, was cloned from B. globigii RUB561, a variant containing an inactivated endonuclease (ENase) gene (bglIIR). Next the ENase protein (R.BglII) was purified to homogeneity from RUB562, a strain expressing the complete R-M system. Oligonucleotide probes specific for the 5' end of the gene were then synthesized and used to locate bglIIR, and the gene was isolated and cloned in a subsequent step. The nucleotide sequence of the system has been determined, and several interesting features have been found. The genes are tandemly arranged, with bglIIR preceding bglIIM. The amino acid sequence of M.BglII is compared to those of other known MTases. A third gene encoding a protein with sequence similarity to known C elements of other R-M systems is found upstream of bglIIR. This is the first instance of a C gene being associated with an R-M system where the R and M genes are collinear. In addition, open reading frames (ORFs) resembling genes involved with DNA mobility are found in close association with BglII. These may shed light on the evolution of the R-M system. PMID:9073062

  7. Simulations and Experiments Reveal the Relative Significance of the Free Chlorine/Nitrite Reaction in Chloraminated Systems

    Science.gov (United States)

    Nitrification can be a problem in distribution systems where chloramines are used as secondary disinfectants. A very rapid monochloramine residual loss is often associated with the onset of nitrification. During nitrification, ammonia-oxidizing bacteria biologically oxidize fre...

  8. Simulations and Experiments Reveal the Relative Significance of the Free Chlorine/Nitrite Reaction in Chloraminated Systems - slides

    Science.gov (United States)

    Nitrification can be a problem in distribution systems where chloramines are used as secondary disinfectants. A very rapid monochloramine residual loss is often associated with the onset of nitrification. During nitrification, ammonia-oxidizing bacteria biologically oxidize fre...

  9. The response of tumour vasculature to angiotensin II revealed by its systemic and local administration to 'tissue-isolated' tumours.

    OpenAIRE

    Tozer, G M; Shaffi, K. M.

    1995-01-01

    A tissue-isolated preparation of the P22 rat carcinosarcoma was used to investigate the tumour vascular response to angiotensin II (ATII). In particular, the relative importance of systemic and local tumour factors was assessed by comparing tumour vascular resistance during systemic administration of ATII and during administration directly into the tumour-supplying artery. The effect of hypervolaemia on tumour vascular resistance was determined as well as the effect of ATII on oxygen metaboli...

  10. Metabolomic analysis reveals the relationship between AZI1 and sugar signaling in systemic acquired resistance of Arabidopsis.

    Science.gov (United States)

    Wang, Xiao-Yan; Li, Dian-Zhen; Li, Qi; Ma, Yan-Qin; Yao, Jing-Wen; Huang, Xuan; Xu, Zi-Qin

    2016-10-01

    The function of AZI1 in systemic acquired resistance of Arabidopsis was confirmed by investigation of the phenotypic features of wild-type Col-0, AZI1 T-DNA knockout and AZI1 overexpressing plants after infection with virulent and avirulent Pseudomonas syringae. Real-time quantitative PCR and Northern blotting analyses showed that the transcript abundances of PR genes increased significantly in local and systemic leaves of wild-type Col-0 and AZI1 overexpressing plants challenged with avirulent P. syringae, whereas the mRNA accumulation of PR genes was obviously attenuated in local and systemic leaves of AZI1 T-DNA knockout plants after localized infiltration with avirulent Psm avrRpm1. The changes of metabolomic profiles in distal leaves of three types of materials infected with avirulent P. syringae were determined by (1)H NMR spectrometry and data mining showed that the soluble carbonhydrates might function as signal substances in the systemic immunity of Arabidopsis. At the same time, the expression of the sugar signaling genes in local and distal leaves after infection of avirulent P. syringae was compared. As a result, it was found that the transcript abundances of sugar signaling genes, including SUS1, SUS2, SUS3, SUS6, SUT1, HXK1, HXK2, SNRK1.2, ERD6, TPS1, TOR, SNRK1.1, SNRK1.3 and bZIP11, were obviously changed in distal leaves of different materials with the modulated AZI1 activities, indicating sugar-related genes are involved in regulation of the systemic immunity mediated by AZI1. These results also illustrated that the immune system associated with sugar molecules probably was an important part of the systemic acquired resistance in Arabidopsis. PMID:27337039

  11. Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells.

    Science.gov (United States)

    Kondo, Yuki; Nurani, Alif Meem; Saito, Chieko; Ichihashi, Yasunori; Saito, Masato; Yamazaki, Kyoko; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Fukuda, Hiroo

    2016-06-01

    Cell differentiation is a complex process involving multiple steps, from initial cell fate specification to final differentiation. Procambial/cambial cells, which act as vascular stem cells, differentiate into both xylem and phloem cells during vascular development. Recent studies have identified regulatory cascades for xylem differentiation. However, the molecular mechanism underlying phloem differentiation is largely unexplored due to technical challenges. Here, we established an ectopic induction system for phloem differentiation named Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL). Our results verified similarities between VISUAL-induced Arabidopsis thaliana phloem cells and in vivo sieve elements. We performed network analysis using transcriptome data with VISUAL to dissect the processes underlying phloem differentiation, eventually identifying a factor involved in the regulation of the master transcription factor gene APL Thus, our culture system opens up new avenues not only for genetic studies of phloem differentiation, but also for future investigations of multidirectional differentiation from vascular stem cells. PMID:27194709

  12. Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB.

    Science.gov (United States)

    Thompson, Nancy E; Glaser, Bryan T; Foley, Katherine M; Burton, Zachary F; Burgess, Richard R

    2009-09-11

    The "B-finger" of transcription factor IIB (TFIIB) is highly conserved and believed to play a role in the initiation process. We performed alanine substitutions across the B-finger of human TFIIB, made change-of-charge mutations in selected residues, and substituted the B-finger sequence from other organisms. Mutant proteins were examined in two minimal promoter systems (containing only RNA polymerase II, TATA-binding protein, and TFIIB) and in a complex system, using TFIIB-immunodepleted HeLa cell nuclear extract (NE). Mutations in conserved residues located on the sides of the B-finger had the greatest effect on activity in both minimal promoter systems, with mutations in residues Glu-51 and Arg-66 eliminating activity. The double change-of-charge mutant (E51R:R66E) did not show activity in either minimal promoter system. Mutations in the nonconserved residues at the tip of the B-finger did not significantly affect activity. However, all of the mutations in the B-finger showed at least 25% activity in the HeLa cell NE. Chimeric proteins, containing B-finger sequences from species with conserved residues on the side of the B-finger, showed wild-type activity in a minimal promoter system and in the HeLa cell NE. However, chimeric proteins whose sequence showed divergence on the sides of the B-finger had reduced activity. Transcription factor IIF (TFIIF) partially restored activity of the inactive mutants in the minimal promoter system, suggesting that TFIIF in HeLa cell NE helps to rescue the inactive mutations by interacting with either the B-finger or another component of the initiation complex that is influenced by the B-finger. PMID:19590095

  13. Structure of the nervous system of Myzostoma cirriferum (Annelida) as revealed by immunohistochemistry and cLSM analyses.

    Science.gov (United States)

    Müller, M C; Westheide, W

    2000-08-01

    The nervous systems of juvenile and adult Myzostoma cirriferum Leuckart, 1836, were stained with antisera against 5-HT (5-hydroxytryptamine, serotonin), FMRFamide, and acetylated alpha-tubulin in combination with the indirect fluorescence technique and analyzed by confocal laser scanning microscopy. The central nervous system consists of two small cerebral ganglia, connected by a dorsal commissure, a ventral nerve mass, and a pair of long circumesophageal connectives joining the former to the latter. The two neuropil cords within the ventral nerve mass curve outward and are joined to one another anteriorly and posteriorly. They are connected by 12 commissures, forming a ladder-like system. A single median nerve runs along the midventral axis. In addition to the circumesophageal connectives, 11 peripheral nerves arise from each main cord. The first innervates the anterior body region. The others form five groups of two nerves each, the first and thicker nerve of which is the parapodial nerve, innervating the parapodium and two corresponding cirri. Except for those in the most posterior group, the second nerves innervate the lateral organs and the body periphery. Serotonergic perikarya are arranged in six more or less distinct clusters, the first lying in front of and the other five between the main nerve cords. The distribution pattern of the FMRFamidergic perikarya is less clear and the somata lie between and outside the cords. One pair of dorsolateral longitudinal nerves was visualized by tubulin staining. Peripheral nerves and the commissures, in particular, demonstrate a segmental organization of the nervous system of M. cirriferum. Furthermore, their arrangement indicates that the body consists of six segments, the first of which is identifiable only by the first pair of peripheral nerves, the first two commissures, and the anteriormost ventral ganglion. The nervous system M. cirriferum thus exhibits several structures also found in the basic plan of the

  14. Minimal Promoter Systems Reveal the Importance of Conserved Residues in the B-finger of Human Transcription Factor IIB*

    OpenAIRE

    Thompson, Nancy E.; GLASER, BRYAN T.; Foley, Katherine M.; Burton, Zachary F.; Burgess, Richard R.

    2009-01-01

    The “B-finger” of transcription factor IIB (TFIIB) is highly conserved and believed to play a role in the initiation process. We performed alanine substitutions across the B-finger of human TFIIB, made change-of-charge mutations in selected residues, and substituted the B-finger sequence from other organisms. Mutant proteins were examined in two minimal promoter systems (containing only RNA polymerase II, TATA-binding protein, and TFIIB) and in a complex system, using TFIIB-immunodepleted HeL...

  15. The pituitary gland of the European eel reveals massive expression of genes involved in the melanocortin system.

    Directory of Open Access Journals (Sweden)

    Eirill Ager-Wick

    Full Text Available Hormones secreted from the pituitary gland regulate important processes such as development, growth and metabolism, reproduction, water balance, and body pigmentation. Synthesis and secretion of pituitary hormones are regulated by different factors from the hypothalamus, but also through feedback mechanisms from peripheral organs, and from the pituitary itself. In the European eel extensive attention has been directed towards understanding the different components of the brain-pituitary-gonad axis, but little is known about the regulation of upstream processes in the pituitary gland. In order to gain a broader mechanistic understanding of the eel pituitary gland, we have performed RNA-seq transcriptome profiling of the pituitary of prepubertal female silver eels. RNA-seq reads generated on the Illumina platform were mapped to the recently assembled European eel genome. The most abundant transcript in the eel pituitary codes for pro-opiomelanocortin, the precursor for hormones of the melanocortin system. Several genes putatively involved in downstream processing of pro-opiomelanocortin were manually annotated, and were found to be highly expressed, both by RNA-seq and by qPCR. The melanocortin system, which affects skin color, energy homeostasis and in other teleosts interacts with the reproductive system, has so far received limited attention in eels. However, since up to one third of the silver eel pituitary's mRNA pool encodes pro-opiomelanocortin, our results indicate that control of the melanocortin system is a major function of the eel pituitary.

  16. THE MINERALOGY OF PB SCALES IN DRINKING WATER DISTRIBUTION SYSTEMS AS REVEALED BY COMBINED XRD AND MICRO-RAMAN SPECTROSCOPY

    Science.gov (United States)

    Dissolving Pb from lead service lines and Pb-containing brasses and solders has become a major health issue for many water distribution systems. Knowledge of the mineralogy of scales in these pipes is key to modeling this dissolution. The traditional method of determining their ...

  17. Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift

    OpenAIRE

    Rato, Claudia; Amirova, Svetlana R.; Bates, Declan G; Stansfield, Ian; Wallace, Heather M.

    2011-01-01

    The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we presen...

  18. Systemic gene transfer reveals distinctive muscle transduction profile of tyrosine mutant AAV-1, -6, and -9 in neonatal dogs

    OpenAIRE

    Hakim, Chady H.; Yue, Yongping; Shin, Jin-Hong; Williams, Regina R; Zhang, Keqing; Smith, Bruce F; Duan, Dongsheng

    2014-01-01

    The muscular dystrophies are a group of devastating genetic disorders that affect both skeletal and cardiac muscle. An effective gene therapy for these diseases requires bodywide muscle delivery. Tyrosine mutant adeno-associated virus (AAV) has been considered as a class of highly potent gene transfer vectors. Here, we tested the hypothesis that systemic delivery of tyrosine mutant AAV can result in bodywide muscle transduction in newborn dogs. Three tyrosine mutant AAV vectors (Y445F/Y731F A...

  19. Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain

    OpenAIRE

    Poggi-Parodi, Dante; Bidard, Frédérique; Pirayre, Aurélie; Portnoy, Thomas; Blugeon, Corinne; Seiboth, Bernhard; Kubicek, Christian P.; Le Crom, Stéphane; Margeot, Antoine

    2014-01-01

    Background The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can ...

  20. A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

    OpenAIRE

    Hvidsten Torgeir R; Jansson Stefan; Street Nathaniel

    2011-01-01

    Abstract Background Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods ...

  1. Four functionally distinct C-type natriuretic peptides found in fish reveal evolutionary history of the natriuretic peptide system

    OpenAIRE

    Inoue, Koji; Naruse, Kiyoshi; Yamagami, Sayaka; Mitani, Hiroshi; Suzuki, Norio; Takei, Yoshio

    2003-01-01

    Natriuretic peptides (NPs) are major cardiovascular and osmoregulatory hormones in vertebrates. Although tetrapods generally have three subtypes, atrial NP (ANP), B-type NP (BNP), and C-type NP (CNP), some teleosts lack BNP, and sharks and hagfish have only one NP. Thus, NPs have diverged during fish evolution, possibly reflecting changes in osmoregulatory systems. In this study, we found, by cDNA cloning, four distinct CNPs (1 through 4) in the medaka (Oryzias latipes...

  2. Identification and functional analysis of olfactory receptor family reveal unusual characteristics of the olfactory system in the migratory locust

    OpenAIRE

    Wang, Zhifeng; Yang, Pengcheng; Chen, Dafeng; Jiang, Feng; Li, Yan; Wang, Xianhui; Kang, Le

    2015-01-01

    Locusts represent the excellent model of insect olfaction because the animals are equipped with an unusual olfactory system and display remarkable density-dependent olfactory plasticity. However, information regarding receptor molecules involved in the olfactory perception of locusts is very limited. On the basis of genome sequence and antennal transcriptome of the migratory locust, we conduct the identification and functional analysis of two olfactory receptor families: odorant receptors (OR...

  3. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity.

    Directory of Open Access Journals (Sweden)

    Michelle R Jones

    2015-08-01

    Full Text Available Genome wide association studies (GWAS have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS, a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS.

  4. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity.

    Science.gov (United States)

    Jones, Michelle R; Brower, Meredith A; Xu, Ning; Cui, Jinrui; Mengesha, Emebet; Chen, Yii-Der I; Taylor, Kent D; Azziz, Ricardo; Goodarzi, Mark O

    2015-08-01

    Genome wide association studies (GWAS) have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS), a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs) therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS. PMID:26305227

  5. Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes.

    Science.gov (United States)

    Lobel, Lior; Herskovits, Anat A

    2016-02-01

    Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs) serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen Listeria monocytogenes revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (e.g., metabolic genes) and functions as a direct activator of the master virulence regulator gene, prfA. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY's regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (i.e., binds DNA) under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., sigB, arg, his, actA, glpF, gadG, gdhA, poxB, glnR and fla genes), integrating metabolism, stress responses, motility and virulence in L. monocytogenes. This study establishes CodY as a multifaceted factor regulating L. monocytogenes physiology in a highly versatile manner. PMID:26895237

  6. Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Lior Lobel

    2016-02-01

    Full Text Available Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen Listeria monocytogenes revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (e.g., metabolic genes and functions as a direct activator of the master virulence regulator gene, prfA. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY's regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (i.e., binds DNA under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., sigB, arg, his, actA, glpF, gadG, gdhA, poxB, glnR and fla genes, integrating metabolism, stress responses, motility and virulence in L. monocytogenes. This study establishes CodY as a multifaceted factor regulating L. monocytogenes physiology in a highly versatile manner.

  7. Systems biology analysis of gene expression during in vivo Mycobacterium avium paratuberculosis enteric colonization reveals role for immune tolerance.

    Directory of Open Access Journals (Sweden)

    Sangeeta Khare

    Full Text Available Survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP in the intestinal mucosa is associated with host immune tolerance. However, the initial events during MAP interaction with its host that lead to pathogen survival, granulomatous inflammation, and clinical disease progression are poorly defined. We hypothesize that immune tolerance is initiated upon initial contact of MAP with the intestinal Peyer's patch. To test our hypothesis, ligated ileal loops in neonatal calves were infected with MAP. Intestinal tissue RNAs were collected (0.5, 1, 2, 4, 8 and 12 hrs post-infection, processed, and hybridized to bovine gene expression microarrays. By comparing the gene transcription responses of calves infected with the MAP, informative complex patterns of expression were clearly visible. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis, and genes were grouped into the specific pathways and gene ontology categories to create a holistic model. This model revealed three different phases of responses: i early (30 min and 1 hr post-infection, ii intermediate (2, 4 and 8 hrs post-infection, and iii late (12 hrs post-infection. We describe here the data that include expression profiles for perturbed pathways, as well as, mechanistic genes (genes predicted to have regulatory influence that are associated with immune tolerance. In the Early Phase of MAP infection, multiple pathways were initiated in response to MAP invasion via receptor mediated endocytosis and changes in intestinal permeability. During the Intermediate Phase, perturbed pathways involved the inflammatory responses, cytokine-cytokine receptor interaction, and cell-cell signaling. During the Late Phase of infection, gene responses associated with immune tolerance were initiated at the level of T-cell signaling. Our study provides evidence that MAP infection resulted in differentially regulated genes, perturbed

  8. Three-dimensional upper crustal structure of the geothermal system in Tarutung (North Sumatra, Indonesia) revealed by seismic attenuation tomography

    Science.gov (United States)

    Muksin, Umar; Haberland, Christian; Bauer, Klaus; Weber, Michael

    2013-12-01

    The geothermal potential in Tarutung is controlled by both the Sumatra Fault system and young arc volcanism. In this study we use the spatial distribution of seismic attenuation, calculated from local earthquake recordings, to image the 3-D seismic attenuation of the area and relate it with the temperature anomalies and the fluid distribution of the subsurface. A temporary seismic network of 42 stations was deployed around Tarutung and Sarulla (south of Tarutung) for a period of 10 months starting in 2011 May. Within this period, the network recorded 2586 local events. A high-quality subset of 229 events recorded by at least 10 stations was used for the attenuation inversion (tomography). Path-average attenuation (tp^{*}) was calculated by using a spectral inversion method. The spread function, the contour lines of the model resolution matrix and the recovery test results show that our 3-D attenuation model (Qp) has good resolution around the Tarutung Basin and along the Sarulla graben. High attenuation (low Qp) related to the geothermal system is found in the northeast of the Tarutung Basin suggesting fluid pathways from below the Sumatra Fault. The upper part of the studied geothermal system in the Tarutung district seems to be mainly controlled by the fault structure rather than by magmatic activities. In the southwest of the Tarutung Basin, the high attenuation zone is associated with the Martimbang volcano. In the Sarulla region, a low-Qp anomaly is found along the graben within the vicinity of the Hopong caldera.

  9. A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems

    Science.gov (United States)

    Blöchliger, Nicolas; Vitalis, Andreas; Caflisch, Amedeo

    2013-11-01

    Advances in IT infrastructure have enabled the generation and storage of very large data sets describing complex systems continuously in time. These can derive from both simulations and measurements. Analysis of such data requires the availability of scalable algorithms. In this contribution, we propose a scalable algorithm that partitions instantaneous observations (snapshots) of a complex system into kinetically distinct sets (termed basins). To do so, we use a combination of ordering snapshots employing the method's only essential parameter, i.e., a definition of pairwise distance, and annotating the resultant sequence, the so-called progress index, in different ways. Specifically, we propose a combination of cut-based and structural annotations with the former responsible for the kinetic grouping and the latter for diagnostics and interpretation. The method is applied to an illustrative test case, and the scaling of an approximate version is demonstrated to be O(NlogN) with N being the number of snapshots. Two real-world data sets from river hydrology measurements and protein folding simulations are then used to highlight the utility of the method in finding basins for complex systems. Both limitations and benefits of the approach are discussed along with routes for future research.

  10. Integration of root phenes revealed by intensive phenotyping of root system architecture, anatomy, and physiology in cereals

    Science.gov (United States)

    York, Larry

    2015-04-01

    Food insecurity is among the greatest challenges humanity will face in the 21st century. Agricultural production in much of the world is constrained by the natural infertility of soil which restrains crops from reaching their yield potential. In developed nations, fertilizer inputs pollute air and water and contribute to climate change and environmental degradation. In poor nations low soil fertility is a primary constraint to food security and economic development. Water is almost always limiting crop growth in any system. Increasing the acquisition efficiency of soil resources is one method by which crop yields could be increased without the use of more fertilizers or irrigation. Cereals are the most widely grown crops, both in terms of land area and in yield, so optimizing uptake efficiency of cereals is an important goal. Roots are the primary interface between plant and soil and are responsible for the uptake of soil resources. The deployment of roots in space and time comprises root system architecture (RSA). Cereal RSA is a complex phenotype that aggregates many elemental phenes (elemental units of phenotype). Integration of root phenes will be determined by interactions through their effects on soil foraging and plant metabolism. Many architectural, metabolic, and physiological root phenes have been identified in maize, including: nodal root number, nodal root growth angle, lateral root density, lateral root length, aerenchyma, cortical cell size and number, and nitrate uptake kinetics. The utility of these phenes needs confirmation in maize and in other cereals. The maize root system is composed of an embryonic root system and nodal roots that emerge in successive whorls as the plant develops, and is similar to other cereals. Current phenotyping platforms often ignore the inner whorls and instead focus on the most visible outer whorls after excavating a maize root crown from soil. Here, an intensive phenotyping platform evaluating phenes of all nodal root

  11. Quantitative evaluation of first, second, and third generation hairpin systems reveals the limit of mammalian vector-based RNAi.

    Science.gov (United States)

    Watanabe, Colin; Cuellar, Trinna L; Haley, Benjamin

    2016-01-01

    Incorporating miRNA-like features into vector-based hairpin scaffolds has been shown to augment small RNA processing and RNAi efficiency. Therefore, defining an optimal, native hairpin context may obviate a need for hairpin-specific targeting design schemes, which confound the movement of functional siRNAs into shRNA/artificial miRNA backbones, or large-scale screens to identify efficacious sequences. Thus, we used quantitative cell-based assays to compare separate third generation artificial miRNA systems, miR-E (based on miR-30a) and miR-3G (based on miR-16-2 and first described in this study) to widely-adopted, first and second generation formats in both Pol-II and Pol-III expression vector contexts. Despite their unique structures and strandedness, and in contrast to first and second-generation RNAi triggers, the third generation formats operated with remarkable similarity to one another, and strong silencing was observed with a significant fraction of the evaluated target sequences within either promoter context. By pairing an established siRNA design algorithm with the third generation vectors we could readily identify targeting sequences that matched or exceeded the potency of those discovered through large-scale sensor-based assays. We find that third generation hairpin systems enable the maximal level of siRNA function, likely through enhanced processing and accumulation of precisely-defined guide RNAs. Therefore, we predict future gains in RNAi potency will come from improved hairpin expression and identification of optimal siRNA-intrinsic silencing properties rather than further modification of these scaffolds. Consequently, third generation systems should be the primary format for vector-based RNAi studies; miR-3G is advantageous due to its small expression cassette and simplified, cost-efficient cloning scheme. PMID:26786363

  12. A novel single virus infection system reveals that influenza virus preferentially infects cells in g1 phase.

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    Ryuta Ueda

    Full Text Available BACKGROUND: Influenza virus attaches to sialic acid residues on the surface of host cells via the hemagglutinin (HA, a glycoprotein expressed on the viral envelope, and enters into the cytoplasm by receptor-mediated endocytosis. The viral genome is released and transported in to the nucleus, where transcription and replication take place. However, cellular factors affecting the influenza virus infection such as the cell cycle remain uncharacterized. METHODS/RESULTS: To resolve the influence of cell cycle on influenza virus infection, we performed a single-virus infection analysis using optical tweezers. Using this newly developed single-virus infection system, the fluorescence-labeled influenza virus was trapped on a microchip using a laser (1064 nm at 0.6 W, transported, and released onto individual H292 human lung epithelial cells. Interestingly, the influenza virus attached selectively to cells in the G1-phase. To clarify the molecular differences between cells in G1- and S/G2/M-phase, we performed several physical and chemical assays. Results indicated that: 1 the membranes of cells in G1-phase contained greater amounts of sialic acids (glycoproteins than the membranes of cells in S/G2/M-phase; 2 the membrane stiffness of cells in S/G2/M-phase is more rigid than those in G1-phase by measurement using optical tweezers; and 3 S/G2/M-phase cells contained higher content of Gb3, Gb4 and GlcCer than G1-phase cells by an assay for lipid composition. CONCLUSIONS: A novel single-virus infection system was developed to characterize the difference in influenza virus susceptibility between G1- and S/G2/M-phase cells. Differences in virus binding specificity were associated with alterations in the lipid composition, sialic acid content, and membrane stiffness. This single-virus infection system will be useful for studying the infection mechanisms of other viruses.

  13. LUT Reveals an Algol-type Eclipsing Binary With Three Additional Stellar Companions in a Multiple System

    Science.gov (United States)

    Zhu, L.-Y.; Zhou, X.; Hu, J.-Y.; Qian, S.-B.; Li, L.-J.; Liao, W.-P.; Tian, X.-M.; Wang, Z.-H.

    2016-04-01

    A complete light curve of the neglected eclipsing binary Algol V548 Cygni in the UV band was obtained with the Lunar-based Ultraviolet Telescope in 2014 May. Photometric solutions are obtained using the Wilson–Devinney method. It is found that solutions with and without third light are quite different. The mass ratio without third light is determined to be q = 0.307, while that derived with third light is q = 0.606. It is shown that V548 Cygni is a semi-detached binary where the secondary component is filling the critical Roche lobe. An analysis of all available eclipse times suggests that there are three cyclic variations in the O–C diagram that are interpreted by the light travel-time effect via the presence of three additional stellar companions. This is in agreement with the presence of a large quantity of third light in the system. The masses of these companions are estimated as m sin i‧ ∼ 1.09, 0.20, and 0.52 M⊙. They are orbiting the central binary with orbital periods of about 5.5, 23.3, and 69.9 years, i.e., in 1:4:12 resonance orbit. Their orbital separations are about 4.5, 13.2, and 26.4 au, respectively. Our photometric solutions suggest that they contribute about 32.4% to the total light of the multiple system. No obvious long-term changes in the orbital period were found, indicating that the contributions of the mass transfer and the mass loss due to magnetic braking to the period variations are comparable. The detection of three possible additional stellar components orbiting a typical Algol in a multiple system make V548 Cygni a very interesting binary to study in the future.

  14. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

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    Ahmad A Mannan

    Full Text Available An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-'omics' steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population.

  15. Characterization of homeobox genes reveals sophisticated regionalization of the central nervous system in the European cuttlefish Sepia officinalis.

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    Laura Focareta

    Full Text Available Cephalopod mollusks possess a number of anatomical traits that often parallel vertebrates in morphological complexity, including a centralized nervous system with sophisticated cognitive functionality. Very little is known about the genetic mechanisms underlying patterning of the cephalopod embryo to arrive at this anatomical structure. Homeodomain (HD genes are transcription factors that regulate transcription of downstream genes through DNA binding, and as such are integral parts of gene regulatory networks controlling the specification and patterning of body parts across lineages. We have used a degenerate primer strategy to isolate homeobox genes active during late-organogenesis from the European cuttlefish Sepia officinalis. With this approach we have isolated fourteen HD gene fragments and examine the expression profiles of five of these genes during late stage (E24-28 embryonic development (Sof-Gbx, Sof-Hox3, Sof-Arx, Sof-Lhx3/4, Sof-Vsx. All five genes are expressed within the developing central nervous system in spatially restricted and largely non-overlapping domains. Our data provide a first glimpse into the diversity of HD genes in one of the largest, yet least studied, metazoan clades and illustrate how HD gene expression patterns reflect the functional partitioning of the cephalopod brain.

  16. Benchmarking of hospital information systems: Monitoring of discharge letters and scheduling can reveal heterogeneities and time trends

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    Eckholt Markus

    2008-04-01

    Full Text Available Abstract Background Monitoring of hospital information system (HIS usage can provide insights into best practices within a hospital and help to assess time trends. In terms of effort and cost of benchmarking, figures derived automatically from the routine HIS system are preferable to manual methods like surveys, in particular for repeated analysis. Methods Due to relevance for quality management and efficient resource utilization we focused on time-to-completion of discharge letters (assessed by CT-plots and usage of patient scheduling. We analyzed these parameters monthly during one year at a major university hospital in Germany. Results We found several distinct patterns of discharge letter documentation indicating a large heterogeneity of HIS usage between different specialties (completeness 51 – 99%, delays 0 – 90 days. Overall usage of scheduling increased during the observation period by 62%, but again showed a considerable variation between departments. Conclusion Regular monitoring of HIS key figures can contribute to a continuous HIS improvement process.

  17. In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems

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    Maiwald Thomas

    2012-02-01

    Full Text Available Abstract Background Mathematical models of dynamical systems facilitate the computation of characteristic properties that are not accessible experimentally. In cell biology, two main properties of interest are (1 the time-period a protein is accessible to other molecules in a certain state - its half-life - and (2 the time it spends when passing through a subsystem - its transit-time. We discuss two approaches to quantify the half-life, present the novel method of in silico labeling, and introduce the label half-life and label transit-time. The developed method has been motivated by laboratory tracer experiments. To investigate the kinetic properties and behavior of a substance of interest, we computationally label this species in order to track it throughout its life cycle. The corresponding mathematical model is extended by an additional set of reactions for the labeled species, avoiding any double-counting within closed circuits, correcting for the influences of upstream fluxes, and taking into account combinatorial multiplicity for complexes or reactions with several reactants or products. A profile likelihood approach is used to estimate confidence intervals on the label half-life and transit-time. Results Application to the JAK-STAT signaling pathway in Epo-stimulated BaF3-EpoR cells enabled the calculation of the time-dependent label half-life and transit-time of STAT species. The results were robust against parameter uncertainties. Conclusions Our approach renders possible the estimation of species and label half-lives and transit-times. It is applicable to large non-linear systems and an implementation is provided within the PottersWheel modeling framework (http://www.potterswheel.de.

  18. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters. PMID:27033205

  19. A New Diagnostic of Active Galactic Nuclei: Revealing Highly-Absorbed Systems at Redshift>0.3

    CERN Document Server

    Juneau, Stéphanie; Alexander, David M; Salim, Samir

    2011-01-01

    We introduce the Mass-Excitation (MEx) diagnostic to identify active galactic nuclei (AGN) in galaxies at intermediate redshift. In the absence of near-infrared spectroscopy, necessary to use traditional nebular line diagrams at z>0.4, we demonstrate that combining [OIII]5007/Hbeta and stellar mass successfully distinguishes between star formation and AGN emission. The MEx classification scheme relies on a novel probabilistic approach splitting galaxies into sub-categories with more confidence than alternative high-z diagnostic diagrams. It recognizes that galaxies near empirical boundaries on traditional diagrams have an uncertain classification and thus a non-zero probability of belonging to more than one category. An outcome of this work is a system of statistical weights that can be used to compute global properties of galaxy samples. We apply the MEx diagram to 2,812 galaxies at 0.3

  20. Exceptionally preserved Cambrian trilobite digestive system revealed in 3D by synchrotron-radiation X-ray tomographic microscopy.

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    Mats E Eriksson

    Full Text Available The Cambrian 'Orsten' fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish 'Orsten' fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the 'Orsten' fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome.

  1. Systems Chemo-Biology and Transcriptomic Meta-Analysis Reveal the Molecular Roles of Bioactive Lipids in Cardiomyocyte Differentiation.

    Science.gov (United States)

    de Faria Poloni, Joice; Bonatto, Diego

    2015-09-01

    Lipids, which are essential constituents of biological membranes, play structural and functional roles in the cell. In recent years, certain lipids have been identified as regulatory signaling molecules and have been termed "bioactive lipids". Subsequently, the importance of bioactive lipids in stem cell differentiation and cardiogenesis has gained increasing recognition. Therefore, the aim of this study was to identify the biological processes underlying murine cardiac differentiation and the mechanisms by which bioactive lipids affect these processes. For this purpose, a transcriptomic meta-analysis of microarray and RNA-seq data from murine stem cells undergoing cardiogenic differentiation was performed. The differentially expressed genes identified via this meta-analysis, as well as bioactive lipids, were evaluated using systems chemo-biology tools. These data indicated that bioactive lipids are associated with the regulation of cell motility, cell adhesion, cytoskeletal rearrangement, and gene expression. Moreover, bioactive lipids integrate the signaling pathways involved in cell migration, the secretion and remodeling of extracellular matrix components, and the establishment of the cardiac phenotype. In conclusion, this study provides new insights into the contribution of bioactive lipids to the induction of cellular responses to various stimuli, which may originate from the extracellular environment and morphogens, and the manner in which this contribution directly affects murine heart morphogenesis. PMID:25752681

  2. Central Nervous System Proteomics in Animal Model of Multiple Sclerosis Revealed Down-Regulation of Mithochondrial Proteins

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    Abolhassan Shahzadeh Fazeli

    2009-01-01

    Full Text Available Objective: Detection of central nervous system (CNS molecular defects in an animal modelof multiple sclerosis.Materials and Methods: Experimental autoimmune encephalomyelitis (EAE was inducedby a myelin oligodendrocyte glycoprotein. Protein expression profiles in the central nervoussystem between healthy clinical scores 1 and 3 of EAE were studied using a two dimensionalelectrophoresis based proteomics approach coupled with MALDI TOF/TOF massspectrometry.Results: We identified 8 mitochondrial proteins that were differentially expressed in CNS, allof them down-regulated in scores 1 and/or 3. Of these, 5 proteins belong to the mitochondrialrespiratory chain including: NADH dehydrogenase (ubiquinone Fe-S protein 8, cytochromec oxidase Va, cytochrome c oxidase Vb, ATP5B, NADH dehydrogenase (ubiquinone flavoprotein2. We also observed down-regulation of three other mitochondrial proteins including:glutaredoxin 5, estradiol 17 beta-dehydrogenase 8 and isocitrate dehydrogenase.Conclusion: Down-regulation of mitochondrial proteins supported the hypothesis thathypoxia-like tissue injury in multiple sclerosis (MS lesions may be due to mitochondrialimpairment.

  3. Disentangling community functional components in a litter-macrodetritivore model system reveals the predominance of the mass ratio hypothesis.

    Science.gov (United States)

    Bílá, Karolína; Moretti, Marco; Bello, Francesco; Dias, André Tc; Pezzatti, Gianni B; Van Oosten, Arend Raoul; Berg, Matty P

    2014-02-01

    RECENT INVESTIGATIONS HAVE SHOWN THAT TWO COMPONENTS OF COMMUNITY TRAIT COMPOSITION ARE IMPORTANT FOR KEY ECOSYSTEM PROCESSES: (i) the community-weighted mean trait value (CWM), related to the mass ratio hypothesis and dominant trait values in the community, and (ii) functional diversity (FD), related to the complementarity hypothesis and the divergence of trait values. However, no experiments controlling for the inherent dependence between CWM and FD have been conducted so far. We used a novel experimental framework to disentangle the unique and shared effects of CWM and FD in a leaf litter-macrodetritivore model system. We manipulated isopod assemblages varying in species number, CWM and FD of litter consumption rate to test the relative contribution of these community parameters in the decomposition process. We showed that CWM, but also the combination of CWM and FD, is a main factor controlling litter decomposition. When we tested individual biodiversity components separately, CWM of litter consumption rate showed a significant effect on decomposition, while FD and species richness alone did not. Our study demonstrated that (i) trait composition rather than species diversity drives litter decomposition, (ii) dominant trait values in the community (CWM) play a chief role in driving ecosystem processes, corroborating the mass ratio hypothesis, and (iii) trait dissimilarity can contribute in modulating the overall biodiversity effects. Future challenge is to assess whether the generality of our finding, that is, that dominant trait values (CWM) predominate over trait dissimilarity (FD), holds for other ecosystem processes, environmental conditions and different spatial and temporal scales. PMID:24634725

  4. The Augustine magmatic system as revealed by seismic tomography and relocated earthquake hypocenters from 1994 through 2009

    Science.gov (United States)

    Syracuse, E.M.; Thurber, C.H.; Power, J.A.

    2011-01-01

    We incorporate 14 years of earthquake data from the Alaska Volcano Observatory with data from a 1975 controlled-source seismic experiment to obtain the three-dimensional P and S wave velocity structure and the first high-precision earthquake locations at Augustine Volcano to be calculated in a fully three-dimensional velocity model. Velocity tomography shows two main features beneath Augustine: a narrow, high-velocity column beneath the summit, extending from ???2 km depth to the surface, and elevated velocities on the south flank. Our relocation results allow a thorough analysis of the spatio-temoral patterns of seismicity and the relationship to the magmatic and eruptive activity. Background seismicity is centered beneath the summit at an average depth of 0.6 km above sea level. In the weeks leading to the January 2006 eruption of Augustine, seismicity focused on a NW-SE line along the trend of an inflating dike. A series of drumbeat earthquakes occurred in the early weeks of the eruption, indicating further magma transport through the same dike system. During the six months following the onset of the eruption, the otherwise quiescent region 1 to 5 km below sea level centered beneath the summit became seismically active with two groups of earthquakes, differentiated by frequency content. The deep longer-period earthquakes occurred during the eruption and are interpreted as resulting from the movement of magma toward the summit, and the post-eruptive shorter-period earthquakes may be due to the relaxation of an emptied magma tube. The seismicity subsequently returned to its normal background rates and patterns. Copyright 2011 by the American Geophysical Union.

  5. Production of the Type IV Secretion System Differs among Brucella Species as Revealed with VirB5- and VirB8-Specific Antisera

    OpenAIRE

    Rouot, Bruno; Alvarez-Martinez, Maria-Teresa; Marius, Carine; Menanteau, Pierrette; Guilloteau, Laurence; Boigegrain, Rose-Anne; Zumbihl, Robert; O'Callaghan, David; Domke, Natalie; Baron, Christian

    2003-01-01

    Expression of the virB operon, encoding the type IV secretion system required for Brucella suis virulence, occurred in the acidic phagocytic vacuoles of macrophages and could be induced in minimal medium at acidic pH values. To analyze the production of VirB proteins, polyclonal antisera against B. suis VirB5 and VirB8 were generated. Western blot analysis revealed that VirB5 and VirB8 were detected after 3 h in acidic minimal medium and that the amounts increased after prolonged incubation. ...

  6. Optical signatures of dissolved organic matter from the Endeavour and Axial vent fields

    Science.gov (United States)

    Stubbins, A.; Butterfield, D.; Rossel, P. E.; Dittmar, T.

    2011-12-01

    Recent studies have revealed that hydrothermal systems in the deep ocean are both sources and processors of dissolved organic matter (DOM). Sub-floor stores of fossil organic carbon may be exported to the deep ocean directly adding fossil C to the deep ocean dissolved organic carbon (DOC) pool and altering its apparent age. Fossil methane and carbon dioxide are also exported from vents. These C sources can then be utilized by chemotrophs and later enter the DOM pool as fossil DOC. Finally, when deep ocean waters are entrained into vent systems, the resultant heating may alter the chemical and optical properties of the DOM in these deep ocean waters. Dissolved organic matter (DOM) samples were collected from vents ranging in temperature from 10 to over 300 degrees centigrade across the Endeavour and Axial fields along the Juan de Fuca ridge. Elevated DOC and protein-like fluorescence reveal the vents to fuel the chemotrophic production of organic matter either in the adjacent water column or local sediments. High DOC and increased humic-like fluorescence in the hottest vent fluids, suggests the thermal degradation of DOM either from buried fossil sources or the entrainment of local waters enriched in DOC due to chemotrophic productivity. Natural and radio-carbon analyses are underway and will provide further insight into the ultimate source of this colored, fluorescent hydrothermal DOM.

  7. System biology analysis of long-term effect and mechanism of Bufei Yishen on COPD revealed by system pharmacology and 3-omics profiling

    Science.gov (United States)

    Li, Jiansheng; Zhao, Peng; Yang, Liping; Li, Ya; Tian, Yange; Li, Suyun

    2016-01-01

    System pharmacology identified 195 potential targets of Bufei Yishen formula (BYF), and BYF was proven to have a short-term therapeutic effect on chronic obstructive pulmonary disease (COPD) rats previously. However, the long-term effect and mechanism of BYF on COPD is still unclear. Herein, we explored its long-term effect and underlying mechanism at system level. We administered BYF to COPD rats from week 9 to 20, and found that BYF could prevent COPD by inhibiting the inflammatory cytokines expression, protease-antiprotease imbalance and collagen deposition on week 32. Then, using transcriptomics, proteomics and metabolomics analysis, we identified significant regulated genes, proteins and metabolites in lung tissues of COPD and BYF-treated rats, which could be mainly attributed to oxidoreductase-antioxidant activity, focal adhesion, tight junction or lipid metabolism. Finally, based on the comprehensive analysis of system pharmacology target, transcript, protein and metabolite data sets, we found a number of genes, proteins, metabolites regulated in BYF-treated rats and the target proteins of BYF were involved in lipid metabolism, inflammatory response, oxidative stress and focal adhension. In conclusion, BYF exerts long-term therapeutic action on COPD probably through modulating the lipid metabolism, oxidative stress, cell junction and inflammatory response pathways at system level. PMID:27146975

  8. Comparative gene expression analysis among vocal learners (Bengalese finch and budgerigar and non-learners (quail and ring dove reveals variable cadherin expressions in the vocal system

    Directory of Open Access Journals (Sweden)

    Eiji eMatsunaga

    2011-04-01

    Full Text Available Birds use various vocalizations to communicate with one another, and some are acquired through learning. So far, three families of birds (songbirds, parrots, and hummingbirds have been identified as having vocal learning ability. Previously, we found that cadherins, a large family of cell-adhesion molecules, show vocal control-area-related expression in a songbird, the Bengalese finch. To investigate the molecular basis of evolution in avian species, we conducted comparative analysis of cadherin expressions in the vocal and other neural systems among vocal learners (Bengalese finch and budgerigar and a non-learner (quail and ring dove. The gene expression analysis revealed that cadherin expressions were more variable in vocal and auditory areas compared to vocally unrelated areas such as the visual areas among these species. Thus, it appears that such diverse cadherin expressions might have been related to generating species diversity in vocal behavior during the evolution of avian vocal learning. 

  9. A colloidal singularity reveals the crucial role of colloidal stability for nanomaterials in-vitro toxicity testing: nZVI-microalgae colloidal system as a case study.

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    Soledad Gonzalo

    Full Text Available Aggregation raises attention in Nanotoxicology due to its methodological implications. Aggregation is a physical symptom of a more general physicochemical condition of colloidal particles, namely, colloidal stability. Colloidal stability is a global indicator of the tendency of a system to reduce its net surface energy, which may be achieved by homo-aggregation or hetero-aggregation, including location at bio-interfaces. However, the role of colloidal stability as a driver of ENM bioactivity has received little consideration thus far. In the present work, which focuses on the toxicity of nanoscaled Fe° nanoparticles (nZVI towards a model microalga, we demonstrate that colloidal stability is a fundamental driver of ENM bioactivity, comprehensively accounting for otherwise inexplicable differential biological effects. The present work throws light on basic aspects of Nanotoxicology, and reveals a key factor which may reconcile contradictory results on the influence of aggregation in bioactivity of ENMs.

  10. The assembly of the halo system of the Milky Way as revealed by SDSS/SEGUE – The CEMP star connection

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    Carollo D.

    2012-02-01

    Full Text Available In recent years, massive new spectroscopic data sets, such as the over half million stellar spectra obtained during the course of SDSS (in particular its sub-survey SEGUE, have provided the quantitative detail required to formulate a coherent story of the assembly and evolution of the Milky Way. The disk and halo systems of our Galaxy have been shown to be both more complex, and more interesting, than previously thought. Here we concentrate on the halo system of the Milky Way. New data from SDSS/SEGUE has revealed that the halo system comprises at least two components, the inner halo and the outer halo, with demonstrably different characteristics (metallicity distributions, density distributions, kinematics, etc.. In addition to suggesting new ways to examine these data, the inner/outer halo dichotomy has enabled an understanding of at least one long-standing observational result, the increase of the fraction of carbon-enhanced metal-poor (CEMP stars with decreasing metallicity.

  11. Three-dimensional brain atlas of pygmy squid, Idiosepius paradoxus, revealing the largest relative vertical lobe system volume among the cephalopods.

    Science.gov (United States)

    Koizumi, Motoki; Shigeno, Shuichi; Mizunami, Makoto; Tanaka, Nobuaki K

    2016-07-01

    Cephalopods have the largest and most complex nervous system of all invertebrates, and the brain-to-body weight ratio exceeds those of most fish and reptiles. The brain is composed of lobe units, the functions of which have been studied through surgical manipulation and electrical stimulation. However, how information is processed in each lobe for the animal to make a behavioral decision has rarely been investigated. To perform such functional analyses, it is necessary to precisely describe how brain lobes are spatially organized and mutually interconnected as a whole. We thus made three-dimensional digital brain atlases of both hatchling and juvenile pygmy squid, Idiosepius paradoxus. I. paradoxus is the smallest squid and has a brain small enough to scan as a whole region in the field-of-view of a low-magnification laser scan microscope objective. Precise analyses of the confocal images of the brains revealed one newly identified lobe and also that the relative volume of the vertical lobe system, the higher association center, in the pygmy squid represents the largest portion compared with the cephalopod species reported previously. In addition, principal component analyses of relative volumes of lobe complexes revealed that the organization of I. paradoxus brain is comparable to those of Decapodiformes species commonly used to analyze complex behaviors such as Sepia officinalis and Sepioteuthis sepioidea. These results suggest that the pygmy squid can be a good model to investigate the brain functions of coleoids utilizing physiological methods. J. Comp. Neurol. 524:2142-2157, 2016. © 2016 Wiley Periodicals, Inc. PMID:26663197

  12. Dysregulation of the descending pain system in temporomandibular disorders revealed by low-frequency sensory transcutaneous electrical nerve stimulation: a pupillometric study.

    Science.gov (United States)

    Monaco, Annalisa; Cattaneo, Ruggero; Mesin, Luca; Ortu, Eleonora; Giannoni, Mario; Pietropaoli, Davide

    2015-01-01

    Using computerized pupillometry, our previous research established that the autonomic nervous system (ANS) is dysregulated in patients suffering from temporomandibular disorders (TMDs), suggesting a potential role for ANS dysfunction in pain modulation and the etiology of TMD. However, pain modulation hypotheses for TMD are still lacking. The periaqueductal gray (PAG) is involved in the descending modulation of defensive behavior and pain through μ, κ, and δ opioid receptors. Transcutaneous electrical nerve stimulation (TENS) has been extensively used for pain relief, as low-frequency stimulation can activate µ receptors. Our aim was to use pupillometry to evaluate the effect of low-frequency TENS stimulation of μ receptors on opioid descending pathways in TMD patients. In accordance with the Research Diagnostic Criteria for TMD, 18 females with myogenous TMD and 18 matched-controls were enrolled. All subjects underwent subsequent pupillometric evaluations under dark and light conditions before, soon after (end of stimulation) and long after (recovery period) sensorial TENS. The overall statistics derived from the darkness condition revealed no significant differences in pupil size between cases and controls; indeed, TENS stimulation significantly reduced pupil size in both groups. Controls, but not TMD patients, displayed significant differences in pupil size before compared with after TENS. Under light conditions, TMD patients presented a smaller pupil size compared with controls; the pupil size was reduced only in the controls. Pupil size differences were found before and during TENS and before and after TENS in the controls only. Pupillometry revealed that stimulating the descending opioid pathway with low-frequency sensory TENS of the fifth and seventh pairs of cranial nerves affects the peripheral target. The TMD patients exhibited a different pattern of response to TENS stimulation compared with the controls, suggesting that impaired modulation of the

  13. Dysregulation of the descending pain system in temporomandibular disorders revealed by low-frequency sensory transcutaneous electrical nerve stimulation: a pupillometric study.

    Directory of Open Access Journals (Sweden)

    Annalisa Monaco

    Full Text Available Using computerized pupillometry, our previous research established that the autonomic nervous system (ANS is dysregulated in patients suffering from temporomandibular disorders (TMDs, suggesting a potential role for ANS dysfunction in pain modulation and the etiology of TMD. However, pain modulation hypotheses for TMD are still lacking. The periaqueductal gray (PAG is involved in the descending modulation of defensive behavior and pain through μ, κ, and δ opioid receptors. Transcutaneous electrical nerve stimulation (TENS has been extensively used for pain relief, as low-frequency stimulation can activate µ receptors. Our aim was to use pupillometry to evaluate the effect of low-frequency TENS stimulation of μ receptors on opioid descending pathways in TMD patients. In accordance with the Research Diagnostic Criteria for TMD, 18 females with myogenous TMD and 18 matched-controls were enrolled. All subjects underwent subsequent pupillometric evaluations under dark and light conditions before, soon after (end of stimulation and long after (recovery period sensorial TENS. The overall statistics derived from the darkness condition revealed no significant differences in pupil size between cases and controls; indeed, TENS stimulation significantly reduced pupil size in both groups. Controls, but not TMD patients, displayed significant differences in pupil size before compared with after TENS. Under light conditions, TMD patients presented a smaller pupil size compared with controls; the pupil size was reduced only in the controls. Pupil size differences were found before and during TENS and before and after TENS in the controls only. Pupillometry revealed that stimulating the descending opioid pathway with low-frequency sensory TENS of the fifth and seventh pairs of cranial nerves affects the peripheral target. The TMD patients exhibited a different pattern of response to TENS stimulation compared with the controls, suggesting that impaired

  14. Ground-based thermography of fluvial systems at low and high discharge reveals potential complex thermal heterogeneity driven by flow variation and bioroughness

    Science.gov (United States)

    Cardenas, M.B.; Harvey, J.W.; Packman, A.I.; Scott, D.T.

    2008-01-01

    Temperature is a primary physical and biogeochemical variable in aquatic systems. Field-based measurement of temperature at discrete sampling points has revealed temperature variability in fluvial systems, but traditional techniques do not readily allow for synoptic sampling schemes that can address temperature-related questions with broad, yet detailed, coverage. We present results of thermal infrared imaging at different stream discharge (base flow and peak flood) conditions using a handheld IR camera. Remotely sensed temperatures compare well with those measured with a digital thermometer. The thermal images show that periphyton, wood, and sandbars induce significant thermal heterogeneity during low stages. Moreover, the images indicate temperature variability within the periphyton community and within the partially submerged bars. The thermal heterogeneity was diminished during flood inundation, when the areas of more slowly moving water to the side of the stream differed in their temperature. The results have consequences for thermally sensitive hydroelogical processes and implications for models of those processes, especially those that assume an effective stream temperature. Copyright ?? 2008 John Wiley & Sons, Ltd.

  15. Illumina MiSeq sequencing reveals long-term impacts of single-walled carbon nanotubes on microbial communities of wastewater treatment systems.

    Science.gov (United States)

    Qu, Yuanyuan; Zhang, Xuwang; Shen, Wenli; Ma, Qiao; You, Shengnan; Pei, Xiaofang; Li, Shuzhen; Ma, Fang; Zhou, Jiti

    2016-07-01

    In this study, phenol wastewater treatment systems treated with different concentrations of single-walled carbon nanotubes (SWCNTs) (0-3.5g/L) were exposed to phenol and carbon nanotubes (CNTs) shock loadings to investigate the long-term impacts of SWCNTs on microbial communities. Phenol removal remained high efficiency (>98%) in SWCNTs-treated groups but decreased in non-treated group (85.1±1.9%) when exposed to high concentration of phenol (500mg/L). However, secondary dosing of SWCNTs in SWCNTs-treated groups would decrease the phenol removal efficiency. Illumina MiSeq sequencing revealed that the diversity, richness and structure of microbial communities were shifted under phenol shock loading, especially under high phenol concentration, but not under CNTs shock loading. In response to phenol and CNTs shock loadings, Rudaea, Burkholderia, Sphingomonas, Acinetobacter, Methylocystis and Thauera became dominant genera, which should be involved in phenol removal. These results suggested that a proper amount of SWCNTs might have positive effects on phenol wastewater treatment systems. PMID:27017131

  16. Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway.

    Directory of Open Access Journals (Sweden)

    Yujiro Tanaka

    Full Text Available Stress-inducible transcription factors play a pivotal role in cellular adaptation to environment to maintain homeostasis and integrity of the genome. Activating transcription factor 3 (ATF3 is induced by a variety of stress and inflammatory conditions and is over-expressed in many kinds of cancer cells. However, molecular mechanisms underlying pleiotropic functions of ATF3 have remained elusive. Here we employed systems analysis to identify genome-wide targets of ATF3 that is either induced by an alkylating agent methyl methanesulfonate (MMS or over-expressed in a prostate tumour cell line LNCaP. We show that stress-induced and cancer-associated ATF3 is recruited to 5,984 and 1,423 targets, respectively, in the human genome, 89% of which are common. Notably, ATF3 targets are highly enriched for not only ATF/CRE motifs but also binding sites of several other stress-inducible transcription factors indicating an extensive network of stress response factors in transcriptional regulation of target genes. Further analysis of effects of ATF3 knockdown on these targets revealed that stress-induced ATF3 regulates genes in metabolic pathways, cell cycle, apoptosis, cell adhesion, and signalling including insulin, p53, Wnt, and VEGF pathways. Cancer-associated ATF3 is involved in regulation of distinct sets of genes in processes such as calcium signalling, Wnt, p53 and diabetes pathways. Notably, stress-induced ATF3 binds to 40% of p53 targets and activates pro-apoptotic genes such as TNFRSF10B/DR5 and BBC3/PUMA. Cancer-associated ATF3, by contrast, represses these pro-apoptotic genes in addition to CDKN1A/p21. Taken together, our data reveal an extensive network of stress-inducible transcription factors and demonstrate that ATF3 has opposing, cell context-dependent effects on p53 target genes in DNA damage response and cancer development.

  17. Nuclear and mitochondrial DNA sequence data reveal the evolutionary history of Barbus (Cyprinidae) in the ancient lake systems of the Balkans.

    Science.gov (United States)

    Marková, Silvia; Sanda, Radek; Crivelli, Alain; Shumka, Spase; Wilson, Iain F; Vukić, Jasna; Berrebi, Patrick; Kotlík, Petr

    2010-05-01

    Freshwater fauna of ancient lakes frequently contain endemic taxa thought to have originated during the long existence of these lakes, yet uncertainties remain as to whether they represent distinct genetic lineages with respect to more widespread relatives and to the relative roles of isolation and dispersal in their evolution. Phylogenetic analyses of sequence variation at nuclear and mitochondrial genes were used to examine these issues for the freshwater fish genus Barbus in two European ancient lake systems on the Balkan Peninsula. The nuclear and mitochondrial data yielded concordant phylogeographic patterns though incomplete sorting of nuclear haplotypes between some mitochondrial clades was detected. The distributions of two currently recognized species investigated here do not match the distributions of evolutionary lineages revealed by phylogenetic analyses. The Prespa barbel, Barbus prespensis, is not endemic to the lakes Prespa as previously thought but is instead found to be widespread in the south-eastern Adriatic Sea basin, with a distribution largely corresponding to the basin of the now extinct Lake Maliq historically connected with Lake Prespa. On the other hand, a cryptic phylogenetic subdivision in a widespread species, B. rebeli, was discovered to be more distant from B. rebeli than from other Barbus species and to be endemic to the system of connected lakes Ohrid and Shkodra. The division coincides with the hydrogeographical boundary delimiting distributions of other freshwater fishes, and we suggest that this newly discovered evolutionary lineage represents a distinct species. These findings support the emerging pattern that endemic taxa have evolved not through isolation of individual lakes, but in systems of currently and historically interconnected lakes and their wider basins. PMID:20139017

  18. A comprehensive set of elemental abundances in damped Ly-alpha systems: revealing the nature of these high-redshift galaxies

    CERN Document Server

    Dessauges-Zavadsky, M; Prochaska, J X; D'Odorico, S; Matteucci, F

    2003-01-01

    By combining our UVES-VLT spectra of a sample of four damped Ly-alpha systems (DLAs) toward the quasars Q0100+13, Q1331+17, Q2231-00 and Q2343+12 with the existing HIRES-Keck spectra, we covered the total spectral range from 3150 to 10000 A for the four quasars. This large wavelength coverage and the high quality of the spectra allowed us to measure the column densities of up to 21 ions, namely of 15 elements - N, O, Mg, Al, Si, P, S, Cl, Ar, Ti, Cr, Mn, Fe, Ni, Zn. Such a large amount of information is necessary to constrain the photoionization and dust depletion effects, two important steps in order to derive the intrinsic chemical abundance patterns of DLAs. We evaluated the photoionization effects with the help of the Al+/Al++, Fe+/Fe++, N0/N+ and Ar/Si,S ratios, and computed dust corrections. Our analysis revealed that the DLA toward Q2343+12 requires important ionization corrections. The access to the complete series of relatively robust intrinsic elemental abundances in the other three DLAs allowed us ...

  19. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect.

    Science.gov (United States)

    Standage, Daniel S; Berens, Ali J; Glastad, Karl M; Severin, Andrew J; Brendel, Volker P; Toth, Amy L

    2016-04-01

    Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects. PMID:26859767

  20. Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries.

    Science.gov (United States)

    Hong, Young-Shick; Martinez, Agathe; Liger-Belair, Gérard; Jeandet, Philippe; Nuzillard, Jean-Marc; Cilindre, Clara

    2012-10-01

    Botrytis cinerea is a fungal plant pathogen of grape berries, leading to economic and quality losses in wine production. The global metabolite changes induced by B. cinerea infection in grape have not been established to date, even though B. cinerea infection is known to cause significant changes in chemicals or metabolites. In order to better understand metabolic mechanisms linked to the infection process and to identify the metabolites associated with B. cinerea infection, (1)H NMR spectroscopy was used in global metabolite profiling and multivariate statistical analysis of berries from healthy and botrytized bunches. Pattern recognition methods, such as principal component analysis, revealed clear metabolic discriminations between healthy and botrytized berries of botrytized bunches and healthy berries of healthy bunches. Significantly high levels of proline, glutamate, arginine, and alanine, which are accumulated upon plant stress, were found in healthy and botrytized berries of botrytized bunches. Moreover, largely degraded phenylpropanoids, flavonoid compounds, and sucrose together with markedly produced glycerol, gluconic acid, and succinate, all being directly associated with B. cinerea growth, were only found in botrytized berries of botrytized bunches. This study reports that B. cinerea infection causes significant metabolic changes in grape berry and highlights that both the metabolic perturbations associated with the plant defence system and those directly derived from fungal pathogen growth should be considered to better understand the interaction between metabolic variation and biotic pathogen stress in plants. PMID:22945941

  1. The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase

    Science.gov (United States)

    Flayhan, Ali; Bergé, Célia; Baïlo, Nathalie; Doublet, Patricia; Bayliss, Richard; Terradot, Laurent

    2015-01-01

    Bacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are translocated by the Dot/Icm type IV secretion system (T4SS) of several Legionella pneumophila strains. We present the crystal structures of an active fragment of the LegK4 protein in apo and substrate-bound states. The structure of LegK41–445 reveals a eukaryotic-like kinase domain flanked by a novel cap domain and a four-helix bundle. The protein self-assembles through interactions mediated by helices αF and αG that generate a dimeric interface not previously observed in a protein kinase. The helix αG is displaced compared to previous kinase structures, and its role in stabilization of the activation loop is taken on by the dimerisation interface. The apo-form of the protein has an open conformation with a disordered P-loop but a structured activation segment in absence of targeted phosphorylation. The nucleotide-binding site of LegK4 contains an unusual set of residues that mediate non-canonical interactions with AMP-PNP. Nucleotide binding results in limited changes in the active site, suggesting that LegK4 constitutive kinase activity does not depend on phosphorylation of the activation loop but on the stabilizing effects of the dimer. PMID:26419332

  2. Pyrosequencing Reveals Bacterial Communities in Unchlorinated Drinking Water Distribution System: An Integral Study of Bulk Water, Suspended Solids, Loose Deposits, and Pipe Wall Biofilm

    KAUST Repository

    Liu, G.

    2014-05-20

    The current understanding of drinking water distribution system (DWDS) microbiology is limited to pipe wall biofilm and bulk water; the contributions of particle-associated bacteria (from suspended solids and loose deposits) have long been neglected. Analyzing the composition and correlation of bacterial communities from different phases helped us to locate where most of the bacteria are and understand the interactions among these phases. In the present study, the bacteria from four critical phases of an unchlorinated DWDS, including bulk water, pipe wall biofilm, suspended solids, and loose deposits, were quantified and identified by adenosine triphosphate analysis and pyrosequencing, respectively. The results showed that the bulk water bacteria (including the contribution of suspended solids) contributed less than 2% of the total bacteria. The bacteria associated with loose deposits and pipe wall biofilm that accumulated in the DWDS accounted for over 98% of the total bacteria, and the contributions of bacteria in loose deposits and pipe wall biofilm were comparable. Depending on the amount of loose deposits, its contribution can be 7-fold higher than the pipe wall biofilm. Pyrosequencing revealed relatively stable bacterial communities in bulk water, pipe wall biofilm, and suspended solids throughout the distribution system; however, the communities present in loose deposits were dependent on the amount of loose deposits locally. Bacteria within the phases of suspended solids, loose deposits, and pipe wall biofilm were similar in phylogenetic composition. The bulk water bacteria (dominated by Polaromonas spp.) were clearly different from the bacteria from the other three phases (dominated by Sphingomonas spp.). This study highlighted that the integral DWDS ecology should include contributions from all of the four phases, especially the bacteria harbored by loose deposits. The accumulation of loose deposits and the aging process create variable microenvironments

  3. Postembryonic lineages of the Drosophila ventral nervous system: Neuroglian expression reveals the adult hemilineage associated fiber tracts in the adult thoracic neuromeres.

    Science.gov (United States)

    Shepherd, David; Harris, Robin; Williams, Darren W; Truman, James W

    2016-09-01

    During larval life most of the thoracic neuroblasts (NBs) in Drosophila undergo a second phase of neurogenesis to generate adult-specific neurons that remain in an immature, developmentally stalled state until pupation. Using a combination of MARCM and immunostaining with a neurotactin antibody, Truman et al. (2004; Development 131:5167-5184) identified 24 adult-specific NB lineages within each thoracic hemineuromere of the larval ventral nervous system (VNS), but because of the neurotactin labeling of lineage tracts disappearing early in metamorphosis, they were unable extend the identification of these lineages into the adult. Here we show that immunostaining with an antibody against the cell adhesion molecule neuroglian reveals the same larval secondary lineage projections through metamorphosis and bfy identifying each neuroglian-positive tract at selected stages we have traced the larval hemilineage tracts for all three thoracic neuromeres through metamorphosis into the adult. To validate tract identifications we used the genetic toolkit developed by Harris et al. (2015; Elife 4) to preserve hemilineage-specific GAL4 expression patterns from larval into the adult stage. The immortalized expression proved a powerful confirmation of the analysis of the neuroglian scaffold. This work has enabled us to directly link the secondary, larval NB lineages to their adult counterparts. The data provide an anatomical framework that 1) makes it possible to assign most neurons to their parent lineage and 2) allows more precise definitions of the neuronal organization of the adult VNS based in developmental units/rules. J. Comp. Neurol. 524:2677-2695, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:26878258

  4. Fetal heart rate variability reveals differential dynamics in the intrauterine development of the sympathetic and parasympathetic branches of the autonomic nervous system

    International Nuclear Information System (INIS)

    The aim of this study was to investigate the hypothesis that fetal beat-to-beat heart rate variability (fHRV) displays the different time scales of sympatho-vagal development prior to and after 32 weeks of gestation (wks GA). Ninety-two magnetocardiograms of singletons with normal courses of pregnancy between 24 + 1 and 41 + 6 wks GA were studied. Heart rate patterns were either quiet/non-accelerative (fHRP I) or active/accelerative (fHRP II) and recording quality sufficient for fHRV. The sample was divided into the GA groups 32 wks GA. Linear parameters of fHRV were calculated: mean heart rate (mHR), SDNN and RMSSD of normal-to-normal interbeat intervals, power in the low (0.04–0.15 Hz) and high frequency range (0.15–0.4 Hz) and the ratios SDNN/RMSSD and LF/HF as markers for sympatho-vagal balance. fHRP I is characterized by decreasing SDNN/RMSSD, LF/HF and mHR. The decrease is more pronounced 32 wks GA. LF/HF increases in fHRP II during the first half of the third trimester. Non-accelerative fHRP are indicative of parasympathetic dominance >32 wks GA. In contrast, the sympathetic accentuation during accelerative fHRP is displayed in the interrelations between mHR, SDNN and SDNN/RMSSD. Prior to 32 wks GA, fHRV reveals the increasing activity of the respective branches of the autonomic nervous system differentiating the types of fHRP

  5. Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

    Directory of Open Access Journals (Sweden)

    Redondo-Nieto Miguel

    2013-01-01

    Full Text Available Abstract Background Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. Results Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. Conclusions The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.

  6. Nitrogen cycling in Yellowstone National Park thermal features: using gene expression to reveal ecological function

    Science.gov (United States)

    Lafree, S. T.; Burton, M. S.; Meyer-Dombard, D. R.

    2010-12-01

    Studies of biodiversity, metabolic strategies, and functional ecology in modern hydrothermal systems have the potential to provide insight into the metabolism and evolution of life. The geochemical and microbial diversity present at Yellowstone National Park (YNP), Wyoming, USA, makes it an ideal place for studying the functional ecology and metabolic processes of prokaryotic organisms. While much work in terrestrial hydrothermal features is focused on phylogenetic and geochemical analyses, a few recent investigations in YNP and other hydrothermal areas have focused on “gene hunting”: screening thermal sediment and biofilm samples for the presence of genes utilized in specific metabolic processes [2, 3, 6, 7, 8]. Although research has evaluated and confirmed the presence of many of these genes in various thermophilic microbial communities, the existence of a gene in the DNA of an organism does not verify its use, and few researchers have done work to confirm the utilization (expression) of the genes discovered in thermal samples [1, 6, 7, 8]. Disequilibrium between reduced hydrothermal fluid of YNP thermal features and the atmosphere provides a copious source of potential energy to be harnessed through microbial metabolic processes, with NO3- and NO2- serving as the preferred electron acceptors and top energy sources after O2 [4, 5]. Consequentially, nitrogen cycling likely plays a vital role in microbial metabolic processes, as well as nutrient availability. This study explores the presence and utilization of functional genes that are key in steps of the nitrogen cycle, such as nitrogen fixation (NifH), denitrification (nirKS), and ammonia oxidation (amoA). Both DNA and RNA were extracted from thermal sediment and streamer biofilm communities collected in the chemosynthetic zone of various thermal features of the Sentinel Meadows Group in Lower Geyser Basin, YNP. Extracted DNA and reverse transcribed RNA (cDNA) were amplified using the polymerase chain

  7. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    Science.gov (United States)

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  8. Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changes.

    Science.gov (United States)

    Oberbach, Andreas; Blüher, Matthias; Wirth, Henry; Till, Holger; Kovacs, Peter; Kullnick, Yvonne; Schlichting, Nadine; Tomm, Janina M; Rolle-Kampczyk, Ulrike; Murugaiyan, Jayaseelan; Binder, Hans; Dietrich, Arne; von Bergen, Martin

    2011-10-01

    , RBP4, PEDF, GLN, and C18:2 showed the strongest correlation to changes in body fat mass. The combined serum proteomic and metabolomic profiling reveals a link between the complement system and obesity and identifies both novel (C3b, CLU, VDBP, and all metabolites) and confirms previously discovered markers (PEDF, RBP4, C3, ATIII, and SAP) of body fat mass changes. PMID:21823675

  9. Quaternary Morphodynamics of Fluvial Dispersal Systems Revealed: The Fly River, PNG, and the Sunda Shelf, SE Asia, simulated with the Massively Parallel GPU-based Model 'GULLEM'

    Science.gov (United States)

    Aalto, R. E.; Lauer, J. W.; Darby, S. E.; Best, J.; Dietrich, W. E.

    2015-12-01

    During glacial-marine transgressions vast volumes of sediment are deposited due to the infilling of lowland fluvial systems and shallow shelves, material that is removed during ensuing regressions. Modelling these processes would illuminate system morphodynamics, fluxes, and 'complexity' in response to base level change, yet such problems are computationally formidable. Environmental systems are characterized by strong interconnectivity, yet traditional supercomputers have slow inter-node communication -- whereas rapidly advancing Graphics Processing Unit (GPU) technology offers vastly higher (>100x) bandwidths. GULLEM (GpU-accelerated Lowland Landscape Evolution Model) employs massively parallel code to simulate coupled fluvial-landscape evolution for complex lowland river systems over large temporal and spatial scales. GULLEM models the accommodation space carved/infilled by representing a range of geomorphic processes, including: river & tributary incision within a multi-directional flow regime, non-linear diffusion, glacial-isostatic flexure, hydraulic geometry, tectonic deformation, sediment production, transport & deposition, and full 3D tracking of all resulting stratigraphy. Model results concur with the Holocene dynamics of the Fly River, PNG -- as documented with dated cores, sonar imaging of floodbasin stratigraphy, and the observations of topographic remnants from LGM conditions. Other supporting research was conducted along the Mekong River, the largest fluvial system of the Sunda Shelf. These and other field data provide tantalizing empirical glimpses into the lowland landscapes of large rivers during glacial-interglacial transitions, observations that can be explored with this powerful numerical model. GULLEM affords estimates for the timing and flux budgets within the Fly and Sunda Systems, illustrating complex internal system responses to the external forcing of sea level and climate. Furthermore, GULLEM can be applied to most ANY fluvial system to

  10. Snap shots from a photo competition: what does it reveal about close-to-community providers, gender and power in health systems?

    Science.gov (United States)

    George, Asha; Theobald, Sally; Morgan, Rosemary; Hawkins, Kate; Molyneux, Sassy

    2015-01-01

    In this commentary, we discuss a photography competition, launched during the summer of 2014, to explore the everyday stories of how gender plays out within health systems around the world. While no submission fees were charged nor financial awards involved, the winning entries were exhibited at the Global Symposium on Health Systems Research in Cape Town, South Africa, in October 2014, with credits to the photographers involved. Anyone who had an experience of, or interest in, gender and health systems was invited to participate. Underlying the aims of the photo competition was a recognition of the importance of participation of community members, health workers and other non-academics in our research engagement and in venues where their perspectives are often missing. The competition elicited participation from a range of stakeholders engaged in health systems: professional photographers, project managers, donors, researchers, activists and community members. In total, 54 photos were submitted by 29 participants from 15 different nationalities and country locations. We unpack what the photos suggest about gender and health systems and the pivotal role of community-level systems that support health, including that of close-to-community health providers. Three themes emerged: women active on the frontlines of service delivery and as primary unpaid carers, the visibility of men in gender and health systems and the inter-sectoral nature and intra-household dynamics of community health that embed close-to-community health providers. The question of who has the right to take and display images, under what contexts and for what purpose also permeated the photo competition. We reflect on how photos can be valuable representations of the worlds that we, health workers and health systems are embedded in. Photographs broaden our horizons by capturing and connecting us to subjects from afar in seemingly unmediated ways but also reflect the politics, values and subjectivities

  11. Controlled expression of nif and isc iron-sulfur protein maturation components reveals target specificity and limited functional replacement between the two systems.

    Science.gov (United States)

    Dos Santos, Patricia C; Johnson, Deborah C; Ragle, Brook E; Unciuleac, Mihaela-Carmen; Dean, Dennis R

    2007-04-01

    The nitrogen-fixing organism Azotobacter vinelandii contains at least two systems that catalyze formation of [Fe-S] clusters. One of these systems is encoded by nif genes, whose products supply [Fe-S] clusters required for maturation of nitrogenase. The other system is encoded by isc genes, whose products are required for maturation of [Fe-S] proteins that participate in general metabolic processes. The two systems are similar in that they include an enzyme for the mobilization of sulfur (NifS or IscS) and an assembly scaffold (NifU or IscU) upon which [Fe-S] clusters are formed. Normal cellular levels of the Nif system, which supplies [Fe-S] clusters for the maturation of nitrogenase, cannot also supply [Fe-S] clusters for the maturation of other cellular [Fe-S] proteins. Conversely, when produced at the normal physiological levels, the Isc system cannot supply [Fe-S] clusters for the maturation of nitrogenase. In the present work we found that such target specificity for IscU can be overcome by elevated production of NifU. We also found that NifU, when expressed at normal levels, is able to partially replace the function of IscU if cells are cultured under low-oxygen-availability conditions. In contrast to the situation with IscU, we could not establish conditions in which the function of IscS could be replaced by NifS. We also found that elevated expression of the Isc components, as a result of deletion of the regulatory iscR gene, improved the capacity for nitrogen-fixing growth of strains deficient in either NifU or NifS. PMID:17237162

  12. Revealing the deeper structure of the end-glacial Pärvie fault system in northern Sweden by seismic reflection profiling

    OpenAIRE

    O. Ahmadi; C. Juhlin; M. Ask; Lund, B.

    2015-01-01

    A new seismic reflection survey for imaging deeper levels of the end-glacial Parvie fault system in northern Sweden was acquired in June 2014. The Parvie fault system hosts the largest fault scarp so far documented in northern Scandinavia, both in terms of its length and calculated magnitude of the earthquake that generated it. Present-day microearthquakes occur along the length of the fault scarp on the eastern side of the scarp, in general agreement with an east-dipping main fault. In the c...

  13. A survey of the Pseudomonas syringae pv. tomato DC3000 type III secretion system effector repertoire reveals several effectors that are deleterious when expressed in Saccharomyces cerevisiae

    Science.gov (United States)

    The injection of nearly 30 effector proteins by the type III secretion system underlies the ability of Pseudomonas syringae pv. tomato strain DC3000 to cause disease in tomato and other host plants. The search for effector functions is complicated by redundancy within the repertoire and by plant R-g...

  14. The structure of the NasR transcription antiterminator reveals a one-component system with a NIT nitrate receptor coupled to an ANTAR RNA-binding effector.

    Science.gov (United States)

    Boudes, Marion; Lazar, Noureddine; Graille, Marc; Durand, Dominique; Gaidenko, Tatiana A; Stewart, Valley; van Tilbeurgh, Herman

    2012-08-01

    The nitrate- and nitrite-sensing NIT domain is present in diverse signal-transduction proteins across a wide range of bacterial species. NIT domain function was established through analysis of the Klebsiella oxytoca NasR protein, which controls expression of the nasF operon encoding enzymes for nitrite and nitrate assimilation. In the presence of nitrate or nitrite, the NasR protein inhibits transcription termination at the factor-independent terminator site in the nasF operon transcribed leader region. We present here the crystal structure of the intact NasR protein in the apo state. The dimeric all-helical protein contains a large amino-terminal NIT domain that associates two four-helix bundles, and a carboxyl-terminal ANTAR (AmiR and NasR transcription antitermination regulator) domain. The analysis reveals unexpectedly that the NIT domain is structurally similar to the periplasmic input domain of the NarX two-component sensor that regulates nitrate and nitrite respiration. This similarity suggests that the NIT domain binds nitrate and nitrite between two invariant arginyl residues located on adjacent alpha helices, and results from site-specific mutagenesis showed that these residues are critical for NasR function. The resulting structural movements in the NIT domain would provoke an active configuration of the ANTAR domains necessary for specific leader mRNA binding. PMID:22690729

  15. Revealing Exo-Zody and Exo-Planets from Solar System Dust Measurements: ALADDIN-2 for the Solar Power Sail Mission

    Science.gov (United States)

    Yano, Hajime; Hirai, Takayuki

    2016-07-01

    The dust structure of our Solar System provides a benchmark information of dust disks of other exo-planetary systems in general, just like the Sun as the closest main sequence G-star that we can study with the most details. Heliocentric dust distributions and gravitational and orbital interactions with planets such as mean motion resonances (MMRs) of dust flux of our Solar System are what we can transfer the knowledge of our Solar System dust apply to infer anisotropic exo-zodiacal brightness, or spatial structures within a exo-planetary dust disks with information about potentially embedded planets inside. In the coming era of disk resolved observations by ALMA, TMT and other new telescopes, we will be able to apply what we find in the Solar System to the rest of planetary systems. In 2010-11, the IKAROS solar sail spacecraft carried the ALADDIN large area dust detector array to study large meteoroids between the Earth and Venus orbits. Yano et al. directly detected both the Earth's and Venus' MMRs dust structures, being consistent with numerical simulations that predict the existence of such local enhancements of dust distribution around these terrestrial planets, as well as Neptune. JAXA's Solar Power Sail mission plans to carry even larger dust detector inherited the technology onboard IKAROS, namely ALADDIN-2 in order to search for such MMRs in the Mars and Jupiter orbits, as predicted by Kuchner et al.(2000), in addition to make a continuous measurement of large dust flux from 1.0 to 5.2 AU crossing the main asteroid belt up to Jupiter Trojan region. It is also noted that recent reanalysis of the Pioneer 10 and 11 photo polarimeter data suggests a small enhancement of the brightness towards the anti-solar direction near Jupiter the largest planet of our Solar System, implying a possible existence of a dust belt related to the planet. The spatial density of dust particles directly measured by the ALADDIN-2 will provide a more conclusive and direct proof due to

  16. The gnotobiotic brine shrimp (Artemia franciscana) model system reveals that the phenolic compound pyrogallol protects against infection through its prooxidant activity.

    Science.gov (United States)

    Baruah, Kartik; Duy Phong, Ho Phuong Pham; Norouzitallab, Parisa; Defoirdt, Tom; Bossier, Peter

    2015-12-01

    The phenolic compound pyrogallol is the functional unit of many polyphenols and currently there has been a growing interest in using this compound in human and animal health owing to its health-promoting effects. The biological actions of pyrogallol moiety (and polyphenols) in inducing health benefitting effects have been studied; however, the mechanisms of action remain unclear yet. Here, we aimed at unravelling the underlying mechanism of action behind the protective effects of pyrogallol against bacterial infection by using the gnotobiotically-cultured brine shrimp Artemia franciscana and pathogenic bacteria Vibrio harveyi as host-pathogen model system. The gnotobiotic test system represents an exceptional system for carrying out such studies because it eliminates any possible interference of microbial communities (naturally present in the experimental system) in mechanistic studies and furthermore facilitates the interpretation of the results in terms of a cause effect relationship. We provided clear evidences suggesting that pyrogallol pretreament, at an optimum concentration, induced protective effects in the brine shrimp against V. harveyi infection. By pretreating brine shrimp with pyrogallol in the presence or absence of an antioxidant enzyme mixture (catalase and superoxide dismutase), we showed that the Vibrio-protective effect of the compound was caused by its prooxidant action (e.g. generation of hydrogen peroxide, H2O2). We showed further that generation of prooxidant is linked to the induction of heat shock protein Hsp70, which is involved in eliciting the prophenoloxidase and transglutaminase immune responses. The ability of pyrogallol to induce protective immunity makes it a potential natural protective agent that might be a potential preventive modality for different host-pathogen systems. PMID:26459033

  17. Accuracy of diagnostic heat and moisture budgets using SESAME-79 field data as revealed by observing system simulation experiments. [Severe Environmental Storm and Mesoscale Experiment

    Science.gov (United States)

    Kuo, Y.-H.; Anthes, R. A.

    1984-01-01

    Observing system simulation experiments are used to investigate the accuracy of diagnostic heat and moisture budgets which employ the AVE-SESAME 1979 data. The time-including, four-dimensional data set of a mesoscale model is used to simulate rawinsonde observations from AVE-SESAME 1979. The 5 C/day (heat budget) and 2 g/kg per day (moisture budget) magnitudes of error obtained indicate difficulties in the diagnosis of the heating rate in weak convective systems. The influences exerted by observational frequency, objective analysis, observational density, vertical interpolation, and observational errors on the budget are also studied, and it is found that the temporal and spatial resolution of the SESAME regional network is marginal for diagnosing convective effects on a horizontal time scale of 550 x 550 km.

  18. Revealing the deeper structure of the end-glacial Pärvie fault system in northern Sweden by seismic reflection profiling

    OpenAIRE

    O. Ahmadi; C. Juhlin; M. Ask; Lund, B.

    2015-01-01

    Fault scarps that extend up to 155 km and have offsets of tens of meters at the surface are present in the northern parts of Finland, Norway and Sweden. These fault scarps are inferred to have formed during earthquakes with magnitudes up to 8 at the time of the last deglaciation. The Pärvie fault system represents the largest earthquake so far documented in northern Scandina...

  19. From Data towards Knowledge: Revealing the Architecture of Signaling Systems by Unifying Knowledge Mining and Data Mining of Systematic Perturbation Data

    OpenAIRE

    Songjian Lu; Bo Jin; L Ashley Cowart; Xinghua Lu

    2013-01-01

    Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically derive knowledge of a cellular signaling system at a conceptual level from systematic perturbation-response data. In this study, we explored a framework that unifies knowledge mining and data mining approaches towards the goal. The framework consists of the...

  20. A Systems Biology Approach Reveals the Dose- and Time-Dependent Effect of Primary Human Airway Epithelium Tissue Culture After Exposure to Cigarette Smoke In Vitro

    OpenAIRE

    Carole Mathis; Stephan Gebel; Carine Poussin; Vincenzo Belcastro; Alain Sewer; Dirk Weisensee; Arnd Hengstermann; Sam Ansari; Sandra Wagner; Peitsch, Manuel C; Julia Hoeng

    2015-01-01

    To establish a relevant in vitro model for systems toxicology-based mechanistic assessment of environmental stressors such as cigarette smoke (CS), we exposed human organotypic bronchial epithelial tissue cultures at the air liquid interface (ALI) to various CS doses. Previously, we compared in vitro gene expression changes with published human airway epithelia in vivo data to assess their similarities. Here, we present a follow-up evaluation of these in vitro transcriptomics data, using comp...

  1. A colloidal singularity reveals the crucial role of colloidal stability for nanomaterials in-vitro toxicity testing: nZVI-microalgae colloidal system as a case study

    OpenAIRE

    Gonzalo, Soledad; Pulido-Reyes, Gerardo; Fernández-Piñas, Francisca; Bonzongo, Jean Claude; Leganés, Francisco; Rosal, Roberto; García-Calvo, Eloy; Rodea-Palomares, Ismael

    2014-01-01

    Aggregation raises attention in Nanotoxicology due to its methodological implications. Aggregation is a physical symptom of a more general physicochemical condition of colloidal particles, namely, colloidal stability. Colloidal stability is a global indicator of the tendency of a system to reduce its net surface energy, which may be achieved by homo-aggregation or hetero-aggregation, including location at bio-interfaces. However, the role of colloidal stability as a driver of ENM bioactivity ...

  2. Tissue-specific root ion profiling reveals essential roles of the CAX and ACA calcium transport systems in response to hypoxia in Arabidopsis.

    Science.gov (United States)

    Wang, Feifei; Chen, Zhong-Hua; Liu, Xiaohui; Colmer, Timothy David; Zhou, Meixue; Shabala, Sergey

    2016-06-01

    Waterlogging is a major abiotic stress that limits the growth of plants. The crucial role of Ca(2+) as a second messenger in response to abiotic and biotic stimuli has been widely recognized in plants. However, the physiological and molecular mechanisms of Ca(2+) distribution within specific cell types in different root zones under hypoxia is poorly understood. In this work, whole-plant physiological and tissue-specific Ca(2+) changes were studied using several ACA (Ca(2+)-ATPase) and CAX (Ca(2+)/proton exchanger) knock-out Arabidopsis mutants subjected to waterlogging treatment. In the wild-type (WT) plants, several days of hypoxia decreased the expression of ACA8, CAX4, and CAX11 by 33% and 50% compared with the control. The hypoxic treatment also resulted in an up to 11-fold tissue-dependent increase in Ca(2+) accumulation in root tissues as revealed by confocal microscopy. The increase was much higher in stelar cells in the mature zone of Arabidopsis mutants with loss of function for ACA8, ACA11, CAX4, and CAX11 In addition, a significantly increased Ca(2+) concentration was found in the cytosol of stelar cells in the mature zone after hypoxic treatment. Three weeks of waterlogging resulted in dramatic loss of shoot biomass in cax11 plants (67% loss in shoot dry weight), while in the WT and other transport mutants this decline was only 14-22%. These results were also consistent with a decline in leaf chlorophyll fluorescence (F v/F m). It is suggested that CAX11 plays a key role in maintaining cytosolic Ca(2+) homeostasis and/or signalling in root cells under hypoxic conditions. PMID:26889007

  3. A systems level analysis reveals transcriptomic and proteomic complexity in Ixodes ricinus midgut and salivary glands during early attachment and feeding.

    Science.gov (United States)

    Schwarz, Alexandra; Tenzer, Stefan; Hackenberg, Michael; Erhart, Jan; Gerhold-Ay, Aslihan; Mazur, Johanna; Kuharev, Jörg; Ribeiro, José M C; Kotsyfakis, Michail

    2014-10-01

    Although pathogens are usually transmitted within the first 24-48 h of attachment of the castor bean tick Ixodes ricinus, little is known about the tick's biological responses at these earliest phases of attachment. Tick midgut and salivary glands are the main tissues involved in tick blood feeding and pathogen transmission but the limited genomic information for I. ricinus delays the application of high-throughput methods to study their physiology. We took advantage of the latest advances in the fields of Next Generation RNA-Sequencing and Label-free Quantitative Proteomics to deliver an unprecedented, quantitative description of the gene expression dynamics in the midgut and salivary glands of this disease vector upon attachment to the vertebrate host. A total of 373 of 1510 identified proteins had higher expression in the salivary glands, but only 110 had correspondingly high transcript levels in the same tissue. Furthermore, there was midgut-specific expression of 217 genes at both the transcriptome and proteome level. Tissue-dependent transcript, but not protein, accumulation was revealed for 552 of 885 genes. Moreover, we discovered the enrichment of tick salivary glands in proteins involved in gene transcription and translation, which agrees with the secretory role of this tissue; this finding also agrees with our finding of lower tick t-RNA representation in the salivary glands when compared with the midgut. The midgut, in turn, is enriched in metabolic components and proteins that support its mechanical integrity in order to accommodate and metabolize the ingested blood. Beyond understanding the physiological events that support hematophagy by arthropod ectoparasites, we discovered more than 1500 proteins located at the interface between ticks, the vertebrate host, and the tick-borne pathogens. Thus, our work significantly improves the knowledge of the genetics underlying the transmission lifecycle of this tick species, which is an essential step for

  4. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription.

    Science.gov (United States)

    Ido, Ayaka; Iwata, Shinya; Iwata, Yuka; Igarashi, Hisako; Hamada, Takahiro; Sonobe, Seiji; Sugiura, Masahiro; Yukawa, Yasushi

    2016-02-01

    In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin). PMID:26662274

  5. Revealing the deeper structure of the end-glacial Pärvie fault system in northern Sweden by seismic reflection profiling

    Science.gov (United States)

    Ahmadi, O.; Juhlin, C.; Ask, M.; Lund, B.

    2015-06-01

    A new seismic reflection survey for imaging deeper levels of the end-glacial Pärvie fault system in northern Sweden was acquired in June 2014. The Pärvie fault system hosts the largest fault scarp so far documented in northern Scandinavia, both in terms of its length and calculated magnitude of the earthquake that generated it. Present-day microearthquakes occur along the length of the fault scarp on the eastern side of the scarp, in general agreement with an east-dipping main fault. In the central section of the fault system, where there is a number of subsidiary faults east of the main Pärvie scarp, it has been unclear how the earthquakes relate to the structures mapped at the surface. A seismic profile across the Pärvie fault system acquired in 2007, with a mechanical hammer as a source, showed a good correlation between the surface mapped faults and moderate to steeply dipping reflections. The most pronounced reflectors could be mapped to about 3 km depth. In the new seismic survey, for deeper penetration an explosive source with a maximum charge size of 8.34 kg in 20 m deep shot holes was used. Reflectors can now be traced to deeper levels with the main 65° east-dipping fault interpreted as a weakly reflective structure. As in the previous profile, there is a strongly reflective 60° west-dipping structure present to the east of the main fault that can now be mapped to about 8 km depth. Extrapolations of the main and subsidiary faults converge at a depth of about 11.5 km, where current earthquake activity is concentrated, suggesting their intersection has created favorable conditions for seismic stress release. Based on the present and previous seismic reflection data, we propose potential locations for future boreholes for scientific drilling into the fault system. These boreholes will provide a better understanding of the reflective nature of the fault structures and stress fields along the faults at depth.

  6. Satellite radar data reveal short-term pre-explosive displacements and a complex conduit system at Volcán de Colima, Mexico

    Directory of Open Access Journals (Sweden)

    Jacqueline T. Salzer

    2014-06-01

    Full Text Available The geometry of the volcanic conduit is a main parameter controlling the dynamics and the style of volcanic eruptions and their precursors, but also one of the main unknowns. Pre-eruptive signals that originate in the upper conduit region include seismicity and deformation of different types and scales. However, the locality of the source of these signals and thus the conduit geometry often remain unconstrained at steep sloped and explosive volcanoes due to the sparse instrumental coverage in the summit region and difficult access. Here we infer the shallow conduit system geometry of Volcán de Colima, Mexico, based on ground displacements detected in high resolution satellite radar data up to seven hours prior to an explosion in January 2013. We use Boundary Element Method modeling to reproduce the data synthetically and constrain the parameters of the deformation source, in combination with an analysis of photographs of the summit. We favour a two-source model, indicative of distinct regions of pressurization at very shallow levels. The location of the upper pressurization source coincides with that of post-explosive extrusion; we therefore attribute the displacements to transient (elastic pre-explosive pressurization of the conduit system. Our results highlight the geometrical complexity of shallow conduit systems at explosive volcanoes and its effect on the distribution of pre-eruptive deformation signals. An apparent absence of such signals at many explosive volcanoes may relate to its small temporal and spatial extent, partly controlled by upper conduit structures. Modern satellite radar instruments allow observations at high spatial and temporal resolution that may be the key for detecting and improving our understanding of the generation of precursors at explosive volcanoes.

  7. New insights into the evolution of the magmatic system of a composite andesite volcano revealed by clasts from distal mass-flow deposits: Ruapehu volcano, New Zealand

    Science.gov (United States)

    Tost, M.; Price, R. C.; Cronin, S. J.; Smith, I. E. M.

    2016-05-01

    Stratovolcanoes characteristically build large composite edifices over long periods with stacked lavas intercalated with pyroclastic deposits. In most cases, only the most recent volcanic products are exposed on the flanks of the volcano, and consequently the search for deposits recording an older eruptive and magmatic history is typically focussed far from the cone, within distal tephra deposits. Clasts within lahar and debris avalanche deposits may also provide unique insights into the earliest eruptive and magmatic history of long-lived volcanoes, especially when widespread fallout is absent. Careful sampling and subsequent petrological and geochemical analyses of lava and pumice clasts from six distal mass-flow deposit sequences (hyperconcentrated flow, debris flows and debris avalanche deposits) from Mt. Ruapehu (New Zealand), combined with detailed stratigraphic studies and radiometric age dating, give new perspectives on the pre-50 ka magmatic system of this complex volcano. A conglomerate emplaced between 340 and 310 ka contains evidence for the oldest episode of Mt. Ruapehu volcanism, and unusually for the composite cone, pumice clasts from this unit contain amphibole-bearing xenoliths. Chemical and petrological data for these oldest Ruapehu clasts indicate that a deep (˜40 km) crustal storage system had already developed under Mt. Ruapehu before ˜340 ka. From the very earliest stages, evolution was largely controlled by magma mixing, along with decoupled assimilation and fractional crystallization within numerous isolated small-scale magma batches stored throughout the crust. From around 340 to 160 ka, there was a progressive shift towards more primitive compositions, suggesting that during this period large-scale replenishment events involving mantle-derived basaltic magmas occurred within the mid- to upper crustal storage system. Subsequent magmas became progressively more evolved due to decoupled fractional crystallization and assimilation processes

  8. Satellite radar data reveal short-term pre-explosive displacements and a complex conduit system at Volcán de Colima, Mexico

    Science.gov (United States)

    Salzer, Jacqueline; Nikkhoo, Mehdi; Walter, Thomas; Sudhaus, Henriette; Reyes-Dávila, Gabriel; Bretón, Mauricio; Arambula, Raúl

    2014-06-01

    The geometry of the volcanic conduit is a main parameter controlling the dynamics and the style of volcanic eruptions and their precursors, but also one of the main unknowns. Pre-eruptive signals that originate in the upper conduit region include seismicity and deformation of different types and scales. However, the locality of the source of these signals and thus the conduit geometry often remain unconstrained at steep sloped and explosive volcanoes due to the sparse instrumental coverage in the summit region and difficult access. Here we infer the shallow conduit system geometry of Volcán de Colima, Mexico, based on ground displacements detected in high resolution satellite radar data up to seven hours prior to an explosion in January 2013. We use Boundary Element Method modeling to reproduce the data synthetically and constrain the parameters of the deformation source, in combination with an analysis of photographs of the summit. We favour a two-source model, indicative of distinct regions of pressurization at very shallow levels. The location of the upper pressurization source coincides with that of post-explosive extrusion; we therefore attribute the displacements to transient (elastic) pre-explosive pressurization of the conduit system. Our results highlight the geometrical complexity of shallow conduit systems at explosive volcanoes and its effect on the distribution of pre-eruptive deformation signals. An apparent absence of such signals at many explosive volcanoes may relate to its small temporal and spatial extent, partly controlled by upper conduit structures. Modern satellite radar instruments allow observations at high spatial and temporal resolution that may be the key for detecting and improving our understanding of the generation of precursors at explosive volcanoes.

  9. Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism

    DEFF Research Database (Denmark)

    Elsemman, Ibrahim; Mardinoglu, Adil; Shoaie, Saeed;

    2016-01-01

    Hepatitis C virus (HCV) infection is a worldwide healthcare problem; however, traditional treatment methods have failed to cure all patients, and HCV has developed resistance to new drugs. Systems biology-based analyses could play an important role in the holistic analysis of the impact of HCV on...... dysplastic nodule and early HCC stages. Our results explained the role of the upregulated expression of BCAT1, PLOD3 and six other methyltransferase genes involved in carnitine biosynthesis and S-adenosylmethionine metabolism in the early and advanced HCC stages. Moreover, GNPAT and BCAP31 expression was...

  10. Revealing the deeper structure of the end-glacial Pärvie fault system in northern Sweden by seismic reflection profiling

    Directory of Open Access Journals (Sweden)

    O. Ahmadi

    2015-02-01

    Full Text Available Fault scarps that extend up to 155 km and have offsets of tens of meters at the surface are present in the northern parts of Finland, Norway and Sweden. These fault scarps are inferred to have formed during earthquakes with magnitudes up to 8 at the time of the last deglaciation. The Pärvie fault system represents the largest earthquake so far documented in northern Scandinavia, both in terms of its length and its calculated magnitude. It is also the longest known glacially induced fault in the world. Present-day microearthquakes occur along the length of the fault scarp on the eastern side of the scarp, in general agreement with an east dipping main fault. In the central section of the fault, where there is a number of subsidiary faults east of the main fault, it has been unclear how the earthquakes relate to the faults mapped at the surface. A seismic profile across the Pärvie Fault system acquired in 2007, with a mechanical hammer as a source, showed a good correlation between the surface mapped faults and moderate to steeply dipping reflectors. The most pronounced reflector could be mapped to about 3 km depth. In an attempt to map the fault system to deeper levels, a new 22 km long 2-D seismic profile which followed the 2007 line was acquired in June 2014. For deeper penetration an explosive source with a maximum charge size of 8.34 kg in 20 m deep shot holes was used. Reflectors can now be traced to deeper levels with the main 65° east dipping fault interpreted as a weakly reflective structure. As in the previous profile, there is a pronounced strongly reflective 60° west dipping structure present to the east of the main fault that can now be mapped to about 8 km depth. Extrapolations of the main and subsidiary faults converge at a depth of about 11.5 km where current earthquake activity is concentrated, suggesting their intersection has created favorable conditions for seismic stress release. Based on the present and previous seismic

  11. Non–invasive sampling of endangered neotropical river otters reveals high levels of dispersion in the Lacantun River System of Chiapas, Mexico

    Directory of Open Access Journals (Sweden)

    Ortega, J.

    2012-01-01

    Full Text Available Patterns of genetic dispersion, levels of population genetic structure, and movement of the neotropical river otter (Lontra longicaudis were investigated by screening eight polymorphic microsatellites from DNA extracted from fecal samples, collected in a hydrologic system of the Lacandon rainforest in Chiapas, Mexico. A total of 34 unique genotypes were detected from our surveys along six different rivers, and the effect of landscape genetic structure was studied. We recovered 16 of the 34 individuals in multiple rivers at multiple times. We found high levels of dispersion and low levels of genetic differentiation among otters from the six surveyed rivers (P > 0.05, except for the pairwise comparison among the Lacantún and José rivers (P < 0.05. We recommend that conservation management plans for the species consider the entire Lacantún River System and its tributaries as a single management unit to ensure the maintenance of current levels of population genetic diversity, because the population analyzed seems to follow a source–sink dynamic mainly determined by the existence of the major river.

  12. The phage λ major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system

    Science.gov (United States)

    Pell, Lisa G.; Kanelis, Voula; Donaldson, Logan W.; Lynne Howell, P.; Davidson, Alan R.

    2009-01-01

    Most bacteriophages possess long tails, which serve as the conduit for genome delivery. We report the solution structure of the N-terminal domain of gpV, the protein comprising the major portion of the noncontractile phage λ tail tube. This structure is very similar to a previously solved tail tube protein from a contractile-tailed phage, providing the first direct evidence of an evolutionary connection between these 2 distinct types of phage tails. A remarkable structural similarity is also seen to Hcp1, a component of the bacterial type VI secretion system. The hexameric structure of Hcp1 and its ability to form long tubes are strikingly reminiscent of gpV when it is polymerized into a tail tube. These data coupled with other similarities between phage and type VI secretion proteins support an evolutionary relationship between these systems. Using Hcp1 as a model, we propose a polymerization mechanism for gpV involving several disorder-to-order transitions. PMID:19251647

  13. Imaging beneath the skin of large tropical rivers: System morphodynamics of the Fly and Beni Rivers revealed by novel sub-surface sonar, deep coring, and modelling

    Science.gov (United States)

    Aalto, R. E.; Grenfell, M.; Lauer, J. W.

    2011-12-01

    Tropical rivers dominate Earth's fluvial fluxes for water, carbon, and mineral sediment. They are characterized by large channels and floodplains, old system histories, prolonged periods of flooding, and a clay-dominated sediment flux. However, the underlying bed & floodplain strata are poorly understood. Available data commonly stem from skin-deep approaches such as GIS analysis of imagery, shallow sampling & topographic profiling during lower river stages. Given the large temporal & spatial scales, new approaches are needed to see below lag deposits on mobile sandy beds & deep into expansive floodbasins. Furthermore, such data are needed to test whether we can interpret large tropical river morphology using analogies to small temperate systems. Systems in a dynamic state of response to sea level rise or an increase/contrast in sediment load would provide especially valuable insight. Last August we conducted a field campaign along the Fly and Strickland Rivers in Papua New Guinea (discharge ~5,350 CMS) and this September we investigated the Beni River in Northern Bolivia (discharge ~3,500 CMS). Results were obtained using a novel measurement method: a high-power (>4kW) dual-frequency SyQwest sub-bottom profiler customized to best image 10-20m below the river/lake bed in shallow water. We were able to distinguish sandy deposits from harder clay and silt lenses and also collected bed grab samples to verify our sonar results. Deep borehole samples (5-15m), bank samples, and push cores confirmed observations from the sonar profiling. We simultaneously collected side-scan sonar imagery plus DGPS records of water/bed elevations that could be used to parameterize numerical models. We have now analyzed these results in some detail. Findings for the Fly River include: 1) The prevalence of hard clay beneath the bed of the Lower Fly River and many locations along the Strickland River, retarding migration; 2) Unusual bed morphology along the lower Middle Fly River, where the

  14. Urticarial vasculitis reveals unsuspected thyroiditis.

    Science.gov (United States)

    Ferreira, Olga; Mota, Alberto; Baudrier, Teresa; Azevedo, Filomena

    2012-01-01

    A 38-year-old woman presented with erythematous, violaceous plaques with a serpiginous and unusual appearance located on the left shoulder, left thigh, and right buttock, evolving for 5 days, which eventually became generalized. A skin biopsy revealed leukocytoclastic vasculitis and a diagnosis of urticarial vasculitis was made. The complete blood count, biochemistry, complement levels, and other immunological test results were unremarkable. However, antithyroid antibody titers were increased. Despite having normal thyroid function tests and an absence of specific symptoms, the patient underwent a thyroid ultrasound, which revealed features of thyroiditis, and was subsequently referred to an endocrinologist. Several diseases can be associated with urticarial vasculitis, namely infections and autoimmune connective-tissue disorders such as systemic lupus erythematosus and Sjögren syndrome. Thyroiditis is an uncommon association. PMID:23000939

  15. Sensing the ups and downs of Las Vegas: InSAR reveals structural control of land subsidence and aquifer-system deformation

    Science.gov (United States)

    Amelung, F.; Galloway, D.L.; Bell, J.W.; Zebker, H.A.; Laczniak, R.J.

    1999-01-01

    Land subsidence in Las Vegas, Nevada, United States, between April 1992 and December 1997 was measured using spaceborne interferometric synthetic aperture radar. The detailed deformation maps clearly show that the spatial extent of subsidence is controlled by geologic structures (faults) and sediment composition (clay thickness). The maximum detected subsidence during the 5.75 yr period is 19 cm. Comparison with leveling data indicates that the subsidence rates declined during the past decade as a result of rising ground-water levels brought about by a net reduction in ground-water extraction. Temporal analysis also detects seasonal subsidence and uplift patterns, which provide information about the elastic and inelastic properties of the aquifer system and their spatial variability.

  16. Sensing the ups and downs of Las Vegas: InSAR reveals structural control of land subsidence and aquifer-system deformation

    Science.gov (United States)

    Amelung, Falk; Galloway, Devin L.; Bell, John W.; Zebker, Howard A.; Laczniak, Randell J.

    1999-06-01

    Land subsidence in Las Vegas, Nevada, United States, between April 1992 and December 1997 was measured using spaceborne interferometric synthetic aperture radar. The detailed deformation maps clearly show that the spatial extent of subsidence is controlled by geologic structures (faults) and sediment composition (clay thickness). The maximum detected subsidence during the 5.75 yr period is 19 cm. Comparison with leveling data indicates that the subsidence rates declined during the past decade as a result of rising ground-water levels brought about by a net reduction in ground-water extraction. Temporal analysis also detects seasonal subsidence and uplift patterns, which provide information about the elastic and inelastic properties of the aquifer system and their spatial variability.

  17. Transcriptome analysis of Sulfolobus solfataricus infected with two related fuselloviruses reveals novel insights into the regulation of CRISPR-Cas system

    DEFF Research Database (Denmark)

    Fusco, Salvatore; Liguori, Rossana; Limauro, Danila;

    2015-01-01

    Fuselloviruses SSV1 and SSV2 are model systems to investigate virus-host relationships in stably infected cells thanks to their temperate nature. Although they are very similar in morphology, genome organization and gene synteny, their replication is induced by different stimuli, i.e.: by UV......-light exposure (for SSV1) and by the growth progression of the host (for SSV2). In this study, we have analysed global gene expression in SSV1- and SSV2-lysogens of Sulfolobus solfataricus P2 in the absence of any stimuli. Additionally, the interplay among SSV1, SSV2 and the host has been investigated in a...... double-infected strain to explore both virus-host and virus-virus interactions. Whereas SSV1 did not induce major changes of the host gene expression, SSV2 elicited a strong host response, which includes the transcriptional activation of CRISPR loci and cas genes. As a consequence, a significant decrease...

  18. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    Science.gov (United States)

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc]. PMID:27261759

  19. In Vivo Quantification of Inflammation in Experimental Autoimmune Encephalomyelitis Rats Using Fluorine-19 Magnetic Resonance Imaging Reveals Immune Cell Recruitment outside the Nervous System.

    Directory of Open Access Journals (Sweden)

    Jia Zhong

    Full Text Available Progress in identifying new therapies for multiple sclerosis (MS can be accelerated by using imaging biomarkers of disease progression or abatement in model systems. In this study, we evaluate the ability to noninvasively image and quantitate disease pathology using emerging "hot-spot" 19F MRI methods in an experimental autoimmune encephalomyelitis (EAE rat, a model of MS. Rats with clinical symptoms of EAE were compared to control rats without EAE, as well as to EAE rats that received daily prophylactic treatments with cyclophosphamide. Perfluorocarbon (PFC nanoemulsion was injected intravenously, which labels predominately monocytes and macrophages in situ. Analysis of the spin-density weighted 19F MRI data enabled quantification of the apparent macrophage burden in the central nervous system and other tissues. The in vivo MRI results were confirmed by extremely high-resolution 19F/1H magnetic resonance microscopy in excised tissue samples and histopathologic analyses. Additionally, 19F nuclear magnetic resonance spectroscopy of intact tissue samples was used to assay the PFC biodistribution in EAE and control rats. In vivo hot-spot 19F signals were detected predominantly in the EAE spinal cord, consistent with the presence of inflammatory infiltrates. Surprising, prominent 19F hot-spots were observed in bone-marrow cavities adjacent to spinal cord lesions; these were not observed in control animals. Quantitative evaluation of cohorts receiving cyclophosphamide treatment displayed significant reduction in 19F signal within the spinal cord and bone marrow of EAE rats. Overall, 19F MRI can be used to quantitatively monitored EAE disease burden, discover unexpected sites of inflammatory activity, and may serve as a sensitive biomarker for the discovery and preclinical assessment of novel MS therapeutic interventions.

  20. The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.

    Directory of Open Access Journals (Sweden)

    Gergő Gógl

    2015-05-01

    Full Text Available Eukaryotic cells commonly use protein kinases in signaling systems that relay information and control a wide range of processes. These enzymes have a fundamentally similar structure, but achieve functional diversity through variable regions that determine how the catalytic core is activated and recruited to phosphorylation targets. "Hippo" pathways are ancient protein kinase signaling systems that control cell proliferation and morphogenesis; the NDR/LATS family protein kinases, which associate with "Mob" coactivator proteins, are central but incompletely understood components of these pathways. Here we describe the crystal structure of budding yeast Cbk1-Mob2, to our knowledge the first of an NDR/LATS kinase-Mob complex. It shows a novel coactivator-organized activation region that may be unique to NDR/LATS kinases, in which a key regulatory motif apparently shifts from an inactive binding mode to an active one upon phosphorylation. We also provide a structural basis for a substrate docking mechanism previously unknown in AGC family kinases, and show that docking interaction provides robustness to Cbk1's regulation of its two known in vivo substrates. Co-evolution of docking motifs and phosphorylation consensus sites strongly indicates that a protein is an in vivo regulatory target of this hippo pathway, and predicts a new group of high-confidence Cbk1 substrates that function at sites of cytokinesis and cell growth. Moreover, docking peptides arise in unstructured regions of proteins that are probably already kinase substrates, suggesting a broad sequential model for adaptive acquisition of kinase docking in rapidly evolving intrinsically disordered polypeptides.

  1. Patterns of the loop current system and regions of sea surface height variability in the eastern Gulf of Mexico revealed by the self-organizing maps

    Science.gov (United States)

    Liu, Yonggang; Weisberg, Robert H.; Vignudelli, Stefano; Mitchum, Gary T.

    2016-04-01

    The Self-Organizing Map (SOM), an unsupervised learning neural network, is employed to extract patterns evinced by the Loop Current (LC) system and to identify regions of sea surface height (SSH) variability in the eastern Gulf of Mexico (GoM) from 23 years (1993-2015) of altimetry data. Spatial patterns are characterized as different LC extensions and different stages in the process of LC eddy shedding. The temporal evolutions and the frequency of occurrences of these patterns are obtained, and the typical trajectories of the LC system progression on the SOM grid are investigated. For an elongated, northwest-extended, or west-positioned LC, it is common for the LC anticyclonic eddy (LCE) to separate and propagate into the western GoM, while an initially separated LCE in close proximity to the west Florida continental slope often reattaches to the LC and develops into an elongated LC, or reduces intensity locally before moving westward as a smaller eddy. Regions of differing SSH variations are also identified using the joint SOM-wavelet analysis. Along the general axis of the LC, SSH exhibits strong variability on time scales of 3 months to 2 years, also with energetic intraseasonal variations, which is consistent with the joint Empirical Orthogonal Function (EOF)-wavelet analysis. In the more peripheral regions, the SSH has a dominant seasonal variation that also projects across the coastal ocean. The SOM, when applied to both space and time domains of the same data, provides a powerful tool for diagnosing ocean processes from such different perspectives.

  2. Proverbs Reveal Culture Diversity

    OpenAIRE

    Hou, Rong

    2013-01-01

    Through the analysis of property of culture and proverb, it can be known that proverb can help one to understand a culture. The way proverb reveals culture diversity can be connected with the patterns of value dimension, which conveys the information of a culture’s deep meaning. From the perspective of uncertainty-avoidance, it can be seen that although Ireland and America both are low-uncertainty-avoidance cultures, they mainly have different life attitudes, because that Americans put more e...

  3. Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

    Directory of Open Access Journals (Sweden)

    Sepil Irem

    2012-05-01

    Full Text Available Abstract Background The critical role of Major Histocompatibility Complex (Mhc genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. Results In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. Conclusions We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help

  4. The Shallow Plumbing System of Piton de la Fournaise Volcano (La Réunion island, Indian Ocean) Revealed by the Major 2007 Caldera Forming Eruption (Invited)

    Science.gov (United States)

    Di Muro, A.; Metrich, N.; Daniele, V.; Rosi, M.; Armienti, P.; Fougeroux, T.; Deloule, E.; Arienzo, I.; Civetta, L.

    2013-12-01

    The 2007 eruption represents a major event in the recent history of Piton de la Fournaise volcano because it produced: i) the most voluminous lava field (at least 0.21 km3), ii) the most intense lava fountaining activity (>200 m high), iii) the largest SO2 plume (>230 kt), iv) the largest summit collapse (1 km wide x 0.34 km deep) and v) the main flank slip event (up to 1.4 m eastwards) ever documented at PdF. The bulk magma volume extruded during the 2007 eruptive sequence is similar to that emitted during the entire 1998-2006 period. As a whole, the volume of magma emitted during the whole 1998-2007 activity cycle is remarkably close to that estimated (~0.35 km3) for the shallow plumbing system of Piton de la Fournaise. The 2007 eruptive sequence consisted of three successive phases (February, March and April). The main caldera forming phase of April ended a 9 years long period (1998-2007) of continuous edifice inflation and frequent eruptive activity (3 eruptions per year on average). On the contrary, post-2007 activity punctuates a trend of continuous deflation and consists of small-volume summit eruptions of moderate/low MgO magmas and frequent shallow magma intrusions. The 2007 lavas and pyroclasts cover the complete range of textures and crystal content an composition typically found in PdF products. The broad range of textures and the large volumes of pyroclasts, lava and gas emitted in 2007 provide an unique and exceptional record of the time-integrated evolution of PdF magma, and represent an unique opportunity to image the volcano plumbing system and bring new constraints on the processes controlling its magmatic and volatile budget. We here address these issues by using an unprecedented geochemical dataset (major, volatile and trace elements, Sr-Nd isotopes) on bulk rocks, minerals, glass inclusions and glass matrices from a very detailed sample set, representative of the time evolution of extruded magma during the entire 2007 eruptive sequence.

  5. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2011-05-01

    Full Text Available Abstract Background The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution. Results The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys. Conclusion A strong reversed asymmetrical mutational constraint in the mitochondrial genome of

  6. The application of isotope and geochemical techniques to reveal contributions of submarine groundwater and septic systems discharges to algal bloom in Boracay Island

    International Nuclear Information System (INIS)

    The study shows that critical areas in Boracay island are contaminated by coliform bacteria and blue green algae (cyanobacteria). The distribution of tritium, 18O, 15N, and 13C in seawater, biota and sediments in the intertidal zone, helped to identify sites with specific sewage outflows and submarine groundwater discharge, SGD, Nitrates (from, 0.0 to 2.3 parts per million, ppm) and nutrients were discovered in seawater, particularly in four identified sites in the bathing zone. Point sources of infiltrating plumes were exposed by anomalies in tritium and 18O in sea water. Septic and canal outflows as well as land based run-offs and submarine groundwater discharge were the identified causes of nutrient enrichments in sites with eminent algal bloom. The isotope composition implied that algae acquire nutrients from septic contamination, while a number of corals assimilate inorganic fertilizer nutrients from land-based plumes and SGD. The elements identified in sediments and corals were related to the natural mineral matrix of calcareous beach zone materials; however, sporadic spikes of lead, chromium and zinc were detected in particular sites at certain depths. These element spikes proxy processes linked to anthropogenic pollution and or organic matter decomposition in the sediment-water interfaces. The practicality of applying isotope-based techniques in conjunction with other chemical methods for the tracking down of the sources of nutrient contamination in polluted systems is demonstrated by the study.

  7. Isotopes of carbon, nitrogen and oxygen reveal contributions of submarine groundwater and septic systems discharges to algal bloom in Boracay Island

    International Nuclear Information System (INIS)

    The study showed that critical areas in Boracay island were contaminated by coliform bacteria and blue green algae (cyanobacteria). The distribution of tritium, 18O,15N and 13C in seawater, biota and sediments in the inter tidal zone, helped to identify sites with septic sewage outflows and submarine groundwater discharge, SGD. Nitrates (from 0.0 to 2.3 parts per million, ppm) and nutrients were discovered in seawater, particularly in four identified sites in the bathing zone. Point sources of infiltrating plumes were exposed by anomalies in tritium and 18O in sea water. Septic and canal outflows as well as land based run-offs and submarine groundwater discharge were the identified causes of nutrient enrichments in sites with eminent algal bloom. The isotope composition implied that algae acquire nutrients from septic contamination, while a number of corals assimilate inorganic fertilizer nutrients from land-based plumes and SGD. The elements identified in sediments and corals were related to the natural mineral matrix of calcareous beach zone materials, however, sporadic spikes of lead, chromium and zinc were detected in particular sites at certain depths. These element spikes proxy processes linked to anthropogenic pollution and or organic matter decomposition in the sediment-water interfaces. The practicality of applying isotope-based techniques in conjunction with other chemical methods for the tracking down of the sources of nutrient contamination in polluted systems in demonstrated by the study.(author)

  8. Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).

    Science.gov (United States)

    Huang, Dingquan; Zhao, Yihong; Cao, Minghao; Qiao, Liang; Zheng, Zhi-Liang

    2016-01-01

    Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control. PMID:27092171

  9. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy

    Science.gov (United States)

    Isserlin, Ruth; Merico, Daniele; Wang, Dingyan; Vuckovic, Dajana; Bousette, Nicolas; Gramolini, Anthony O.; Bader, Gary D.; Emili, Andrew

    2016-01-01

    Apoptosis is a hallmark of multiple etiologies of heart failure, including dilated cardiomyopathy. Since microRNAs are master regulators of cardiac development and key effectors of intracellular signaling, they represent novel candidates for understanding the mechanisms driving the increased dysfunction and loss of cardiomyocytes during cardiovascular disease progression. To determine the role of cardiac miRNAs in the apoptotic response, we used microarray technology to monitor miRNA levels in a validated murine phospholambam mutant model of dilated cardiomyopathy. 24 miRNAs were found to be differentially expressed, most of which have not been previously linked to dilated cardiomyopathy. We showed that individual silencing of 7 out of 8 significantly down-regulated miRNAs (mir-1, −29c, −30c, −30d, −149, −486, −499) led to a strong apoptotic phenotype in cell culture, suggesting they repress pro-apoptotic factors. To identify putative miRNA targets most likely relevant to cell death, we computationally integrated transcriptomic, proteomic and functional annotation data. We showed the dependency of prioritized target abundance on miRNA expression using RNA interference and quantitative mass spectrometry. We concluded that down regulation of key pro-survival miRNAs causes up-regulation of apoptotic signaling effectors that contribute to cardiac cell loss, potentially leading to system decompensation and heart failure. PMID:25361207

  10. Geometric and Kinematic Structure of the Outflow/Envelope System of L1527 Revealed by Subarcsecond-resolution Observation of CS

    CERN Document Server

    Oya, Yoko; Lefloch, Bertrand; López-Sepulvre, Ana; Watanabe, Yoshimasa; Ceccarelli, Cecilia; Yamamoto, Satoshi

    2016-01-01

    Subarcsecond-resolution images of the rotational line emissions of CS and c-C$_3$H$_2$ obtained toward the low-mass protostar IRAS 04368$+$2557 in L1527 with the Atacama Large Millimeter/submillimeter Array are investigated to constrain the orientation of the outflow/envelope system. The distribution of CS consists of an envelope component extending from north to south and a faint butterfly-shaped outflow component. The kinematic structure of the envelope is well reproduced by a simple ballistic model of an infalling rotating envelope. Although the envelope has a nearly edge-on configuration, the inclination angle of the rotation axis from the plane of the sky is found to be 5$^\\circ$, where we find that the western side of the envelope faces the observer. This configuration is opposite to the direction of the large-scale ($\\sim$ 10$^4$ AU) outflow suggested previously from the $^{12}$CO ($J$=3$-$2) observation, and to the morphology of infrared reflection near the protostar ($\\sim$ 200 AU). The latter discre...

  11. Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole.

    Directory of Open Access Journals (Sweden)

    Xuwang Zhang

    Full Text Available Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1, phenol plus indole (G2 and indole only (G3, were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H-ylidene indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05. Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole.

  12. Investigation of Swedish cases reveals an outbreak of cryptosporidiosis at a Norwegian hotel with possible links to in-house water systems

    Directory of Open Access Journals (Sweden)

    Krogh Truls

    2008-11-01

    Full Text Available Abstract Background In March 2007, the Norwegian Institute of Public Health was notified of Swedish individuals diagnosed with cryptosporidiosis after staying at a Norwegian hotel. In Norway, cryptosporidiosis is not reportable, and human infections are rarely diagnosed. Methods A questionnaire on illness and exposure history was e-mailed to seven organised groups who had visited the hotel in March. Cases were defined as persons with diarrhoea for more than two days or laboratory-confirmed cryptosporidiosis during or within two weeks of the hotel visit. The risk factor analysis was restricted to two groups with the highest attack rates (AR and same hotel stay period. Local food safety authorities conducted environmental investigations. Results In total, 25 diarrhoeal cases (10 laboratory-confirmed were identified among 89 respondents. Although environmental samples were negative, epidemiological data suggest an association with in-house water consumption. In one group, the AR was higher amongst consumers of water from hotel dispenser (relative risk [RR] = 3.0; 95% confidence interval [CI]: 0.9–9.8, tap water (RR = 2.3; CI: 0.9–5.8, and lower amongst commercial bottled water drinkers (RR = 0.6; CI: 0.4–1.0. Consumption of ice cubes was a risk-factor (RR = 7.1; CI: 1.1–45.7 in the two groups combined. Conclusion This outbreak would probably have remained undetected without the alert from Swedish health authorities, illustrating the difficulties in outbreak detection due to low health care seeking behaviour for diarrhoea and limited parasite diagnostics in Norway. Awareness of cryptosporidiosis should be raised amongst Norwegian medical personnel to improve case and outbreak detection, and possible risks related to in-house water systems should be assessed.

  13. Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks

    Directory of Open Access Journals (Sweden)

    Zarnescu Daniela C

    2008-11-01

    Full Text Available Abstract Background In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermore, in mammalian systems, both genes have been implicated in neuronal development. Given these genetic and functional similarities, we tested Drosophila sticky and dFmr1 for a genetic interaction and measured whole genome expression in both mutants to assess similarities in gene regulation. Results We found that sticky mutations can dominantly suppress a dFmr1 gain-of-function phenotype in the developing eye, while phenotypes produced by RNAi knock-down of sticky were enhanced by dFmr1 RNAi and a dFmr1 loss-of-function mutation. We also identified a large number of transcripts that were misexpressed in both mutants suggesting that sticky and dFmr1 gene products similarly regulate gene expression. By integrating gene expression data with a protein-protein interaction network, we found that mutations in sticky and dFmr1 resulted in misexpression of common gene networks, and consequently predicted additional specific phenotypes previously not known to be associated with either gene. Further phenotypic analyses validated these predictions. Conclusion These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.

  14. Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism.

    Science.gov (United States)

    Elsemman, Ibrahim E; Mardinoglu, Adil; Shoaie, Saeed; Soliman, Taysir H; Nielsen, Jens

    2016-04-26

    Hepatitis C virus (HCV) infection is a worldwide healthcare problem; however, traditional treatment methods have failed to cure all patients, and HCV has developed resistance to new drugs. Systems biology-based analyses could play an important role in the holistic analysis of the impact of HCV on hepatocellular metabolism. Here, we integrated HCV assembly reactions with a genome-scale hepatocyte metabolic model to identify metabolic targets for HCV assembly and metabolic alterations that occur between different HCV progression states (cirrhosis, dysplastic nodule, and early and advanced hepatocellular carcinoma (HCC)) and healthy liver tissue. We found that diacylglycerolipids were essential for HCV assembly. In addition, the metabolism of keratan sulfate and chondroitin sulfate was significantly changed in the cirrhosis stage, whereas the metabolism of acyl-carnitine was significantly changed in the dysplastic nodule and early HCC stages. Our results explained the role of the upregulated expression of BCAT1, PLOD3 and six other methyltransferase genes involved in carnitine biosynthesis and S-adenosylmethionine metabolism in the early and advanced HCC stages. Moreover, GNPAT and BCAP31 expression was upregulated in the early and advanced HCC stages and could lead to increased acyl-CoA consumption. By integrating our results with copy number variation analyses, we observed that GNPAT, PPOX and five of the methyltransferase genes (ASH1L, METTL13, SMYD2, TARBP1 and SMYD3), which are all located on chromosome 1q, had increased copy numbers in the cancer samples relative to the normal samples. Finally, we confirmed our predictions with the results of metabolomics studies and proposed that inhibiting the identified targets has the potential to provide an effective treatment strategy for HCV-associated liver disorders. PMID:27040643

  15. Quaternary evolution of the delta systems and the coast line of Lake Ohrid (FYROM/Albania) revealed by shallow geophysical and drilling data

    Science.gov (United States)

    Hoffmann, Nadine; Reicherter, Klaus; Gruetzner, Christoph

    2010-05-01

    The Lake Ohrid Basin (40°54´ - 41°10`N, 20°38`- 20°48`E) is a cross boundary lake (FYROM/Albania) stretching over a length of c. 30 km and a width of c. 15 km. It is situated in a karstic environment in the Balkanides, an active tectonic region. The general geodynamic setting of the Lake Ohrid area can be described as a "basin and range" situation which is influenced by the northern part of the Hellenic trench and is underlain by ongonig extension so that the Ohrid basin is still actively subsiding. Typical sedimentation patterns supported by the topography give evidence for a tectonically controlled regime. Inactive, Pleistocene lobe-shaped fans are cut off relatively linear by the lake. Drowned alluvial fans along the west coast give evidence for lake-level fluctuations or tectonic subsidence along the western basin margin. In contrast the Struga plain in the North is a vast dried up area, which acts either as a sedimentary catchment for a fan system or as a tectonic basement which is subject to subsidence. Thus, the investigation areas concentrated close to the shorelines including extensive parts at the west coast, in the Struga Plain to the North, the deltas of the inflowing rivers and mass movement bodies at the east coast. Ground Penetrating Radar and Electric Resistivity have been applied, as a non-invasive shallow subsurface mapping methods, to image the sedimentary and tectonic structures. Sediment cores were taken and grain size and sediment composition were analysed. In the aggradation and deltaic plains of the Dajan river in the north and of the Cerava river in the south sets of channels cutting into horizontal layers were identified close to the shoreline. Several S-ward dipping foreset-like structures were found in the north near Struga. The cores show sequences of grain sizes varying between clay and gravel intersected by intervals that are fining upward, and are interpreted as fluvial sediments. No evidences for a higher lake-level were found

  16. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  17. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  18. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    This work presents a method for designing facial interfaces for sociable android robots with respect to the fundamental rules of human affect expression. Extending the work of Paul Ekman towards a robotic direction, we follow the judgment-based approach for evaluating facial expressions to test in...... which case an android robot like the Geminoid|DK –a duplicate of an Original person- reveals emotions convincingly; when following an empirical perspective, or when following a theoretical one. The methodology includes the processes of acquiring the empirical data, and gathering feedback on them. Our...... findings are based on the results derived from a number of judgments, and suggest that before programming the facial expressions of a Geminoid, the Original should pass through the proposed procedure. According to our recommendations, the facial expressions of an android should be tested by judges, even in...

  19. Chemistry of plutonium revealed

    International Nuclear Information System (INIS)

    In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. In this paper the work carried out at Berkeley from the spring of 1942 to the summer of 1945 is described briefly. The aqueous chemistry of plutonium is quite remarkable. Important insights were obtained from tracer experiments, but the full complexity was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were based on aqueous solutions, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, an equilibrium was rapidly established among the four aqueous oxidation states, while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element are reported

  20. Revealing Cosmic Rotation

    CERN Document Server

    Yadav, Amit P S; Keating, Brian G

    2012-01-01

    Cosmological Birefringence (CB), a rotation of the polarization plane of radiation coming to us from distant astrophysical sources, may reveal parity violation in either the electromagnetic or gravitational sectors of the fundamental interactions in nature. Until only recently this phenomenon could be probed with only radio observations or observations at UV wavelengths. Recently, there is a substantial effort to constrain such non-standard models using observations of the rotation of the polarization plane of cosmic microwave background (CMB) radiation. This can be done via measurements of the $B$-modes of the CMB or by measuring its TB and EB correlations which vanish in the standard model. In this paper we show that $EB$ correlations-based estimator is the best for upcoming polarization experiments. The $EB$ based estimator surpasses other estimators because it has the smallest noise and of all the estimators is least affected by systematics. Current polarimeters are optimized for the detection of $B$-mode...

  1. What the voice reveals.

    NARCIS (Netherlands)

    Ko, Sei Jin

    2007-01-01

    Given that the voice is our main form of communication, we know surprisingly little about how it impacts judgment and behavior. Furthermore, the modern advancement in telecommunication systems, such as cellular phones, has meant that a large proportion of our everyday interactions are conducted voca

  2. What the voice reveals.

    OpenAIRE

    Ko, Sei Jin

    2007-01-01

    Given that the voice is our main form of communication, we know surprisingly little about how it impacts judgment and behavior. Furthermore, the modern advancement in telecommunication systems, such as cellular phones, has meant that a large proportion of our everyday interactions are conducted vocally and these interactions can have important consequences. For example, imagine two people, who met through an internet-dating service, having their first phone conversation or potential employees...

  3. Puerto Rico Revealed Preference data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Revealed preference models provide insights into recreational angler behavior and the economic value of recreational fishing trips. Revealed preference data is...

  4. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem.

    Directory of Open Access Journals (Sweden)

    Wesley D Swingley

    Full Text Available We have constructed a conceptual model of biogeochemical cycles and metabolic and microbial community shifts within a hot spring ecosystem via coordinated analysis of the "Bison Pool" (BP Environmental Genome and a complementary contextual geochemical dataset of ~75 geochemical parameters. 2,321 16S rRNA clones and 470 megabases of environmental sequence data were produced from biofilms at five sites along the outflow of BP, an alkaline hot spring in Sentinel Meadow (Lower Geyser Basin of Yellowstone National Park. This channel acts as a >22 m gradient of decreasing temperature, increasing dissolved oxygen, and changing availability of biologically important chemical species, such as those containing nitrogen and sulfur. Microbial life at BP transitions from a 92 °C chemotrophic streamer biofilm community in the BP source pool to a 56 °C phototrophic mat community. We improved automated annotation of the BP environmental genomes using BLAST-based Markov clustering. We have also assigned environmental genome sequences to individual microbial community members by complementing traditional homology-based assignment with nucleotide word-usage algorithms, allowing more than 70% of all reads to be assigned to source organisms. This assignment yields high genome coverage in dominant community members, facilitating reconstruction of nearly complete metabolic profiles and in-depth analysis of the relation between geochemical and metabolic changes along the outflow. We show that changes in environmental conditions and energy availability are associated with dramatic shifts in microbial communities and metabolic function. We have also identified an organism constituting a novel phylum in a metabolic "transition" community, located physically between the chemotroph- and phototroph-dominated sites. The complementary analysis of biogeochemical and environmental genomic data from BP has allowed us to build ecosystem-based conceptual models for this hot

  5. Revealed Cores: Characterizations and Structure

    OpenAIRE

    Stefano Vannucci

    2010-01-01

    Characterizations of the choice functions that select the cores or the externally stable cores induced by an underlying revealed dominance digraph are provided. Relying on such characterizations, the basic order-theoretic structure of the corresponding sets of revealed cores is also analyzed

  6. A multi-layer, closed-loop system for continuous measurement of CO2 concentrations and its isotopic signature in forest soils as a basis for CO2 efflux calculation and for revealing its controls

    Science.gov (United States)

    Jochheim, Hubert; Wirth, Stephan

    2015-04-01

    We present a setup of measurement devices that allows the application of the soil CO2 gradient approach for CO2 efflux calculation in combination with the analysis of isotopic signature (δ13C). Vertical profiles of CO2 concentrations in air-filled pores of soil were measured using miniature NDIR sensors within a 16-channel closed-loop system where equilibrium with soil air can be achieved using hydrophobic, gas-permeable porous polypropylene tubes circulating gas using peristaltic pumps. A 16-position multiplexer allows the connection to an isotopic CO2 analyser. This setup was applied at two ICP Forest intensive monitoring sites, a beech and a pine forest on sandy soils located in Brandenburg, Germany. CO2 concentrations in air-filled pores of soils were measured on top of soil surface, below the humus layer, and in 10cm, 20cm, 30cm and 100 cm depths every 30 min. At both sites, soil moisture and temperature were measured continuously in the respective soil depths in identical time intervals. Isotopic signatures of soil CO2 was detected by measurement campaigns. After two years of measurements, our results provided evidence for distinct seasonal dynamics and vertical gradients of soil CO2 concentration and δ13C values. Varying impacts of soil temperature and moisture on CO2 concentration were revealed, highlighting its impact on soil physical and soil biological controls. Higher levels of CO2 concentration and a more distinct seasonal dynamics were detected at the beech site compared to the pine site. The collected data provide a suitable database for calculation of CO2 efflux and modelling of soil respiration.

  7. REVEAL: Software Documentation and Platform Migration

    Science.gov (United States)

    Wilson, Michael A.; Veibell, Victoir T.

    2011-01-01

    The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

  8. Driven Rydberg atoms reveal quartic level repulsion

    OpenAIRE

    Sacha, Krzysztof; Zakrzewski, Jakub

    2001-01-01

    The dynamics of Rydberg states of a hydrogen atom subject simultaneously to uniform static electric field and two microwave fields with commensurate frequencies is considered in the range of small fields amplitudes. In the certain range of the parameters of the system the classical secular motion of the electronic ellipse reveals chaotic behavior. Quantum mechanically, when the fine structure of the atom is taken into account, the energy level statistics obey predictions appropriate for the s...

  9. Driven Rydberg atoms reveal quartic level repulsion

    CERN Document Server

    Sacha, K; Sacha, Krzysztof; Zakrzewski, Jakub

    2001-01-01

    The dynamics of Rydberg states of a hydrogen atom subject simultaneously to uniform static electric field and two microwave fields with commensurate frequencies is considered in the range of small fields amplitudes. In the certain range of the parameters of the system the classical secular motion of the electronic ellipse reveals chaotic behavior. Quantum mechanically, when the fine structure of the atom is taken into account, the energy level statistics obey predictions appropriate for the symplectic Gaussian random matrix ensemble.

  10. Decision Making and Revealed Preference

    DEFF Research Database (Denmark)

    de la Rosa, Leonidas Enrique

    If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis. ....... Given advances in evolutionary psychology and neuroscience, I propose one way to model those evolutionary pressures that will hopefully prove useful in expanding normative economics.......If our decision-making processes are to some extent shaped by evolutionary pressures and our environment is different from that to which we adapted, some of our choices will not be in our best interest. But revealed preference is the only tool that we have so far to conduct a normative analysis...

  11. Lipid sorting revealed by SANS

    International Nuclear Information System (INIS)

    We have investigated the lipid sorting in a binary small unilamellar vesicle (SUV) composed of cone-shaped (1,2-dihexanoyl-sn-glycero-3-phosphocholine: DHPC) and cylinder-shaped (1,2-dipalmitoyl-sn-glycero-3-phosphocholine: DPPC) lipids. In order to reveal the lipid sorting we adopted a contrast matching technique of small angle neutron scattering (SANS), which extracts the distribution of deuterated lipids in the bilayer quantitatively. The SANS profile of deuterated SUVs at the contrast matching condition showed a characteristic scattering profile, indicating an asymmetric distribution of cone-shaped lipids in the bilayer. The fitting of the observed SANS profile revealed that most DHPC molecules are localized in the outer leaflet, which supports that the shape of the lipid is strongly coupled with the membrane curvature. We compared the obtained asymmetric distribution of the cone-shaped lipids in the bilayer with the theoretical prediction based on the curvature energy model. (author)

  12. Revealing and Concealing in Antiquity

    DEFF Research Database (Denmark)

    Secrecy and the act of concealing and revealing knowledge effectually segregate the initiated and the uninitiated. The act of sharing or hiding knowledge plays a central role in all human relations private or public, political or religious. This volume explores the concept of secrecy and its impl...... the concept of secrecy and its potential for illuminating the agendas behind identity constructions, political propaganda, literary works, religous practices and shared history....

  13. Transparency masters for mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1980-01-01

    Transparency Masters for Mathematics Revealed focuses on master diagrams that can be used for transparencies for an overhead projector or duplicator masters for worksheets. The book offers information on a compilation of master diagrams prepared by John R. Stafford, Jr., audiovisual supervisor at the University of Missouri at Kansas City. Some of the transparencies are designed to be shown horizontally. The initial three masters are number lines and grids that can be used in a mathematics course, while the others are adaptations of text figures which are slightly altered in some instances. The

  14. Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol:coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila.

    Science.gov (United States)

    Ding, Yan-Huai R; Zhang, Shi-Ping; Tomb, Jean-Francois; Ferry, James G

    2002-09-24

    Each of the genomic sequences of Methanosarcina acetivorans, Methanosarcina mazei, and Methanosarcina thermophila revealed two homologs of mtaA, three homologs of mtaB, and three homologs of mtaC encoding enzymes specific for methanogenesis from methanol. Two-dimensional gel electrophoretic analyses of polypeptides from M. thermophila established that methanol induces the expression of mtaA-1, mtaB-1, mtaB-2, mtaB-3, mtaC-1, mtaC-2, and mtaC-3 whereas mtaB-3 and mtaC-3 are constitutively expressed in acetate-grown cells. The gene product of one of three mttC homologs, encoding trimethylamine-specific methyltransferase I, was detected in methanol- but not acetate-grown M. thermophila. A postulated role for the multiple homologs is discussed. PMID:12393212

  15. Plan competitions reveal entrepreneurial talent

    Energy Technology Data Exchange (ETDEWEB)

    Madison, Alison L.

    2011-05-15

    Monthly economic diversity column for Tri-City Herald business section. Excerpt below: There’s something to be said for gaining valuable real-world experience in a structured, nurturing environment. Take for instance learning to scuba dive in the comfort of my resort pool rather than immediately hanging out with sharks while I figure out little things like oxygen tanks and avoiding underwater panic attacks. Likewise, graduate students are getting some excellent, supportive real-world training through university business plan competitions. These competitions are places where smart minds, new technologies, months of preparation and coaching, and some healthy pre-presentation jitters collide to reveal not only solid new business ideas, but also some promising entrepreneurial talent. In fact, professionals from around our region descend upon college campuses every spring to judge these events, which help to bridge the gap between academics and the real technology and business-driven economy.

  16. The chemistry of plutonium revealed

    International Nuclear Information System (INIS)

    In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. Important insights were obtained from tracer experiments, but the full complexity of plutonium chemistry was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were aqueous solution based, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, it was found that an equilibrium was rapidly established among the four aqueous oxidation states while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element will be reported

  17. Archimedes: Accelerator Reveals Ancient Text

    International Nuclear Information System (INIS)

    Archimedes (287-212 BC), who is famous for shouting 'Eureka' (I found it) is considered one of the most brilliant thinkers of all times. The 10th-century parchment document known as the 'Archimedes Palimpsest' is the unique source for two of the great Greek's treatises. Some of the writings, hidden under gold forgeries, have recently been revealed at the Stanford Synchrotron Radiation Laboratory at SLAC. An intense x-ray beam produced in a particle accelerator causes the iron in original ink, which has been partly erased and covered, to send out a fluorescence glow. A detector records the signal and a digital image showing the ancient writings is produced. Please join us in this fascinating journey of a 1,000-year-old parchment from its origin in the Mediterranean city of Constantinople to a particle accelerator in Menlo Park.

  18. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  19. Revealing effective classifiers through network comparison

    CERN Document Server

    Gallos, Lazaros K

    2014-01-01

    The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two networks for structural similarity, based on the distribution of edge density in network subgraphs. We demonstrate that this method can efficiently introduce comparative analysis into network science and opens the road for many new applications. For example, we show how the construction of a phylogenetic tree across animal taxa according to their social structure can reveal commonalities in the behavioral ecology of the populations, or how students create similar networks according to the University size. Our method can be expanded to study a multitude of additional properties, such as network classification, changes during time evolution, convergence of growth models, and detection of structural changes during damage.

  20. Revealing effective classifiers through network comparison

    Science.gov (United States)

    Gallos, Lazaros K.; Fefferman, Nina H.

    2014-11-01

    The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured, in ways that are otherwise inaccessible to observation. Here, we introduce the n-tangle method to directly compare two networks for structural similarity, based on the distribution of edge density in network subgraphs. We demonstrate that this method can efficiently introduce comparative analysis into network science and opens the road for many new applications. For example, we show how the construction of a “phylogenetic tree” across animal taxa according to their social structure can reveal commonalities in the behavioral ecology of the populations, or how students create similar networks according to the University size. Our method can be expanded to study many additional properties, such as network classification, changes during time evolution, convergence of growth models, and detection of structural changes during damage.

  1. Social patterns revealed through random matrix theory

    Science.gov (United States)

    Sarkar, Camellia; Jalan, Sarika

    2014-11-01

    Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

  2. Ceres Revealed in a Grain of Salt

    Science.gov (United States)

    Zolensky, M. E.; Bodnar, R. J.; Chan, Q. H.-S.; Hagiya, K.; Komatsu, M.; Steele, A.; Fries, M.; Kebukawa, Y.; Mikouchi, T.; Ohsumi, K.

    2016-01-01

    Introduction: Zag and Monahans (1998) are H chondrite regolith breccias containing 4.5 giga-year-old halite crystals which contain abundant inclusions of aqueous fluids, solids and organics. These all originated on a cryo-volcanically-active C class asteroid, probably 1 Ceres; the halite was transported to the regolith of the H chondrite parent asteroid, potentially 6 Hebe. Detailed analysis of these solids will thus potentially reveal the mineralogy of Ceres. Mineralogy of solids in the Monahans Halite Solid grains are present in the halites, which were entrained within the mother brines during eruption, including material from the interior and surface of the erupting body. The solids include abundant, widely variable organics that could not have been significantly heated (which would have resulted in the loss of fluids from the halite). Our analyses by Raman microprobe, SEM/EDX, synchrotron X-ray diffraction, UPLC-FD/QToF-MS, C-XANES and TEM reveal that these trapped grains include macromolecular carbon (MMC) similar in structure to CV3 chondrite matrix carbon, aliphatic carbon compounds, olivine (Fo99-59), high- and low-Ca pyroxene, feldspars, phyllosilicates, magnetite, sulfides, metal, lepidocrocite, carbonates, diamond, apatite and zeolites. Conclusions: The halite in Monahans and Zag derive from a water and carbon-rich object that was cryo-volcanically active in the early solar system, probably Ceres. The Dawn spacecraft found that Ceres includes C chondrite materials. Our samples include both protolith and aqueously-altered samples of the body, permitting understanding of alteration conditions. Whatever the halite parent body, it was rich in a wide variety of organics and warm, liquid water at the solar system's dawn.

  3. Focus groups reveal consumer ambivalence.

    Science.gov (United States)

    1983-01-01

    According to qualitative research, Salvadoreans are ambivalent about the use of contraceptives. Since complete responsibility for management of the CSM project was accepted by the Association Demografica Salvadorena (ADS), the agency which operates the contraceptive social marketing project in El Salvador, in November 1980, the need for decisions in such areas as product price increases, introduction of new condom brands, promotion of the vaginal foaming tablet, and assessment of product sales performance had arisen. The ICSMP funded market research, completed during 1983, was intended to provide the data on which such decisions by ADS could be based. The qualitative research involved 8 focus groups, comprised of men and women, aged 18-45, contraceptive users and nonusers, from the middle and lower socioeconomic strata of the city of San Salvador and other suburban areas. In each group a moderator led discussion of family planning and probed respondents for specific attitudes, knowledge, and behavior regarding the use of contraceptives. To assess attitudes at a more emotional level, moderators asked respondents to "draw" their ideas on certain issues. A marked discrepancy was revealed between respondents' intellectual responses to the issues raised in group discussion, as opposed to their feelings expressed in the drawings. Intellectually, participants responded very positively to family planning practice, but when they were asked to draw their perceptions, ambivalent feelings emerged. Drawings of both the user and the nonuser convey primarily negative aspects for either choice. The user is tense and moody toward her children; the nonuser loses her attractiveness and "dies." Figures also show drawings of some of the attitudes of single and married male participants. 1 drawing shows an incomplete and a complete circle, symbolizing a sterilized man (incomplete) and a nonsterilized man (complete). Another picture depicts a chained man who has lost his freedom

  4. Imaging beneath the skin of large tropical rivers: Clay controls on system morphodynamics revealed by novel CHIRP sub-surface sonar and deep coring along the Fly and Strickland Rivers, Papua New Guinea (Invited)

    Science.gov (United States)

    Aalto, R. E.; Grenfell, M.; Lauer, J. W.

    2010-12-01

    Tropical rivers dominate Earth’s fluvial fluxes for water, carbon, and mineral sediment. They are characterized by large channels and floodplains, old system histories (in comparison to many temperate rivers), frequent and prolonged periods of flooding, and a clay-dominated sediment flux transported above a sandy bed. However, limited insight is available regarding the underlying bed & floodplain strata -- material that underpins system mobility and morphodynamics. Available data commonly stems from “skin-deep” approaches such as GIS analysis of imagery, shallow sampling of a surface veneer, & topographic profiling during lower river stages. Given the large temporal & spatial scales of such systems, new approaches are needed to see below lag deposits on mobile sandy beds & deep into expansive floodbasins. Furthermore, such data are needed to test whether we can usefully interpret large tropical river morphology using direct analogies to observations from small temperate sytems. Systems responding to sea level rise, pending avulsions, or an increase/contrast in sediment load would provide especially valuable insight. We conducted a field campaign along the Fly and Strickland Rivers in Papua New Guinea (discharge ~ 5,400 CMS). Immediate results were obtained using a dual-frequency CHIRP sub-bottom profiler optimized for fluvial environments, with which we were able to image 10-20m below the river/lake bed. We were able to distinguish sandy deposits from harder clay and silt lenses and also collected bed grab samples to verify our sonar results. Deep borehole samples (5-15m), push cores, and cutbank profiles of material strength confirmed observations from the sonar profiling. We simultaneously collected side-scan sonar imagery plus DGPS water/bed elevations. Findings include: 1) The prevalence of hard clay beneath the bed at many locations along the Lower Fly and Strickland Rivers, retarding migration; 2) Unusual bed morphology along the lower Middle Fly River

  5. Radioactivity reveals how crisps mix

    International Nuclear Information System (INIS)

    Many of the ''fluids'' processed in the food industry have strange flow properties that cannot easily be predicted. This is an important question in industry, since engineers need to know how such systems flow through pipes in production plants or how different components mix together. To counter this lack of knowledge, the fluids are generally processed for longer than necessary, which often proves expensive and may affect the quality of the final product. The University of Birmingham Positron Imaging Centre has developed a powerful technique to study the behaviour of crisps, yoghurt and ice cream - together with many other granular materials and viscous fluids - in a variety of industrial processes. In one case, the group labelled a single crisp using a positron-emitting radioisotope and added it to a rotating drum full of crisps. By tracking the movement of the labelled crisp, they could determine how uniformly the crisps were exposed to the flavouring that was added in the mixing process. In this article the author describes the research at the university's Positron Imaging Centre. (UK)

  6. Connecting Metabolic Potential with Thermodynamic Reality: Lithotrophic Microbial Communities of the Frasassi Cave System

    Science.gov (United States)

    McCauley, R. L.; Macalady, J. L.; Schaperdoth, I.

    2013-12-01

    If Martian life evolved during the Noachian period, it likely would have retreated to liquid water refuges where redox chemistry provided metabolically viable substrates. Present-day Mars appears to have such a refuge with data suggesting that liquid water may persist in the subsurface, however limited data is available with regards to subsurface Martian geochemistry and hydrogeology. On Earth, we find microbial communities thriving in subsurface environments utilizing a multitude of lithoautotrophic metabolisms. The Frasassi cave system in Italy hosts many such lithotrophic microbial communities, which are isolated from surface carbon, sunlight, and oxygen similar to possible Martian microbial populations. By studying the community structure, geochemistry and thermodynamics of the system, as well as the metabolic capabilities using metagenomics, we hope to discover microbes are capable of thriving in so-called 'energy-limited' environments and inform the search for life in the solar system. Two subsurface cave lakes in the Frasassi cave system, Lago Infinito and Lago dell'Orsa, have anoxic waters that host rope-like biofilm communities dominated by Deltaproteobacteria, Chloroflexi, and Planctomycetes clades. Thermodynamic calculations based on in situ geochemistry of waters surrounding the biofilms suggest very few metabolisms are energetically-feasible including: 1) anaerobic oxidation of methane (AOM) coupled with sulfate reduction 2) anaerobic ammonia oxidation (anammox) coupled with sulfate reduction 3) methanogenesis (Lago dell'Orsa only) 4) chemotrophic sulfate reduction AOM and anammox were only recently discovered and appear to have low energy yields associated with slow growth rates. AOM coupled with sulfate reduction has been shown to occur in a syntrophy between sulfate-reducing bacteria (SRB) and methanotrophic Archaea. However, these rope-like biofilms have a small (Metagenomics and carbon isotope data verify that autotrophic SRB are important in

  7. Toponome imaging system: in situ protein network mapping in normal and cancerous colon from the same patient reveals more than five-thousand cancer specific protein clusters and their subcellular annotation by using a three symbol code.

    Science.gov (United States)

    Bhattacharya, Sayantan; Mathew, George; Ruban, Ernie; Epstein, David B A; Krusche, Andreas; Hillert, Reyk; Schubert, Walter; Khan, Michael

    2010-12-01

    In a proof of principle study, we have applied an automated fluorescence toponome imaging system (TIS) to examine whether TIS can find protein network structures, distinguishing cancerous from normal colon tissue present in a surgical sample from the same patient. By using a three symbol code and a power of combinatorial molecular discrimination (PCMD) of 2(21) per subcellular data point in one single tissue section, we demonstrate an in situ protein network structure, visualized as a mosaic of 6813 protein clusters (combinatorial molecular phenotype or CMPs), in the cancerous part of the colon. By contrast, in the histologically normal colon, TIS identifies nearly 5 times the number of protein clusters as compared to the cancerous part (32 009). By subcellular visualization procedures, we found that many cell surface membrane molecules were closely associated with the cell cytoskeleton as unique CMPs in the normal part of the colon, while the same molecules were disassembled in the cancerous part, suggesting the presence of dysfunctional cytoskeleton-membrane complexes. As expected, glandular and stromal cell signatures were found, but interestingly also found were potentially TIS signatures identifying a very restricted subset of cells expressing several putative stem cell markers, all restricted to the cancerous tissue. The detection of these signatures is based on the extreme searching depth, high degree of dimensionality, and subcellular resolution capacity of TIS. These findings provide the technological rationale for the feasibility of a complete colon cancer toponome to be established by massive parallel high throughput/high content TIS mapping. PMID:20822185

  8. The 'revealed preferences' theory: Assumptions and conjectures

    International Nuclear Information System (INIS)

    Being kind of intuitive psychology the 'Revealed-Preferences'- theory based approaches towards determining the acceptable risks are a useful method for the generation of hypotheses. In view of the fact that reliability engineering develops faster than methods for the determination of reliability aims the Revealed-Preferences approach is a necessary preliminary help. Some of the assumptions on which the 'Revealed-Preferences' theory is based will be identified and analysed and afterwards compared with experimentally obtained results. (orig./DG)

  9. Trophic spectra reveal the community structure of a terrestrial system

    Science.gov (United States)

    Recent advances in compound-specific isotopic ratio analysis (CSI-AA) have allowed researchers to measure trophic fractionation of 15N in specific amino acids, namely glutamic acid and phenylalanine. These amino acids have proven useful in food web studies because of the wide and consistent disparit...

  10. Distributed neural system for emotional intelligence revealed by lesion mapping

    OpenAIRE

    Aron K Barbey; Colom, Roberto; Grafman, Jordan

    2012-01-01

    Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-base...

  11. systems

    Directory of Open Access Journals (Sweden)

    Alexander Leonessa

    2000-01-01

    Full Text Available A nonlinear robust control-system design framework predicated on a hierarchical switching controller architecture parameterized over a set of moving nominal system equilibria is developed. Specifically, using equilibria-dependent Lyapunov functions, a hierarchical nonlinear robust control strategy is developed that robustly stabilizes a given nonlinear system over a prescribed range of system uncertainty by robustly stabilizing a collection of nonlinear controlled uncertain subsystems. The robust switching nonlinear controller architecture is designed based on a generalized (lower semicontinuous Lyapunov function obtained by minimizing a potential function over a given switching set induced by the parameterized nominal system equilibria. The proposed framework robustly stabilizes a compact positively invariant set of a given nonlinear uncertain dynamical system with structured parametric uncertainty. Finally, the efficacy of the proposed approach is demonstrated on a jet engine propulsion control problem with uncertain pressure-flow map data.

  12. Revealing advantage in a quantum network

    Science.gov (United States)

    Mukherjee, Kaushiki; Paul, Biswajit; Sarkar, Debasis

    2016-07-01

    The assumption of source independence was used to reveal nonlocal (apart from standard Bell-CHSH scenario) nature of correlations generated in entanglement swapping experiments. In this work, we have discussed the various utilities of this assumption to reveal nonlocality (via generation of nonbilocal correlations) and thereby exploiting quantumness under lesser requirements compared to some standard means of doing the same. We have also provided with a set of sufficient criteria, imposed on the states (produced by the sources) under which source independence can reveal nonbilocal nature of correlations in a quantum network.

  13. Saturn's Rings Reveal Unexpected Phenomena

    Institute of Scientific and Technical Information of China (English)

    李颖

    2004-01-01

    Safely in orbit around Saturn, NASA's Cassini spacecraft sent back its first close-up images of the massive planet's rings on July 1, revealing an unexpectedly varied terrain featuring surprisingly sharp edges, braids and delicate ridges.

  14. Do markets reveal preferences or shape them?

    OpenAIRE

    Isoni, Andrea; Brooks, Peter; Loomes, Graham; Sugden, Robert

    2016-01-01

    We contrast the proposition that markets reveal independently-existing preferences with the alternative possibility that they may help to shape them. Using demand-revealing experimental market institutions, we separate the shaping effects of price cues from the effects of market discipline. We find that individual valuations and prevailing prices are systematically affected by both exogenous manipulations of price expectations and endogenous but divergent price feedback. These effects persist...

  15. Spinal Cord Compression Revealing an Intraosseous Schwannoma

    OpenAIRE

    Leila Metoui; Faïda Ajili; Mouna Maiza; Mehdi Ben Ammar; Imen Gharsallah; Issam M'sakni; Bassem Louzir; Salah Othmani

    2013-01-01

    A 68-year-old female presented with inflammatory lumbalgia and cruralgia. Physical examination revealed a lumbar stiffness without neurological deficit. Secondarily, paraplegia and urinary retention appeared. Magnetic resonance imaging showed a vertebral compaction of L3 vertebra with medullar compression. Emergent surgery revealed an epidural tumor involving largely the L3 vertebral body. Histology found schwannoma with positive protein S100 on the immunohistochemical study. Metastasis scree...

  16. Cardiac hydatid cyst revealed by ventricular tachycardia

    OpenAIRE

    Ibn Elhadj, Zied; Boukhris, Marouane; Kammoun, Ikram; Halima, Afef Ben; Addad, Faouzi; Kachboura, Salem

    2013-01-01

    Hydatid disease is a human parasitic infestation caused by the larval stage of Echinococcus Granulosus. The liver and the lungs are the most common locations. Cardiac involvement is rare and accounts for 0.5–2% of all hydatid disease. We report an unusual presentation of cardiac hydatid cyst revealed by ventricular tachycardia in a patient with a history of cerebral hydatid cyst.

  17. Consumer choice and revealed bounded rationality

    OpenAIRE

    Manzini, Paola; Mariotti, Marco

    2006-01-01

    We study two boundedly rational procedures in consumer behavior. We show that these procedures can be detected by conditions on observable demand data of the same type as standard revealed preference axioms. This provides the basis for a non-parametric analysis of boundedly rational consumer behavior mirroring the classical one for utility maximization.

  18. Eye Movements Reveal Dynamics of Task Control

    Science.gov (United States)

    Mayr, Ulrich; Kuhns, David; Rieter, Miranda

    2013-01-01

    With the goal to determine the cognitive architecture that underlies flexible changes of control settings, we assessed within-trial and across-trial dynamics of attentional selection by tracking of eye movements in the context of a cued task-switching paradigm. Within-trial dynamics revealed a switch-induced, discrete delay in onset of…

  19. Botswana’s revealed comparative advantage

    OpenAIRE

    Makochekanwa, Albert

    2007-01-01

    Analysis of Botswana’s competitiveness in world trade has been presented based on indices of revealed comparative advantage (RCA) calculated for the period 1999 and 2004. Results show that Botswana has RCA in diamonds, copper matte, and meat of bovine animals, among other products. Changes in values of RCA over time reinforce the dynamic nature of comparative advantage. The study established that the country gained comparative specialization in the following products: sugar products; copper o...

  20. Mammalian phylogeny reveals recent diversification rate shifts

    OpenAIRE

    Stadler, Tanja

    2011-01-01

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous–Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveal...

  1. Mediastinal Mature Teratoma Revealed by Empyema

    Directory of Open Access Journals (Sweden)

    Mohammed Raoufi

    2016-01-01

    Full Text Available Teratomas are germ cell tumors, manifested with a great variety of clinical features; the most common extragonadal site is the anterior mediastinum. In this case, we report the patient with a large mature mediastinal teratoma with several components of ectodermal and endothermal epithelium. A 24-year-old female patient presented with history of persistent chest pain and progressively aggravating dyspnea for the previous 3 months. A chest X-ray showed a large opacity of the entire left hemithorax. Transcutaneous needle aspiration revealed a purulent fluid. The tube thoracostomy was introduced and the effusion was evacuated. Some weeks later, patient was seen in emergency for persistent cough and lateral chest pain. CT scan revealed a mass of the left hemithorax. The mass showed heterogeneous density, without compressing mediastinum great vessels and left hilar structures. Lipase value was elevated in needle aspiration. The patient underwent a total resection of the mediastinum mass via a left posterolateral thoracotomy. Microscopy revealed a mature teratoma with cystic structures. The patient subsequently made a full recovery. This case provide benign mediastinal teratoma with total atelectasis of left lung and elevated lipase value in needle transcutaneous aspiration; this event is explained by pancreatic component in the cystic tumor. Total removal of the tumor is adequate treatment for this type of teratoma and the prognosis is excellent.

  2. Mediastinal Mature Teratoma Revealed by Empyema.

    Science.gov (United States)

    Raoufi, Mohammed; Herrak, Laila; Benali, Anas; Achaachi, Leila; El Ftouh, Mustapha; Bellarbi, Salma; Tilfine, Charaf; Taouarsa, Firdaous

    2016-01-01

    Teratomas are germ cell tumors, manifested with a great variety of clinical features; the most common extragonadal site is the anterior mediastinum. In this case, we report the patient with a large mature mediastinal teratoma with several components of ectodermal and endothermal epithelium. A 24-year-old female patient presented with history of persistent chest pain and progressively aggravating dyspnea for the previous 3 months. A chest X-ray showed a large opacity of the entire left hemithorax. Transcutaneous needle aspiration revealed a purulent fluid. The tube thoracostomy was introduced and the effusion was evacuated. Some weeks later, patient was seen in emergency for persistent cough and lateral chest pain. CT scan revealed a mass of the left hemithorax. The mass showed heterogeneous density, without compressing mediastinum great vessels and left hilar structures. Lipase value was elevated in needle aspiration. The patient underwent a total resection of the mediastinum mass via a left posterolateral thoracotomy. Microscopy revealed a mature teratoma with cystic structures. The patient subsequently made a full recovery. This case provide benign mediastinal teratoma with total atelectasis of left lung and elevated lipase value in needle transcutaneous aspiration; this event is explained by pancreatic component in the cystic tumor. Total removal of the tumor is adequate treatment for this type of teratoma and the prognosis is excellent. PMID:27144046

  3. Complex Hydrocarbon Chemistry in Interstellar and Solar System Ices Revealed: A Combined Infrared Spectroscopy and Reflectron Time-of-flight Mass Spectrometry Analysis of Ethane (C2H6) and D6-Ethane (C2D6) Ices Exposed to Ionizing Radiation

    Science.gov (United States)

    Abplanalp, Matthew J.; Kaiser, Ralf I.

    2016-08-01

    The irradiation of pure ethane (C2H6/C2D6) ices at 5.5 K, under ultrahigh vacuum conditions was conducted to investigate the formation of complex hydrocarbons via interaction with energetic electrons simulating the secondary electrons produced in the track of galactic cosmic rays. The chemical modifications of the ices were monitored in situ using Fourier transform infrared spectroscopy (FTIR) and during temperature-programmed desorption via mass spectrometry exploiting a quadrupole mass spectrometer with electron impact ionization (EI-QMS) as well as a reflectron time-of-flight mass spectrometer coupled to a photoionization source (PI-ReTOF-MS). FTIR confirmed previous ethane studies by detecting six molecules: methane (CH4), acetylene (C2H2), ethylene (C2H4), the ethyl radical (C2H5), 1-butene (C4H8), and n-butane (C4H10). However, the TPD phase, along with EI-QMS, and most importantly, PI-ReTOF-MS, revealed the formation of at least 23 hydrocarbons, many for the first time in ethane ice, which can be arranged in four groups with an increasing carbon-to-hydrogen ratio: C n H2n+2 (n = 3, 4, 6, 8, 10), C n H2n (n = 3–10), {{{C}}}n{{{H}}}2n-2 (n = 3–10), and {{{C}}}n{{{H}}}2n-4 (n = 4–6). The processing of simple ethane ices is relevant to the hydrocarbon chemistry in the interstellar medium, as ethane has been shown to be a major product of methane, as well as in the outer solar system. These data reveal that the processing of ethane ices can synthesize several key hydrocarbons such as C3H4 and C4H6 isomers, which ha­ve been found to synthesize polycyclic aromatic hydrocarbons like indene (C9H8) and naphtha­lene (C10H8) in the ISM and in hydrocarbon-rich atmospheres of planets and their moons such as Titan.

  4. Transient light-induced intracellular oxidation revealed by redox biosensor

    International Nuclear Information System (INIS)

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition

  5. Transient light-induced intracellular oxidation revealed by redox biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Kolossov, Vladimir L., E-mail: viadimer@illinois.edu [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Beaudoin, Jessica N. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Hanafin, William P. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); DiLiberto, Stephen J. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Kenis, Paul J.A. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801 (United States); Rex Gaskins, H. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 S. Lincoln Avenue, Urbana, IL 61801 (United States); Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 S. Goodwin Avenue, Urbana, IL 61801 (United States)

    2013-10-04

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition.

  6. Is Romanian Rural Tourism Sustainable? Revealing Particularities

    OpenAIRE

    Daniela Ruxandra Andrei; Rodica-Manuela Gogonea; Marian Zaharia; Jean-Vasile Andrei

    2014-01-01

    Research on sustainable tourism involves developing an appropriate framework to highlight the interdependences of economic, social and environmental systems. The interdependence is based on the entropy of the system while respecting the principle of holism and diversity of rural tourism sustainability. In this context, sustainability in general and rural tourism in particular can be considered a complex system of development, which in some ways can be studied by statistical and econometric me...

  7. Midface swelling reveals nasofrontal dermal sinus

    International Nuclear Information System (INIS)

    Nasofrontal dermal sinuses are very rare and generally occur in children. This congenital malformation can be revealed by midface swelling, which can be complicated by local infection or neuromeningitis. Such complications make the dermal sinus a life-threatening disease. Two cases of nasofrontal dermal sinuses are reported in this work. The first case is an 11-month-old girl who presented with left orbitonasal soft tissue swelling accompanied by inflammation. Physical examination found fever, left orbitonasal thickening, and a puncture hole letting out pus. Computed tomography revealed microabscesses located at the left orbitonasal soft tissues, a frontal bone defect, and an intracranial cyst. Magnetic resonance imaging showed the transosseous tract between the glabella and the brain and affirmed the epidermoid nature of the intracranial cyst. The second case is a 7-year-old girl who presented with a nasofrontal non-progressive mass that intermittently secreted a yellow liquid through an external orifice located at the glabella. MRI revealed a cystic mass located in the deep layer of the glabellar skin related to an epidermoid cyst with a nasofrontal dermal sinus tract. In both cases, surgical excision was performed, and pathological confirmation was made for the diagnoses of dermal sinuses. The postoperative course was favorable. Through these cases, the authors stress the role of imaging methods in confirming the diagnosis and looking for associated cysts (dermoid and epidermoid) to improve recognition of this rare disease. Knowledge of the typical clinical presentations, imaging manifestations, and most common sites of occurrence of this malformation are needed to formulate a differential diagnosis.

  8. Revealing digital documents. Concealed structures in data

    CERN Document Server

    Voß, Jakob

    2011-01-01

    This short paper gives an introduction to a research project to analyze how digital documents are structured and described. Using a phenomenological approach, this research will reveal common patterns that are used in data, independent from the particular technology in which the data is available. The ability to identify these patterns, on different levels of description, is important for several applications in digital libraries. A better understanding of data structuring will not only help to better capture singular characteristics of data by metadata, but will also recover intended structures of digital objects, beyond long term preservation.

  9. Interior Evolution of Ceres Revealed by Dawn

    Science.gov (United States)

    Raymond, Carol A.; Park, Ryan S.; Konopliv, Alex S.; Bland, Michael T.; Marchi, Simone; Castillo-Rogez, Julie C.; McCord, Thomas B.; Jaumann, Ralf; Russell, Christopher T.; Prettyman, Thomas H.

    2015-11-01

    Dawn's exploration of Ceres has revealed its geophysical characteristics, informing the processes that have shaped it. Dawn has determined the average diameter of Ceres to be 940 km, smaller than the previously estimated 975 km [1]. This implies a density of 2160 kg/m3, indicating that Ceres is less differentiated than predicted [2]. The low-degree gravity field is consistent with the body being in hydrostatic equilibrium and the magnitude of J2 implies some central condensation. Ceres' entire surface is cratered, implying the lack of a thick (10's of km) water ice layer at the surface. Variability in Ceres' crater morphology indicates that the near-surface layer has variable strength and rheology, likely due to heterogeneity in the near-surface mixture of rock, ice and salt. The lack of a number of expected large impact basins on Ceres can be interpreted to be the result of viscous relaxation, resurfacing or a combination of both. These data provide insights into Ceres' thermal evolution and mechanical properties, which appear to be unique to this warm, icy body.[1] Thomas, P. C., et al., Differentiation of the asteroid Ceres as revealed by its shape, Nature, 437, 224-226, 2005; [2] McCord et al., Ceres: Its Origin, Evolution and Structure and Dawn's Potential Contribution, Space Sci Rev DOI 10.1007/s11214-010-9729-9, 2011.

  10. Narratives and Emotions: Revealing and Concealing Laughter

    Directory of Open Access Journals (Sweden)

    Lena Marander-Eklund

    2008-08-01

    Full Text Available My paper deals with laughter as an expression of emotions in stories.I study laughter both as a communicative factor in fieldwork and as a stylistic device in narratives. When is laughter used as an effect in storytelling and what does this laughter mean? Is laughter always an expression of humour and comics? What else can it be an expression of? The stories that I use for analysing laughter are personal experience stories of giving birth. In these stories women use laughter in many ways, both in contact with me as an interviewer, together with me, and as a way of marking the meaning of the story. The women often laugh when they talk about corporeality, pain and difficulties during labour, but also when they perform a self-presentation with elements that “almost” happened during birth. What do they reveal or conceal with laughter in narratives and what can the laughter reveal about the point of their narration?

  11. North Korea's nuclear power programme revealed

    International Nuclear Information System (INIS)

    The extent of the nuclear programme in the Democratic People's Republic of Korea (DPRK) was revealed in May 1992: reports on the country's facilities were handed to the International Atomic Energy Agency and an Agency group visited Korea on a ''familiarisation visit''. DPRK's nuclear programme had been the subject of speculation for some time. While the country had signed the Non-Proliferation Treaty and two facilities were already under IAEA safeguards - a research reactor and a critical facility, both at the Institute of Nuclear Physics - there were a number of indicators that DPRK was pursuing a nuclear programme aimed at military use. The new openness was prompted by a number of factors including discussions on closer relations with South Korea. DPRK signed a comprehensive Safeguards Agreement on 30 January 1992. On the familiarisation visit by the IAEA director general in May the DPRK revealed nuclear facilities in operation or under construction at five sites. At Pakchon and Pyongsan: each site housed a uranium mine and uranium-ore concentration plant. At Pyongyang: the two facilities already under safeguards at the Institute of Nuclear Physics; and a sub critical facility at Kim Il Sung university. At Nyongbyon: a fuel fabrication plant; an 5MWe experimental power reactor, in operation; a 50MWe prototype power reactor under construction; and a facility ultimately intended as a reprocessing plant, but described by North Korea, because of its unfinished state, as a laboratory. At Taechon: a 200MWe power reactor under construction. (author)

  12. Transcriptome classification reveals molecular subtypes in psoriasis

    Directory of Open Access Journals (Sweden)

    Ainali Chrysanthi

    2012-09-01

    Full Text Available Abstract Background Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phenotypes, such as plaque psoriasis, are well defined, it is currently unclear whether there are molecular subtypes that might impact on prognosis or treatment outcomes. Results We present a pipeline for patient stratification through a comprehensive analysis of gene expression in paired lesional and non-lesional psoriatic tissue samples, compared with controls, to establish differences in RNA expression patterns across all tissue types. Ensembles of decision tree predictors were employed to cluster psoriatic samples on the basis of gene expression patterns and reveal gene expression signatures that best discriminate molecular disease subtypes. This multi-stage procedure was applied to several published psoriasis studies and a comparison of gene expression patterns across datasets was performed. Conclusion Overall, classification of psoriasis gene expression patterns revealed distinct molecular sub-groups within the clinical phenotype of plaque psoriasis. Enrichment for TGFb and ErbB signaling pathways, noted in one of the two psoriasis subgroups, suggested that this group may be more amenable to therapies targeting these pathways. Our study highlights the potential biological relevance of using ensemble decision tree predictors to determine molecular disease subtypes, in what may initially appear to be a homogenous clinical group. The R code used in this paper is available upon request.

  13. Revealing Hidden Coherence in Partially Coherent Light

    CERN Document Server

    Svozilík, Jiří; Peřina, Jan; Torres, Juan P

    2015-01-01

    The coherence of a system can be ultimately related to the nature of its correlations with the surroundings (outside world). The system can be, for instance, the polarization of a photon, which forms part of a polarization-entangled two-photon state, or the spatial shape of a coherent beam, where each spatial mode bears different polarizations. Whereas a local unitary transformation of the system do not affect its coherence, global unitary transformations modifying both the system and its surroundings can enhance its coherence transforming mutual correlations into coherence. The question naturally arises of what is the best measure that quantifies the correlations that can be turned into coherence, and how much coherence can be extracted. We answer both questions, and illustrate its application for some typical simple systems, with the aim at illuminating the general concept of enhancing coherence by modifying correlations.

  14. Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints

    Directory of Open Access Journals (Sweden)

    Grigory Genikhovich

    2015-03-01

    Full Text Available BMP signaling plays a crucial role in the establishment of the dorso-ventral body axis in bilaterally symmetric animals. However, the topologies of the bone morphogenetic protein (BMP signaling networks vary drastically in different animal groups, raising questions about the evolutionary constraints and evolvability of BMP signaling systems. Using loss-of-function analysis and mathematical modeling, we show that two signaling centers expressing different BMPs and BMP antagonists maintain the secondary axis of the sea anemone Nematostella. We demonstrate that BMP signaling is required for asymmetric Hox gene expression and mesentery formation. Computational analysis reveals that network parameters related to BMP4 and Chordin are constrained both in Nematostella and Xenopus, while those describing the BMP signaling modulators can vary significantly. Notably, only chordin, but not bmp4 expression needs to be spatially restricted for robust signaling gradient formation. Our data provide an explanation of the evolvability of BMP signaling systems in axis formation throughout Eumetazoa.

  15. Chemotaxis: new role for Ras revealed

    Institute of Scientific and Technical Information of China (English)

    Jianshe Yan; Dale Hereld; Tian Jin

    2010-01-01

    @@ A recent study of chemotaxis revealed a new role for the proto-oncogene Ras in the social ameba Dictyostelium discoideum.Chemotaxis,the directional movement of cells toward chemokines and other chemoattractants,plays critical roles in diverse physiological processes,such as mobilization of immune cells to fight invading microorganisms,targeting of metastatic cancer cells to specific tissues,and guidance of sperm cells to ova during fertilization.This work,published in the July 26 issue of The Journal of Cell Biology,was conducted in Dr.Devreotes' lab at John Hopkins University and Dr.Parent's lab at National Cancer Institute.This research team demonstrated that RasC functions as an upstream regulator of TORC2 and thereby governs the effects of TORC2-PKB signaling on the cytoskeleton and cell migration.

  16. Revealed Quantum Information in Weak Interaction Processes

    CERN Document Server

    Hiesmayr, B C

    2014-01-01

    We analyze the achievable limits of the quantum information processing of the weak interaction revealed by hyperons with spin. We find that the weak decay process corresponds to an interferometric device with a fixed visibility and fixed phase difference for each hyperon. Nature chooses rather low visibilities expressing a preference to parity conserving or violating processes (except for the decay $\\Sigma^+\\longrightarrow p \\pi^0$). The decay process can be considered as an open quantum channel that carries the information of the hyperon spin to the angular distribution of the momentum of the daughter particles. We find a simple geometrical information theoretic interpretation of this process: two quantization axes are chosen spontaneously with probabilities $\\frac{1\\pm\\alpha}{2}$ where $\\alpha$ is proportional to the visibility times the real part of the phase shift. Differently stated the weak interaction process corresponds to spin measurements with an imperfect Stern-Gerlach apparatus. Equipped with this...

  17. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Jeffrey [ORNL; Bilheux, Hassina Z [ORNL; Kang, Misun [ORNL; Voisin, Sophie [ORNL; Cheng, Chu-Lin [ORNL; Horita, Jusuke [ORNL; Perfect, Edmund [ORNL

    2013-01-01

    Many terrestrial ecosystem processes are constrained by water availability and transport within the soil. Knowledge of plant water fluxes is thus critical for assessing mechanistic processes linked to biogeochemical cycles, yet resolution of root structure and xylem water transport dynamics has been a particularly daunting task for the ecologist. Through neutron imaging, we demonstrate the ability to non-invasively monitor individual root functionality and water fluxes within Zea mays L. (maize) and Panicum virgatum L. (switchgrass) seedlings growing in a sandy medium. Root structure and growth were readily imaged by neutron radiography and neutron computed tomography. Seedlings were irrigated with water or deuterium oxide and imaged through time as a growth lamp was cycled on to alter leaf demand for water. Sub-millimeter scale resolution reveals timing and magnitudes of root water uptake, redistribution within the roots, and root-shoot hydraulic linkages, relationships not well characterized by other techniques.

  18. New mechanism revealed for regulation of autoimmunity

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ A healthy human body is equipped with a powerful immune system for resisting the attack of invading microorganisms. Unfortunately, the system sometimes goes awry and attacks the body itself.Autoimmunity is the failure of an organism to recognize its own constituent parts as"self," resulting in an immune response against its own cells and tissues. A disorder that results from such an aberrant immune response is termed an autoimmune disease.

  19. Is Romanian Rural Tourism Sustainable? Revealing Particularities

    Directory of Open Access Journals (Sweden)

    Daniela Ruxandra Andrei

    2014-12-01

    Full Text Available Research on sustainable tourism involves developing an appropriate framework to highlight the interdependences of economic, social and environmental systems. The interdependence is based on the entropy of the system while respecting the principle of holism and diversity of rural tourism sustainability. In this context, sustainability in general and rural tourism in particular can be considered a complex system of development, which in some ways can be studied by statistical and econometric methods that allow the analysis of the interdependences between the variables of rural tourism at county level and at the level of rural communities. Conducting such studies involves identifying the rural communities where rural tourism has reached significant levels. Based on this consideration, this paper aims to identify the development regions and counties of Romania where the trends of development of rural tourism are significantly above the average recorded at country level, as a first step towards particular studies of sustainability in rural communities.

  20. Spectrins in axonal cytoskeletons: Dynamics revealed by extensions and fluctuations

    Science.gov (United States)

    Lai, Lipeng; Cao, Jianshu

    2014-07-01

    The macroscopic properties, the properties of individual components, and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the study of complex systems. Using axonal cytoskeleton as an example system, here we perform a theoretical study of slender structures that can be coarse-grained as a simple smooth three-dimensional curve. We first present a generic model for such systems based on the fundamental theorem of curves. We use this generic model to demonstrate the applicability of the well-known worm-like chain (WLC) model to the network level and investigate the situation when the system is stretched by strong forces (weakly bending limit). We specifically studied recent experimental observations that revealed the hitherto unknown periodic cytoskeleton structure of axons and measured the longitudinal fluctuations. Instead of focusing on single molecules, we apply analytical results from the WLC model to both single molecule and network levels and focus on the relations between extensions and fluctuations. We show how this approach introduces constraints to possible local dynamics of the spectrin tetramers in the axonal cytoskeleton and finally suggests simple but self-consistent dynamics of spectrins in which the spectrins in one spatial period of axons fluctuate in-sync.

  1. NMR Revealed Activated Alumina-Water Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHOU Rui; ZHOU Yan; HU Kai; JI Zhen-ping; CHENG Gong-zhen

    2005-01-01

    Three different spin-lattice relaxation times (T1) of water were obtained in activated alumina-water slurry system, which indicate that there exist three states of water: bound water, pore water and bulk water. The chemical shift (δH) decreases as the amount of water added to the system increases due to the differences in contribution of these three states of water in the samples. The δH value for adsorbed water decreases nearly linearly and T1 increases with elevating temperature, which result from the decrease in the content of bound water by the increase in thermal motion.

  2. What School Financial Reports Reveal and Hide.

    Science.gov (United States)

    Walters, Donald L.

    The problem of full disclosure of the financial operation and position of a school system is discussed in this paper. Techniques described for analyzing revenue and expenditure patterns include percentage changes and index numbers for horizontal analysis and proportions for vertical analysis. Also discussed are how financial reports are affected…

  3. Polyradiculoneuritis revealing an acute monoblastic leukemia 5

    OpenAIRE

    Wafa Allam; Hassan Errihani; Yahya Hsaini

    2010-01-01

    Acute polyradiculoneuritis has been frequently reported in association with malignant disorders, especially those of the lymphoid system. To date, there have been no reported cases of acute monoblastic leukemia associated with this polyradiculopathy. The authors tell us about a very rare case of leukemia presenting as acute monoblastic leukemia 5 (AML5) in a 28 years old patient from Morroco

  4. Revealing source signatures in ambient BTEX concentrations

    International Nuclear Information System (INIS)

    Management of ambient concentrations of Volatile Organic Compounds (VOCs) is essential for maintaining low ozone levels in urban areas where its formation is under a VOC-limited regime. The significant decrease in traffic-induced VOC emissions in many developed countries resulted in relatively comparable shares of traffic and non-traffic VOC emissions in urban airsheds. A key step for urban air quality management is allocating ambient VOC concentrations to their pertinent sources. This study presents an approach that can aid in identifying sources that contribute to observed BTEX concentrations in areas characterized by low BTEX concentrations, where traditional source apportionment techniques are not useful. Analysis of seasonal and diurnal variations of ambient BTEX concentrations from two monitoring stations located in distinct areas reveal the possibility to identify source categories. Specifically, the varying oxidation rates of airborne BTEX compounds are used to allocate contributions of traffic emissions and evaporative sources to observed BTEX concentrations. - BTEX sources are identified from temporal variations of ambient concentration

  5. Revealing the values behind convenience food consumption.

    Science.gov (United States)

    Botonaki, Anna; Mattas, Konstadinos

    2010-12-01

    The increasing importance of convenience in consumer food choices has attracted researchers' interest. In the effort to understand how convenience affects consumers' food preferences, values are believed to play an important role. The present study attempts to examine the way personal values suggested by Schwartz (1992) are associated with behaviour and attitudes regarding convenience food. A number of constructs describing food related attitudes and behaviours were developed and their relationship with personal values was analyzed following the methodology proposed by Brunsø, Scholderer, and Grunert (2004). Data were collected through a questionnaire survey from a random sample of consumers in Thessaloniki city, Greece. The results reveal that convenience food consumption and convenience orientation in the food domain are mainly connected with values that motivate people to seek new experiences, act independently and enhance their own personal interests, while are in conflict with values of conservation and self-transcendence. The opposite holds for other food related attitudes and behaviours like involvement with cooking and variety in diet. The findings seem to be of particular interest not only for marketers of food products, but also for food policy makers. PMID:20875475

  6. ERYTHEMA NODOSUM REVEALING ACUTE MYELOID LEUKEMIA

    Directory of Open Access Journals (Sweden)

    Chebbi Wafa

    2013-07-01

    Full Text Available Introduction: Erythema nodosum (EN is the most common type of panniculitis. It may be idiopathic or secondary to various etiologies. However, the occurrence of erythema nodosum in malignant hemopathy had rarely been reported. Case report: A 42 year-old woman presented with a four week history of recurrent multiple painful erythematous nodules developed on the lower limbs associated with arthralgia of the ankles and fever. The clinical features of skin lesions with contusiform color evolution allowed establishing the diagnosis of EN. No underlying cause was found. The skin lesions were improved with non-steroidal anti-inflammatory drugs and colchicine. Three months later, the patient consulted for recurrence of EN associated with fever, inflammatory polyarthralgia and hepatosplenomegaly. The peripheral blood count revealed pancytopenia. A bone marrow examination confirmed the diagnosis of acute myeloid leukemia type 2. Initiation of chemotherapy was followed by the complete disappearance of skin lesions of EN. Conclusion: Paraneoplastic erythema nodosum is a rare entity. In the literature, a few cases of association with leukemia have been reported. Exploration for solid neoplasms or hemopathy in case of recurrent EN or resistance to conventional treatment should be systematic

  7. VISTA Reveals the Secret of the Unicorn

    Science.gov (United States)

    2010-10-01

    A new infrared image from ESO's VISTA survey telescope reveals an extraordinary landscape of glowing tendrils of gas, dark clouds and young stars within the constellation of Monoceros (the Unicorn). This star-forming region, known as Monoceros R2, is embedded within a huge dark cloud. The region is almost completely obscured by interstellar dust when viewed in visible light, but is spectacular in the infrared. An active stellar nursery lies hidden inside a massive dark cloud rich in molecules and dust in the constellation of Monoceros. Although it appears close in the sky to the more familiar Orion Nebula it is actually almost twice as far from Earth, at a distance of about 2700 light-years. In visible light a grouping of massive hot stars creates a beautiful collection of reflection nebulae where the bluish starlight is scattered from parts of the dark, foggy outer layers of the molecular cloud. However, most of the new-born massive stars remain hidden as the thick interstellar dust strongly absorbs their ultraviolet and visible light. In this gorgeous infrared image taken from ESO's Paranal Observatory in northern Chile, the Visible and Infrared Survey Telescope for Astronomy (VISTA [1], eso0949) penetrates the dark curtain of cosmic dust and reveals in astonishing detail the folds, loops and filaments sculpted from the dusty interstellar matter by intense particle winds and the radiation emitted by hot young stars. "When I first saw this image I just said 'Wow!' I was amazed to see all the dust streamers so clearly around the Monoceros R2 cluster, as well as the jets from highly embedded young stellar objects. There is such a great wealth of exciting detail revealed in these VISTA images," says Jim Emerson, of Queen Mary, University of London and leader of the VISTA consortium. With its huge field of view, large mirror and sensitive camera, VISTA is ideal for obtaining deep, high quality infrared images of large areas of the sky, such as the Monoceros R2 region

  8. Differential metabolism of Mycoplasma species as revealed by their genomes

    Directory of Open Access Journals (Sweden)

    Fabricio B.M. Arraes

    2007-01-01

    Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

  9. Neuropeptide Receptor Transcriptome Reveals Unidentified Neuroendocrine Pathways

    OpenAIRE

    Yamanaka, Naoki; Yamamoto, Sachie; Žitňan, Dušan; Watanabe, Ken; Kawada, Tsuyoshi; Satake, Honoo; Kaneko, Yu; Hiruma, Kiyoshi; Tanaka, Yoshiaki; Shinoda, Tetsuro; Kataoka, Hiroshi

    2008-01-01

    Neuropeptides are an important class of molecules involved in diverse aspects of metazoan development and homeostasis. Insects are ideal model systems to investigate neuropeptide functions, and the major focus of insect neuropeptide research in the last decade has been on the identification of their receptors. Despite these vigorous efforts, receptors for some key neuropeptides in insect development such as prothoracicotropic hormone, eclosion hormone and allatotropin (AT), remain undefined. ...

  10. NASA's Hyperwall Revealing the Big Picture

    Science.gov (United States)

    Sellers, Piers

    2011-01-01

    NASA:s hyperwall is a sophisticated visualization tool used to display large datasets. The hyperwall, or video wall, is capable of displaying multiple high-definition data visualizations and/or images simultaneously across an arrangement of screens. Functioning as a key component at many NASA exhibits, the hyperwall is used to help explain phenomena, ideas, or examples of world change. The traveling version of the hyperwall is typically comprised of nine 42-50" flat-screen monitors arranged in a 3x3 array (as depicted below). However, it is not limited to monitor size or number; screen sizes can be as large as 52" and the arrangement of screens can include more than nine monitors. Generally, NASA satellite and model data are used to highlight particular themes in atmospheric, land, and ocean science. Many of the existing hyperwall stories reveal change across space and time, while others display large-scale still-images accompanied by descriptive, story-telling captions. Hyperwall content on a variety of Earth Science topics already exists and is made available to the public at: eospso.gsfc.nasa.gov/hyperwall. Keynote and PowerPoint presentations as well as Summary of Story files are available for download on each existing topic. New hyperwall content and accompanying files will continue being developed to promote scientific literacy across a diverse group of audience members. NASA invites the use of content accessible through this website but requests the user to acknowledge any and all data sources referenced in the content being used.

  11. Revealing of Mycobacterium marinum transcriptome by RNA-seq.

    Directory of Open Access Journals (Sweden)

    Sen Wang

    Full Text Available Transcriptome analysis has played an essential role for revealing gene expression and the complexity of regulations at transcriptional level. RNA-seq is a powerful tool for transcriptome profiling, which uses deep-sequencing technologies to directly determine the cDNA sequence. Here, we utilized RNA-seq to explore the transcriptome of Mycobacteriummarinum (M. marinum, which is a useful model to study the pathogenesis of Mycobacterium tuberculosis (Mtb. Two profiles of exponential and early stationary phase cultures were generated after a physical ribosome RNA removal step. We systematically described the transcriptome and analyzed the functions for the differentiated expressed genes between the two phases. Furthermore, we predicted 360 operons throughout the whole genome, and 13 out of 17 randomly selected operons were validated by qRT-PCR. In general, our study has primarily uncovered M. marinum transcriptome, which could help to gain a better understanding of the regulation system in Mtb that underlines disease pathogenesis.

  12. Cyp1a reporter zebrafish reveals target tissues for dioxin

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kun-Hee [Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju (Korea, Republic of); Department of Microbiology, Chonnam National University Medical School, Gwangju (Korea, Republic of); Park, Hye-Jeong [Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju (Korea, Republic of); Kim, Jin Hee [Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju (Korea, Republic of); Department of Microbiology, Chonnam National University Medical School, Gwangju (Korea, Republic of); Kim, Suhyun [Graduate School of Medicine, Korea University, Ansan (Korea, Republic of); Williams, Darren R. [New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju (Korea, Republic of); Kim, Myeong-Kyu [Department of Neurology, Chonnam National University Medical School, Gwangju (Korea, Republic of); Jung, Young Do [Department of Biochemistry, Chonnam National University Medical School, Gwangju (Korea, Republic of); Teraoka, Hiroki [School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu (Japan); Park, Hae-Chul [Graduate School of Medicine, Korea University, Ansan (Korea, Republic of); Choy, Hyon E., E-mail: hyonchoy@chonnam.ac.kr [Department of Microbiology, Chonnam National University Medical School, Gwangju (Korea, Republic of); Shin, Boo Ahn, E-mail: bashin@chonnam.ac.kr [Department of Microbiology, Chonnam National University Medical School, Gwangju (Korea, Republic of); Choi, Seok-Yong, E-mail: zebrafish@chonnam.ac.kr [Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju (Korea, Republic of); School of Biological Sciences and Technology, Chonnam National University, Gwangju (Korea, Republic of)

    2013-06-15

    Highlights: •2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is the most toxic anthropogenic substance ever identified. •Transgenic cyp1a reporter zebrafish reveals target tissues for TCDD. •The retinal bipolar cells, otic vesicle, lateral line, pancreas, cloaca and pectoral fin bud are novel targets in zebrafish for TCDD. •Our findings will further understanding of human health risks by TCDD. -- Abstract: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is the unintentional byproduct of various industrial processes, is classified as human carcinogen and could disrupt reproductive, developmental and endocrine systems. Induction of cyp1a1 is used as an indicator of TCDD exposure. We sought to determine tissues that are vulnerable to TCDD toxicity using a transgenic zebrafish (Danio rerio) model. We inserted a nuclear enhanced green fluorescent protein gene (EGFP) into the start codon of a zebrafish cyp1a gene in a fosmid clone using DNA recombineering. The resulting recombineered fosmid was then used to generate cyp1a reporter zebrafish, embryos of which were exposed to TCDD. Expression pattern of EGFP in the reporter zebrafish mirrored that of endogenous cyp1a mRNA. In addition, exposure of the embryos to TCDD at as low as 10 pM for 72 h, which does not elicit morphological abnormalities of embryos, markedly increased GFP expression. Furthermore, the reporter embryos responded to other AhR ligands as well. Exposure of the embryos to TCDD revealed previously reported (the cardiovascular system, liver, pancreas, kidney, swim bladder and skin) and unreported target tissues (retinal bipolar cells, otic vesicle, lateral line, cloaca and pectoral fin bud) for TCDD. Transgenic cyp1a reporter zebrafish we have developed can further understanding of ecotoxicological relevance and human health risks by TCDD. In addition, they could be used to identify agonists of AhR and antidotes to TCDD toxicity.

  13. Passive seismology reveals biannual calving periodicity

    Science.gov (United States)

    Bartholomaus, T. C.; Larsen, C. F.; West, M. E.; Oneel, S.

    2013-12-01

    Iceberg calving is a large and variable component of the total mass loss from marine-terminating glaciers worldwide. However, the processes that control the size and variability of calving fluxes are poorly understood. Even more basic descriptions of iceberg calving, such as its seasonality, are uncertain. Here, we present nearly two years of automatically-estimated calving fluxes at Yahtse Glacier, a tidewater glacier whose terminus flows at ~7 km/yr towards the Gulf of Alaska. At the terminus, ice losses to calving and submarine melt total approximately 1.5 km^3/yr. In order to identify temporal variability in this mean rate, we develop a statistical model of calving size based on characteristics of calving-generated icequakes. These characteristics include 4 amplitude-based variables and 5 variables related to the shape of the icequake envelope. We build our model by combining automatically-detected icequakes (O'Neel et al., 2007) located at the terminus of Yahtse Glacier (Jones et al., 2013) with a training set of 1400 icequakes produced by visually-observed calving events (Bartholomaus et al., 2012). In each of the models tested (regression trees, multinomial logistic regression and multiple linear regession), icequake duration emerges as the single best predictor of iceberg size, consistent with past studies (Qamar, 1988; O'Neel et al., 2007). Additional predictors, such as the mean icequake amplitude and the kurtosis of the icequake envelope improve the predictive capability of the model and reduce the mean squared error to well-within the error of the in-person classification. Once validated, we apply our model to ~ 400,000 icequakes produced by calving events at Yahtse Glacier between June 2009 and September 2011. These results reveal fluctuations in calving rate at a range of timescales, including twice per year. We suggest that the roughly 50%, biannual variation in calving rate is the result of the trade-off between two competing processes at the

  14. Microradiometers Reveal Ocean Health, Climate Change

    Science.gov (United States)

    2013-01-01

    When NASA researcher Stanford Hooker is in the field, he pays close attention to color. For Hooker, being in the field means being at sea. On one such research trip to the frigid waters of the Arctic, with a Coast Guard icebreaker looming nearby and the snow-crusted ice shelf a few feet away, Hooker leaned over the edge of his small boat and lowered a tethered device into the bright turquoise water, a new product devised by a NASA partner and enabled by a promising technology for oceanographers and atmospheric scientists alike. Color is a function of light. Pure water is clear, but the variation in color observed during a visit to the beach or a flight along a coastline depends on the water s depth and the constituents in it, how far down the light penetrates and how it is absorbed and scattered by dissolved and suspended material. Hooker cares about ocean color because of what it can reveal about the health of the ocean, and in turn, the health of our planet. "The main thing we are interested in is the productivity of the water," Hooker says. The seawater contains phytoplankton, microscopic plants, which are the food base for the ocean s ecosystems. Changes in the water s properties, whether due to natural seasonal effects or human influence, can lead to problems for delicate ecosystems such as coral reefs. Ocean color can inform researchers about the quantities and distribution of phytoplankton and other materials, providing clues as to how the world ocean is changing. NASA s Coastal Zone Color Scanner, launched in 1978, was the first ocean color instrument flown on a spacecraft. Since then, the Agency s ocean color research capabilities have become increasingly sophisticated with the launch of the SeaWiFS instrument in 1997 and the twin MODIS instruments carried into orbit on NASA s Terra (1999) and Aqua (2002) satellites. The technology provides sweeping, global information on ocean color on a scale unattainable by any other means. One issue that arises from

  15. Abrasive supply for ancient Egypt revealed

    International Nuclear Information System (INIS)

    In the framework of the major research scheme 'Synchronization of Civilizations in the Eastern Mediterranean Region in the 2nd Millennium B.C' instrumental neutron activation analysis (INAA) was used to determine 30 elements in pumice from archaeological excavations to reveal their specific volcanic origin. In ancient time, the widespread pumiceous products of several eruptions in the Aegean region have been used as abrasive tools and were therefore popular trade objects. The correlation of such archaeological findings to a specific eruption of known age would therefore allow to certify a maximum age of the respective stratum ('dating by first appearance'). Pumices from the Aegean region can easily be distinguished by their trace element distribution patterns. This has been shown by previous studies of the group. The elements Al, Ba, Ca, Ce, Co, Cr, Cs, Dy, Eu, Fe, Hf, K, La, Lu, Mn, Na, Nd, Rb, Sb, Sc, Sm, Ta, Tb, Th, Ti, U, V, Yb, Zr and Zn were determined in 16 samples of pumice lumps from excavations in Tell-el-Dab'a and Tell-el-Herr (Egypt). Two irradiation cycles and five measurement runs were applied. To show the accuracy of the results obtained, typical samples of the most important pumice sources in the Aegean region, particularly from Milos, Nisyros, Kos and Thera were analyzed together with the Egyptian samples of unknown origin. A reliable identification of the samples is achieved by comparing these results to the database compiled in previous studies. The geographical positions of these islands are shown. Within the error range, most of the elements determined in typical representatives of Milos, Nisyros, Kos and Santorini were in perfect agreement with values from the literature. On the basis of the Cluster graphics presented, it is possible to relate unknown pumice to its primary source, just by comparing the relation of a few elements, like Ta-Eu and Th-Hf. One concludes that all samples except one can be related to the Minoan eruption of Thera

  16. SOUTH POL: Revealing the Polarized Southern Sky

    Science.gov (United States)

    Magalhães, A. M.

    2014-10-01

    SOUTH POL will be a survey of the Southern sky in optical polarized light. It will use a newly designed polarimeter for an 80cm Robotic Telescope. Telescope and polarimeter will be installed at CTIO, Chile. The initial goal is to cover the sky south of declination -15° in about two years of observing time, aiming at a polarimetric accuracy ≤ 0.1% down to V=15, with a camera covering a field of about 2.0 square degrees. SOUTH POL will impact areas such as Cosmology, Extragalactic Astronomy, Interstellar Medium of the Galaxy and Magellanic Clouds, Star Formation, Stellar Envelopes, Stellar Explosions and Solar System, among others. The polarimeter is currently being built and its optics and electronics assembled. We will describe the current status of the project. This project is supported by FAPESP. AMM is also supported by CNPq.

  17. Chandra Data Reveal Rapidly Whirling Black Holes

    Science.gov (United States)

    2008-01-01

    A new study using results from NASA's Chandra X-ray Observatory provides one of the best pieces of evidence yet that many supermassive black holes are spinning extremely rapidly. The whirling of these giant black holes drives powerful jets that pump huge amounts of energy into their environment and affects galaxy growth. A team of scientists compared leading theories of jets produced by rotating supermassive black holes with Chandra data. A sampling of nine giant galaxies that exhibit large disturbances in their gaseous atmospheres showed that the central black holes in these galaxies must be spinning at near their maximum rates. People Who Read This Also Read... NASA’s Swift Satellite Catches First Supernova in The Act of Exploding Black Holes Have Simple Feeding Habits Jet Power and Black Hole Assortment Revealed in New Chandra Image Erratic Black Hole Regulates Itself "We think these monster black holes are spinning close to the limit set by Einstein's theory of relativity, which means that they can drag material around them at close to the speed of light," said Rodrigo Nemmen, a visiting graduate student at Penn State University, and lead author of a paper on the new results presented at American Astronomical Society in Austin, Texas. The research reinforces other, less direct methods previously used which have indicated that some stellar and supermassive black holes are spinning rapidly. According to Einstein's theory, a rapidly spinning black hole makes space itself rotate. This effect, coupled with gas spiraling toward the black hole, can produce a rotating, tightly wound vertical tower of magnetic field that flings a large fraction of the inflowing gas away from the vicinity of the black hole in an energetic, high-speed jet. Computer simulations by other authors have suggested that black holes may acquire their rapid spins when galaxies merge, and through the accretion of gas from their surroundings. "Extremely fast spin might be very common for large

  18. "Wonderful" Star Reveals its Hot Nature

    Science.gov (United States)

    2005-04-01

    For the first time an X-ray image of a pair of interacting stars has been made by NASA's Chandra X-ray Observatory. The ability to distinguish between the interacting stars - one a highly evolved giant star and the other likely a white dwarf - allowed a team of scientists to observe an X-ray outburst from the giant star and find evidence that a bridge of hot matter is streaming between the two stars. "Before this observation it was assumed that all the X-rays came from a hot disk surrounding a white dwarf, so the detection of an X-ray outburst from the giant star came as a surprise," said Margarita Karovska of the Harvard-Smithsonian Center for Astrophysics in Cambridge, Mass., and lead author article in the latest Astrophysical Journal Letters describing this work. An ultraviolet image made by the Hubble Space Telescope was a key to identifying the location of the X-ray outburst with the giant star. X-ray studies of this system, called Mira AB, may also provide better understanding of interactions between other binary systems consisting of a "normal" star and a collapsed star such as a white dwarf, black hole or a neutron star, where the stellar objects and gas flow cannot be distinguished in an image. HST Ultraviolet Image of Mira HST Ultraviolet Image of Mira The separation of the X-rays from the giant star and the white dwarf was made possible by the superb angular resolution of Chandra, and the relative proximity of the star system at about 420 light years from Earth. The stars in Mira AB are about 6.5 billion miles apart, or almost twice the distance of Pluto from the Sun. Mira A (Mira) was named "The Wonderful" star in the 17th century because its brightness was observed to wax and wane over a period of about 330 days. Because it is in the advanced, red giant phase of a star's life, it has swollen to about 600 times that of the Sun and it is pulsating. Mira A is now approaching the stage where its nuclear fuel supply will be exhausted, and it will collapse

  19. Exposing the Dark Microbial Biosphere

    OpenAIRE

    Hubalek, Valerie

    2015-01-01

    Dark biosphere research has been widely neglected, although by volume this biome comprises the lion’s share of habitats on our planet. In these systems the main metabolic strategies are of chemotrophic nature, leading to gradual depletion of redox gradients essential for sustaining life. Thus these environments are regarded more or less close to chemical equilibrium. Here, we use sequence data of whole community metagenomes and taxonomic marker approaches to study the ecology of environments ...

  20. MYSTERIES OF THE HUMAN FETUS REVEALED.

    Science.gov (United States)

    Sandman, Curt A

    2015-09-01

    The impressive program of research from the DiPietro laboratory succeeds in its aim to document the ontogeny of human fetal neurobehavioral development. From studies of great depth and breadth, and wielding creative methods of assessment, DiPietro et al. open a window into the largely inaccessible developing human fetal brain. This commentary, with reference to the seminal cardiovascular studies of the Laceys, supports the measures of the fetal heart to index fetal well-being and to provide evidence of stimulus processing. A separate case is made that the DiPietro program provides unique and invaluable information for assessing the influential Developmental Origins of Health and Disease or Fetal Programming Models. The goal of these models, to predict or understand the influences of early experience or response patterns on later postnatal life, is identical to the ultimate goal of the DiPietro program. Because human fetal behavior is uncontaminated by socialization or parenting or peers, it may be the best reflection of fetal exposures. The remarkable neurobehavioral profiles generated by the DiPietro program can make a critical contribution to the Fetal Programming Model in terms of sensitive and critical periods of nervous system vulnerability and to specify gestational periods of neurobehavioral risk. PMID:26303720

  1. Neuropeptide receptor transcriptome reveals unidentified neuroendocrine pathways.

    Science.gov (United States)

    Yamanaka, Naoki; Yamamoto, Sachie; Zitnan, Dusan; Watanabe, Ken; Kawada, Tsuyoshi; Satake, Honoo; Kaneko, Yu; Hiruma, Kiyoshi; Tanaka, Yoshiaki; Shinoda, Tetsuro; Kataoka, Hiroshi

    2008-01-01

    Neuropeptides are an important class of molecules involved in diverse aspects of metazoan development and homeostasis. Insects are ideal model systems to investigate neuropeptide functions, and the major focus of insect neuropeptide research in the last decade has been on the identification of their receptors. Despite these vigorous efforts, receptors for some key neuropeptides in insect development such as prothoracicotropic hormone, eclosion hormone and allatotropin (AT), remain undefined. In this paper, we report the comprehensive cloning of neuropeptide G protein-coupled receptors from the silkworm, Bombyx mori, and systematic analyses of their expression. Based on the expression patterns of orphan receptors, we identified the long-sought receptor for AT, which is thought to stimulate juvenile hormone biosynthesis in the corpora allata (CA). Surprisingly, however, the AT receptor was not highly expressed in the CA, but instead was predominantly transcribed in the corpora cardiaca (CC), an organ adjacent to the CA. Indeed, by using a reverse-physiological approach, we purified and characterized novel allatoregulatory peptides produced in AT receptor-expressing CC cells, which may indirectly mediate AT activity on the CA. All of the above findings confirm the effectiveness of a systematic analysis of the receptor transcriptome, not only in characterizing orphan receptors, but also in identifying novel players and hidden mechanisms in important biological processes. This work illustrates how using a combinatorial approach employing bioinformatic, molecular, biochemical and physiological methods can help solve recalcitrant problems in neuropeptide research. PMID:18725956

  2. CRISPR loci reveal networks of gene exchange in archaea

    Directory of Open Access Journals (Sweden)

    Brodt Avital

    2011-12-01

    Full Text Available Abstract Background CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. Results Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. Open peer review This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten

  3. Revealing hidden regularities with a general approach to fission

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Karl-Heinz; Jurado, Beatriz [Chemin du Solarium, CENBG, CNRS/IN2P3, B. P. 120, Gradignan (France)

    2015-12-15

    Selected aspects of a general approach to nuclear fission are described with the focus on the possible benefit of meeting the increasing need of nuclear data for the existing and future emerging nuclear applications. The most prominent features of this approach are the evolution of quantum-mechanical wave functions in systems with complex shape, memory effects in the dynamics of stochastic processes, the influence of the Second Law of thermodynamics on the evolution of open systems in terms of statistical mechanics, and the topological properties of a continuous function in multi-dimensional space. It is demonstrated that this approach allows reproducing the measured fission barriers and the observed properties of the fission fragments and prompt neutrons. Our approach is based on sound physical concepts, as demonstrated by the fact that practically all the parameters have a physical meaning, and reveals a high degree of regularity in the fission observables. Therefore, we expect a good predictive power within the region extending from Po isotopes to Sg isotopes where the model parameters have been adjusted. Our approach can be extended to other regions provided that there is enough empirical information available that allows determining appropriate values of the model parameters. Possibilities for combining this general approach with microscopic models are suggested. These are supposed to enhance the predictive power of the general approach and to help improving or adjusting the microscopic models. This could be a way to overcome the present difficulties for producing evaluations with the required accuracy. (orig.)

  4. Molecular Mechanisms Regulating Hepcidin Revealed by Hepcidin Disorders

    Directory of Open Access Journals (Sweden)

    Clara Camaschella

    2011-01-01

    Full Text Available Iron is essential for human life, but toxic if present in excess. To avoid iron overload and maintain iron homeostasis, all cells are able to regulate their iron content through the post-transcriptional control of iron genes operated by the cytosolic iron regulatory proteins that interact with iron responsive elements on iron gene mRNA. At the systemic level, iron homeostasis is regulated by the liver peptide hepcidin. Disruption of these regulatory loops leads to genetic diseases characterized by iron deficiency (iron-refractory iron-deficiency anemia or iron overload (hemochromatosis. Alterations of the same systems are also found in acquired disorders, such as iron-loading anemias characterized by ineffective erythropoiesis and anemia of chronic diseases (ACD associated with common inflammatory conditions. In ACD, iron is present in the body, but maldistributed, being deficient for erythropoiesis, but sequestered in macrophages. Studies of the hepcidin regulation by iron and inflammatory cytokines are revealing new pathways that might become targets of new therapeutic intervention in iron disorders.

  5. Can strong correlations be experimentally revealed for Ҡ -mesons?

    Directory of Open Access Journals (Sweden)

    Hiesmayr Beatrix C.

    2014-01-01

    Full Text Available In 1964 the physicists John St. Bell working at CERN took the 1935-idea of Einstein-Podolsky-Rosen seriously and found that all theories based on local realism have to satisfy a certain inequality, nowadays dubbed Bell’s inequality. Experiments with ordinary matter systems or light show violations of Bell’s inequality favouring the quantum theory though a loophole free experiment has not yet been performed. This contribution presents an experimentally feasible Bell inequality for systems at higher energy scales, i.e. entangled neutral Ҡ -meson pairs that are typically produced in Φ -mesons decays or proton-antiproton annihilation processes. Strong requirements have to be overcome in order to achieve a conclusive tests, such a proposal was recently published. Surprisingly, this new Bell inequality reveals new features for weakly decaying particles, in particular, a strong sensitivity to the combined charge-conjugation-parity (CP symmetry. Here-with, a puzzling relation between a symmetry breaking for mesons and Bell’s inequality—which is a necessary and sufficient condition for the security of quantum cryptography protocols— is established. This becomes the more important since CP symmetry is related to the cosmological question why the antimatter disappeared after the Big Bang.

  6. Strategy revealing phenotypic differences among synthetic oscillator designs.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2014-09-19

    Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested. PMID:25019938

  7. Revealing hidden regularities with a general approach to fission

    International Nuclear Information System (INIS)

    Selected aspects of a general approach to nuclear fission are described with the focus on the possible benefit of meeting the increasing need of nuclear data for the existing and future emerging nuclear applications. The most prominent features of this approach are the evolution of quantum-mechanical wave functions in systems with complex shape, memory effects in the dynamics of stochastic processes, the influence of the Second Law of thermodynamics on the evolution of open systems in terms of statistical mechanics, and the topological properties of a continuous function in multi-dimensional space. It is demonstrated that this approach allows reproducing the measured fission barriers and the observed properties of the fission fragments and prompt neutrons. Our approach is based on sound physical concepts, as demonstrated by the fact that practically all the parameters have a physical meaning, and reveals a high degree of regularity in the fission observables. Therefore, we expect a good predictive power within the region extending from Po isotopes to Sg isotopes where the model parameters have been adjusted. Our approach can be extended to other regions provided that there is enough empirical information available that allows determining appropriate values of the model parameters. Possibilities for combining this general approach with microscopic models are suggested. These are supposed to enhance the predictive power of the general approach and to help improving or adjusting the microscopic models. This could be a way to overcome the present difficulties for producing evaluations with the required accuracy. (orig.)

  8. Revealing hidden regularities with a general approach to fission

    Science.gov (United States)

    Schmidt, Karl-Heinz; Jurado, Beatriz

    2015-12-01

    Selected aspects of a general approach to nuclear fission are described with the focus on the possible benefit of meeting the increasing need of nuclear data for the existing and future emerging nuclear applications. The most prominent features of this approach are the evolution of quantum-mechanical wave functions in systems with complex shape, memory effects in the dynamics of stochastic processes, the influence of the Second Law of thermodynamics on the evolution of open systems in terms of statistical mechanics, and the topological properties of a continuous function in multi-dimensional space. It is demonstrated that this approach allows reproducing the measured fission barriers and the observed properties of the fission fragments and prompt neutrons. Our approach is based on sound physical concepts, as demonstrated by the fact that practically all the parameters have a physical meaning, and reveals a high degree of regularity in the fission observables. Therefore, we expect a good predictive power within the region extending from Po isotopes to Sg isotopes where the model parameters have been adjusted. Our approach can be extended to other regions provided that there is enough empirical information available that allows determining appropriate values of the model parameters. Possibilities for combining this general approach with microscopic models are suggested. These are supposed to enhance the predictive power of the general approach and to help improving or adjusting the microscopic models. This could be a way to overcome the present difficulties for producing evaluations with the required accuracy.

  9. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  10. Architecture of cognitive flexibility revealed by lesion mapping.

    Science.gov (United States)

    Barbey, Aron K; Colom, Roberto; Grafman, Jordan

    2013-11-15

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n=149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism-Extraversion-Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R(2)=0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  11. Subfield profitability analysis reveals an economic case for cropland diversification

    Science.gov (United States)

    Brandes, E.; McNunn, G. S.; Schulte, L. A.; Bonner, I. J.; Muth, D. J.; Babcock, B. A.; Sharma, B.; Heaton, E. A.

    2016-01-01

    Public agencies and private enterprises increasingly desire to achieve ecosystem service outcomes in agricultural systems, but are limited by perceived conflicts between economic and ecosystem service goals and a lack of tools enabling effective operational management. Here we use Iowa—an agriculturally homogeneous state representative of the Maize Belt—to demonstrate an economic rationale for cropland diversification at the subfield scale. We used a novel computational framework that integrates disparate but publicly available data to map ˜3.3 million unique potential management polygons (9.3 Mha) and reveal subfield opportunities to increase overall field profitability. We analyzed subfield profitability for maize/soybean fields during 2010-2013—four of the most profitable years in recent history—and projected results for 2015. While cropland operating at a loss of US 250 ha-1 or more was negligible between 2010 and 2013 at 18 000-190 000 ha (<2% of row-crop land), the extent of highly unprofitable land increased to 2.5 Mha, or 27% of row-crop land, in the 2015 projection. Aggregation of these areas to the township level revealed ‘hotspots’ for potential management change in Western, Central, and Northeast Iowa. In these least profitable areas, incorporating conservation management that breaks even (e.g., planting low-input perennials), into low-yielding portions of fields could increase overall cropland profitability by 80%. This approach is applicable to the broader region and differs substantially from the status quo of ‘top-down’ land management for conservation by harnessing private interest to align profitability with the production of ecosystem services.

  12. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.

    Science.gov (United States)

    Cuomo, Christina A; Desjardins, Christopher A; Bakowski, Malina A; Goldberg, Jonathan; Ma, Amy T; Becnel, James J; Didier, Elizabeth S; Fan, Lin; Heiman, David I; Levin, Joshua Z; Young, Sarah; Zeng, Qiandong; Troemel, Emily R

    2012-12-01

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites. PMID:22813931

  13. VLBA Reveals Dust-Enshrouded "Supernova Factory"

    Science.gov (United States)

    2003-05-01

    1, 2003, showed that this new object has typical characteristics of a supernova explosion by a young, massive star. Multiwavelength image of Arp 299 Multiwavelength Image of the colliding-galaxy pair Arp 299 using data from the VLA and Hubble Space Telescope. Here, radio emission is shown as red, infrared as green, and ultraviolet as blue. CREDIT: NRAO/AUI/NSF, STScI, NASA (Click on Image for Larger Version) Artist's Conception of Supernova Factory Artist's Conception of the dust-enshrouded supernova factory in Arp 299. Bright circles are the shocks from new supernova explosions. CREDIT: NASA/Walt Feimer (Click on Image for Larger Version) "This supernova is exploding in a very dense environment, quite different from the environments of supernova explosions that can be seen in visible light," Teng said. "This is the kind of dense environment in which stars likely formed in the early Universe," she added. The astronomers believe the super star cluster in Arp 299 saw its most recent peak of star formation some 6-8 million years ago, and now its massive stars, 10-20 times (or more) as massive as the Sun, are ending their lives in supernova explosions. Super star clusters typically contain up to a million stars, which is why the scientists think Source A will see frequent supernova explosions. "We plan to keep watching this region, and hope that we can study numerous supernovae, and gain important new information about the processes of star formation, both in the early Universe and at the present time," Neff said. "Because of the dust and the distance, only a radio telescope with the VLBA's ability to see fine detail can find the supernovae in this region," Ulvestad said. The VLBA is a continent-wide system of ten radio- telescope antennas, ranging from Hawaii in the west to the U.S. Virgin Islands in the east, providing the greatest resolving power, or ability to see fine detail, in astronomy. Dedicated in 1993, the VLBA is operated from the NRAO's Array Operations

  14. Cosmic Lens Reveals Distant Galactic Violence

    Science.gov (United States)

    2008-10-01

    , that the galaxy has merged with another. "This whole picture, of massive galaxies and supermassive black holes assembling themselves through major galaxy mergers so early in the Universe, is a new paradigm in galaxy formation. This gravitationally lensed system allows us to see this process in unprecedented detail," said Chris Carilli, of the National Radio Astronomy Observatory. In 2003, astronomers studied PSS J2322+1944, finding the Einstein Ring by observing radio waves emitted by molecules of Carbon Monoxide (CO). When astronomers see large amounts of CO gas in a galaxy, they conclude that there also is a large amount of molecular Hydrogen present, and thus a large reservoir of fuel for star formation. In the latest study, scientists painstakingly produced a physical model of the lensing intermediate galaxy. By knowing the mass, structure and orientation of this galaxy, they could then deduce the details of how it bends the light and radio waves from the more-distant galaxy. This allowed them to reconstruct a picture of the distant object. By doing this with multiple VLA images made at different radio frequencies, they were able to measure the motions of the gas in the distant galaxy. "The lensing galaxy was, in effect, part of our telescope. By projecting backward through the lens, we determined the structure and dynamics of the galaxy behind it," said Fabian Walter of the Max-Planck Institute for Astronomy in Germany. PSS J2322+1944 was first discovered by George Djorgovski of Caltech, using the digitized Palomar Observatory Sky Survey. Later radio and optical studies showed that it had a huge reservoir of dust and molecular gas, and indicated gravitational lensing. Gravitational lenses were predicted, based on Albert Einstein's General Theory of Relativity, in 1919. Einstein himself showed in 1936 that a perfectly-aligned gravitational lens would produce a circular image, but felt that the chances of actually observing such an object were nearly zero. The first

  15. MicroRNA sequence motifs reveal asymmetry between the stem arms

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Havgaard, Jakob Hull; Ensterö, M.; Sawera, Milena; Jensen, Peter; Öhman, M.; Fredholm, Merete

    2006-01-01

    The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their gen...

  16. Many-objective optimization and visual analytics reveal key trade-offs for London's water supply

    OpenAIRE

    Matrosov, E. S.; Huskova, I.; Kasprzyk, J. R.; J. J. Harou; Lambert, C; Reed, P. M.

    2015-01-01

    In this study, we link a water resource management simulator to multi-objective search to reveal the key trade-offs inherent in planning a real-world water resource system. We consider new supplies and demand management (conservation) options while seeking to elucidate the trade-offs between the best portfolios of schemes to satisfy projected water demands. Alternative system designs are evaluated using performance measures that minimize capital and operating costs and energy use while maximi...

  17. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    OpenAIRE

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

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

    Science.gov (United States)

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

    2016-06-01

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

  19. Note on generated choice and axioms of revealed preference

    OpenAIRE

    Magyarkuti, Gyula

    2000-01-01

    In this article, we study the axiomatic foundations of revealed preference theory. Let P denote the strict and R the weak revealed preference, respectively. The purpose of the paper is to show that weak, strong, and Hansson's axioms of revealed preference can be given as identities using the generated choices with respect to P and R in terms of maximality and in terms of greatestness.

  20. Revealed Preference Tests using Supermarket Data: the Money Pump

    OpenAIRE

    Echenique, Federico; Lee, Sangmok; Shum, Matthew

    2010-01-01

    We use a money pump argument to measure deviations from the revealed preference axioms. Using a panel data set of food expenditures, we find a large number of violations of the weak axiom of revealed preference. The money pump costs are small, which indicate that the violations of revealed preference are not severe. While most households' behavior deviates from rationality, by our measure they are close to being rational.

  1. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

    LENUS (Irish Health Repository)

    Potnis, Neha

    2011-03-11

    Abstract Background Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10. Results We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity. Conclusions Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster

  2. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

    Directory of Open Access Journals (Sweden)

    Koebnik Ralf

    2011-03-01

    Full Text Available Abstract Background Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10. Results We sequenced the genomes of X. vesicatoria (Xv strain 1111 (ATCC 35937, X. perforans (Xp strain 91-118 and X. gardneri (Xg strain 101 (ATCC 19865. The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity. Conclusions Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the

  3. Ecoinformatics reveals effects of crop rotational histories on cotton yield.

    Directory of Open Access Journals (Sweden)

    Matthew H Meisner

    Full Text Available Crop rotation has been practiced for centuries in an effort to improve agricultural yield. However, the directions, magnitudes, and mechanisms of the yield effects of various crop rotations remain poorly understood in many systems. In order to better understand how crop rotation influences cotton yield, we used hierarchical Bayesian models to analyze a large ecoinformatics database consisting of records of commercial cotton crops grown in California's San Joaquin Valley. We identified several crops that, when grown in a field the year before a cotton crop, were associated with increased or decreased cotton yield. Furthermore, there was a negative association between the effect of the prior year's crop on June densities of the pest Lygus hesperus and the effect of the prior year's crop on cotton yield. This suggested that some crops may enhance L. hesperus densities in the surrounding agricultural landscape, because residual L. hesperus populations from the previous year cannot continuously inhabit a focal field and attack a subsequent cotton crop. In addition, we found that cotton yield declined approximately 2.4% for each additional year in which cotton was grown consecutively in a field prior to the focal cotton crop. Because L. hesperus is quite mobile, the effects of crop rotation on L. hesperus would likely not be revealed by small plot experimentation. These results provide an example of how ecoinformatics datasets, which capture the true spatial scale of commercial agriculture, can be used to enhance agricultural productivity.

  4. Integrative modelling reveals mechanisms linking productivity and plant species richness

    Science.gov (United States)

    Grace, James B.; Anderson, T. Michael; Seabloom, Eric W.; Borer, Elizabeth T.; Adler, Peter B.; Harpole, W. Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M.; Pärtel, Meelis; Bakker, Jonathan D.; Buckley, Yvonne M.; Crawley, Michael J.; Damschen, Ellen I.; Davies, Kendi F.; Fay, Philip A.; Firn, Jennifer; Gruner, Daniel S.; Hector, Andy; Knops, Johannes M. H.; MacDougall, Andrew S.; Melbourne, Brett A.; Morgan, John W.; Orrock, John L.; Prober, Suzanne M.; Smith, Melinda D.

    2016-01-01

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

  5. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

    Science.gov (United States)

    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  6. Basin Formation and Cratering on Mercury Revealed by MESSENGER

    Science.gov (United States)

    Chapman, C. R.; Fassett, C.; Marchi, S.; Merline, W. J.; Ostrach, L. R.; Prockter, L. M.

    2015-12-01

    Mercury has been bombarded by asteroids and comets throughout its history. The resulting craters and basins are the dominant topographic features on the planet. Although visible basins contain some of the most interesting tectonic features, plains, and evidence of vertical stratigraphy, they fall far short of saturating the surface. Nevertheless, Mercury has a greater spatial density of peak-ring basins and protobasins than any other Solar System body, partly because these morphologies begin at smaller sizes than on most bodies. Cratering at approximately three times the cratering rate on the Moon, combined with likely plains-forming volcanism, prevents recognition of surface features older than 4.0 to 4.1 Ga. Severe losses of craters Mercury suggest that most plains formation ended about 3.6 to 3.7 Ga, though activity has continued in a few small regions until much more recently (e.g., inside the Rachmaninoff basin). Mercury, compared with other terrestrial bodies, is struck by projectiles impacting at much higher velocities, which is probably responsible for the formation of abundant secondary craters that dominate the numbers of craters Mercury-specific impactors ("vulcanoids") cannot be excluded, imaging searches by MESSENGER have revealed no remaining vulcanoids and no other evidence suggests that Mercury has been bombarded by anything other than the same populations of asteroids and comets that have impacted the Moon and other terrestrial planets from the end of the period of heavy bombardment 3.8 to 3.9 Ga to the present.

  7. Time-resolved metabolomics reveals metabolic modulation in rice foliage

    Directory of Open Access Journals (Sweden)

    Arita Masanori

    2008-06-01

    Full Text Available Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS and capillary electrophoresis diode-array detection (CE-DAD, we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the

  8. PCR-based plasmid typing in Enterococcus faecium strains reveals widely distributed pRE25-, pRUM-, pIP501-and pHT beta-related replicons associated with glycopeptide resistance and stabilizing toxin-antitoxin systems

    DEFF Research Database (Denmark)

    Rosvoll, T.C.S.; Pedersen, T.; Sletvold, H.;

    2010-01-01

    AM373, pMBB1 or pEF418 were not detected. Furthermore, 61% of the strains contained the axe-txe (n=42) or/and the omega-epsilon-zeta (n=18) plasmid stabilization loci. Sequence analyses divided the omega-epsilon-zeta operon into two distinct phylogenetic groups. The present typing scheme accounted for......A PCR-based typing scheme was applied to identify plasmids in an epidemiologically and geographically diverse strain collection of Enterococcus faecium (n=93). Replicon types of pRE25 (n=56), pRUM (n=41), pIP501 (n=17) and pHT beta (n=14) were observed in 83% of the strains, while pS86, pCF10, p...... about 60% of the total number of plasmids detected by S1 nuclease analyses, which revealed zero to seven plasmids (10 kb to > 200 kb) per isolate. Interestingly, strains belonging to the clinically important clonal complex 17 (CC17) yielded a significantly higher number of plasmids (3.1) and p...

  9. Early revealing of neurogenic disorders of urination in patients with anorectal anomalies

    Directory of Open Access Journals (Sweden)

    Makedonsky I.O.

    2013-03-01

    Full Text Available 148 patients with anorectal malformations (ARM were examined. Using clinical, X-ray, ultrasound and urodynamical methods of detections, factors which can cause bladder dysfunction in anorectal malformations are revealed. It was noted that patients with high and low forms of this defect have significant percentage of neurogenec disorders of urination. Absence of anomalies of spinal column development does not exclude these children from the group of scheduled profound urologic investigation. We propose ultrasound measurement of bladder wall thickness and 4-hour monitoring of voiding, urodynamic examination as early diagnostic methods of neurogenic bladder dysfunctions. For timely revealing and treatment of neurogenic disorders of urination we recommend urologic inves¬tigation to all ARM patients. Improvement of diagnostic methods and development of algorithm of revealing mentioned pathologies against ARM with the aim to prevent com¬plications in the urinary system, being perspective in decreasing lethality and disability.

  10. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Science.gov (United States)

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  11. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

    Science.gov (United States)

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

  12. Molecular profiling reveals primary mesothelioma cell lines recapitulate human disease.

    Science.gov (United States)

    Chernova, T; Sun, X M; Powley, I R; Galavotti, S; Grosso, S; Murphy, F A; Miles, G J; Cresswell, L; Antonov, A V; Bennett, J; Nakas, A; Dinsdale, D; Cain, K; Bushell, M; Willis, A E; MacFarlane, M

    2016-07-01

    Malignant mesothelioma (MM) is an aggressive, fatal tumor strongly associated with asbestos exposure. There is an urgent need to improve MM patient outcomes and this requires functionally validated pre-clinical models. Mesothelioma-derived cell lines provide an essential and relatively robust tool and remain among the most widely used systems for candidate drug evaluation. Although a number of cell lines are commercially available, a detailed comparison of these commercial lines with freshly derived primary tumor cells to validate their suitability as pre-clinical models is lacking. To address this, patient-derived primary mesothelioma cell lines were established and characterized using complementary multidisciplinary approaches and bioinformatic analysis. Clinical markers of mesothelioma, transcriptional and metabolic profiles, as well as the status of p53 and the tumor suppressor genes CDKN2A and NF2, were examined in primary cell lines and in two widely used commercial lines. Expression of MM-associated markers, as well as the status of CDKN2A, NF2, the 'gatekeeper' in MM development, and their products demonstrated that primary cell lines are more representative of the tumor close to its native state and show a degree of molecular diversity, thus capturing the disease heterogeneity in a patient cohort. Molecular profiling revealed a significantly different transcriptome and marked metabolic shift towards a greater glycolytic phenotype in commercial compared with primary cell lines. Our results highlight that multiple, appropriately characterised, patient-derived tumor cell lines are required to enable concurrent evaluation of molecular profiles versus drug response. Furthermore, application of this approach to other difficult-to-treat tumors would generate improved cellular models for pre-clinical evaluation of novel targeted therapies. PMID:26891694

  13. Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

    Science.gov (United States)

    Steele, Joshua A; Countway, Peter D; Xia, Li; Vigil, Patrick D; Beman, J Michael; Kim, Diane Y; Chow, Cheryl-Emiliane T; Sachdeva, Rohan; Jones, Adriane C; Schwalbach, Michael S; Rose, Julie M; Hewson, Ian; Patel, Anand; Sun, Fengzhu; Caron, David A; Fuhrman, Jed A

    2011-09-01

    Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes. PMID:21430787

  14. "Missing Link" Revealing Fast-Spinning Pulsar Mysteries

    Science.gov (United States)

    2009-05-01

    telescope during a large sky survey in 1998, and had been observed in visible light by the Sloan Digital Sky Survey in 1999, revealing a Sun-like star. When observed again in 2000, the object had changed dramatically, showing evidence for a rotating disk of material, called an accretion disk, surrounding the neutron star. By May of 2002, the evidence for this disk had disappeared. "This strange behavior puzzled astronomers, and there were several different theories for what the object could be," said Ingrid Stairs of the University of British Columbia, who has been visiting the Australia Telescope National Facility and Swinburne University this year. The 2007 GBT observations showed that the object is a millisecond pulsar, spinning 592 times per second. "No other millisecond pulsar has ever shown evidence for an accretion disk," Archibald said. "We know that another type of binary-star system, called a low-mass X-ray binary (LMXB), also contains a fast-spinning neutron star and an accretion disk, but these don't emit radio waves. We've thought that LMXBs probably are in the process of getting spun up, and will later emit radio waves as a pulsar. This object appears to be the 'missing link' connecting the two types of systems," she explained. "It appears this thing has flipped from looking like an LMXB to looking like a pulsar, as it experienced an episode during which material pulled from the companion star formed an accretion disk around the neutron star. Later, that mass transfer stopped, the disk disappeared, and the pulsar emerged," said Scott Ransom of the NRAO. The scientists have studied J1023 in detail with the GBT, with the Westerbork radio telescope in the Netherlands, with the Arecibo radio telescope in Puerto Rico, and with the Parkes radio telescope in Australia. Their results indicate that the neutron star's companion has less than half the Sun's mass, and orbits the neutron star once every four hours and 45 minutes. "This system gives us an unparalled 'cosmic

  15. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    Science.gov (United States)

    ... 1999 Spotlight on Research 2012 July 2012 (historical) Genome-Wide Scan Reveals Mutation Associated with Melanoma A ... out to see if a technology called whole genome sequencing would help them find other genetic risk ...

  16. [An original revealing mode of sarcoidosis: Sweet's syndrome].

    Science.gov (United States)

    Bricha, Myriem; Sqalli, Fatimazzahra; Hammi, Sanae; Bourkadi, Jamal Eddine

    2016-01-01

    Sweet's syndrome is a neutrophilic dermatosis which usually presents as an idiopathic disorder. The combination of Sweet's syndrome and sarcoidosis is rare. We report the clinical case of a Sweet's syndrome revealing sarcoidosis. PMID:27279949

  17. Revealing ecological networks using Bayesian network inference algorithms.

    Science.gov (United States)

    Milns, Isobel; Beale, Colin M; Smith, V Anne

    2010-07-01

    Understanding functional relationships within ecological networks can help reveal keys to ecosystem stability or fragility. Revealing these relationships is complicated by the difficulties of isolating variables or performing experimental manipulations within a natural ecosystem, and thus inferences are often made by matching models to observational data. Such models, however, require assumptions-or detailed measurements-of parameters such as birth and death rate, encounter frequency, territorial exclusion, and predation success. Here, we evaluate the use of a Bayesian network inference algorithm, which can reveal ecological networks based upon species and habitat abundance alone. We test the algorithm's performance and applicability on observational data of avian communities and habitat in the Peak District National Park, United Kingdom. The resulting networks correctly reveal known relationships among habitat types and known interspecific relationships. In addition, the networks produced novel insights into ecosystem structure and identified key species with high connectivity. Thus, Bayesian networks show potential for becoming a valuable tool in ecosystem analysis. PMID:20715607

  18. Facial cellulitis revealing choreo-acanthocytosis: a case report

    OpenAIRE

    Samia, Younes; Yosra, Cherif; Foued, Bellazreg; Mouna, Aissi; Olfa, Berriche; Jihed, Souissi; Hammadi, Braham; Mahbouba, Frih-Ayed; Amel, Letaief; Habib, Sfar Mohamed

    2014-01-01

    We report a 62 year-old-man with facial cellulitis revealing choreo-acanthocytosis (ChAc). He showed chorea that started 20 years ago. The orofacial dyskinisia with tongue and cheek biting resulted in facial cellulitis. The peripheral blood smear revealed acanthocytosis of 25%. The overall of chorea, orofacial dyskinetic disorder, peripheral neuropathy, disturbed behavior, acanthocytosis and the atrophy of caudate nuclei was suggestive of a diagnosis of ChAc. To our knowledge no similar cases...

  19. The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

    OpenAIRE

    Fernando Dini Andreote; Diego Javier Jiménez; Diego Chaves; Armando Cavalcante Franco Dias; Danice Mazzer Luvizotto; Francisco Dini-Andreote; Cristiane Cipola Fasanella; Maryeimy Varon Lopez; Sandra Baena; Rodrigo Gouvêa Taketani; Itamar Soares de Melo

    2012-01-01

    Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed high...

  20. Maps of sparse Markov chains efficiently reveal community structure in network flows with memory

    CERN Document Server

    Persson, Christian; Edler, Daniel; Rosvall, Martin

    2016-01-01

    To better understand the flows of ideas or information through social and biological systems, researchers develop maps that reveal important patterns in network flows. In practice, network flow models have implied memoryless first-order Markov chains, but recently researchers have introduced higher-order Markov chain models with memory to capture patterns in multi-step pathways. Higher-order models are particularly important for effectively revealing actual, overlapping community structure, but higher-order Markov chain models suffer from the curse of dimensionality: their vast parameter spaces require exponentially increasing data to avoid overfitting and therefore make mapping inefficient already for moderate-sized systems. To overcome this problem, we introduce an efficient cross-validated mapping approach based on network flows modeled by sparse Markov chains. To illustrate our approach, we present a map of citation flows in science with research fields that overlap in multidisciplinary journals. Compared...

  1. Interior Layered Deposits in Tithonium Chasma Reveal Diverse Compositions

    Science.gov (United States)

    2008-01-01

    reveals diversity in the mineral content of this light-colored material. Some areas have no signature in the data, indicating dust-like spectral properties, while other areas have signatures of monohydrated or polyhydrated sulfate. This signifies a variety of compositions within these layered deposits. CRISM is one of six science instruments on NASA's Mars Reconnaissance Orbiter. Led by The Johns Hopkins University Applied Physics Laboratory, Laurel, Md., the CRISM team includes expertise from universities, government agencies and small businesses in the United States and abroad. NASA's Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, manages the Mars Reconnaissance Orbiter and the Mars Science Laboratory for NASA's Science Mission Directorate, Washington. Lockheed Martin Space Systems, Denver, built the orbiter.

  2. Axonal Transport Proteomics Reveals Mobilization of Translation Machinery to the Lesion Site in Injured Sciatic Nerve*

    OpenAIRE

    Michaelevski, Izhak; Medzihradszky, Katalin F.; Lynn, Aenoch; Burlingame, Alma L.; Fainzilber, Mike

    2009-01-01

    Investigations of the molecular mechanisms underlying responses to nerve injury have highlighted the importance of axonal transport systems. To obtain a comprehensive view of the protein ensembles associated with axonal transport in injured axons, we analyzed the protein compositions of axoplasm concentrated at ligatures following crush injury of rat sciatic nerve. LC-MS/MS analyses of iTRAQ-labeled peptides from axoplasm distal and proximal to the ligation sites revealed protein ensembles tr...

  3. Reconstituting pancreas development from purified progenitor cells reveals genes essential for islet differentiation

    OpenAIRE

    Sugiyama, Takuya; Benitez, Cecil M.; Ghodasara, Amar; Liu, Lucy; McLean, Graeme W.; Lee, Jonghyeob; Blauwkamp, Timothy A; Nusse, Roeland; Wright, Christopher V.E.; Gu, Guoqiang; Kim, Seung K.

    2013-01-01

    Developmental biology is challenged to reveal the function of numerous candidate genes implicated by recent genome-scale studies as regulators of organ development and diseases. Recapitulating organogenesis from purified progenitor cells that can be genetically manipulated would provide powerful opportunities to dissect such gene functions. Here we describe systems for reconstructing pancreas development, including islet β-cell and α-cell differentiation, from single fetal progenitor cells. A...

  4. General Mutagenesis of F Plasmid TraI Reveals Its Role in Conjugative Regulation

    OpenAIRE

    Haft, Rembrandt J F; Palacios, Gilberto; Nguyen, Tran; Mally, Manuela; Gachelet, Eliora G.; Zechner, Ellen L.; Traxler, Beth

    2006-01-01

    Bacteria commonly exchange genetic information by the horizontal transfer of conjugative plasmids. In gram-negative conjugation, a relaxase enzyme is absolutely required to prepare plasmid DNA for transit into the recipient via a type IV secretion system. Here we report a mutagenesis of the F plasmid relaxase gene traI using in-frame, 31-codon insertions. Phenotypic analysis of our mutant library revealed that several mutant proteins are functional in conjugation, highlighting regions of TraI...

  5. Single cell transcriptional analysis reveals novel innate immune cell types

    Directory of Open Access Journals (Sweden)

    Linda E. Kippner

    2014-06-01

    Full Text Available Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription

  6. The neurobiology of offensive aggression: Revealing a modular view.

    Science.gov (United States)

    de Boer, S F; Olivier, B; Veening, J; Koolhaas, J M

    2015-07-01

    Experimental studies aimed at understanding the neurobiology of aggression started in the early 20th century, and by employing increasingly sophisticated tools of functional neuroanatomy (i.e., from electric/chemical lesion and stimulation techniques to neurochemical mapping and manipulations) have provided the important framework for the functional brain circuit organization of aggressive behaviors. Recently, newly emerging technologies for mapping,measuring and manipulating neural circuitry at the level of molecular and genetically defined neuronal subtypes promise to further delineate the precise neural microcircuits mediating the initiation and termination of aggressive behavior, and characterize its dynamic neuromolecular functioning. This paper will review some of the behavioral, neuroanatomical and neurochemical evidence in support of a modular view of the neurobiology of offensive aggressive behavior. Although aggressive behavior likely arises from a specific concerted activity within a distributed neural network across multiple brain regions, emerging opto- and pharmacogenetic neuronal manipulation studies make it clear that manipulation of molecularly-defined neurons within a single node of this global interconnected network seems to be both necessary and sufficient to evoke aggressive attacks. However, the evidence so far also indicates that in addition to behavior-specific neurons there are neuronal systems that should be considered as more general behavioral control modules. The answer to the question of behavioral specificity of brain structures at the level of individual neurons requires a change of the traditional experimental setup. Studies using c-fos expression mapping usually compare the activation patterns induced by for example aggression with a home cage control. However, to reveal the behavioral specificity of this neuronal activation pattern, a comparison with other social and non-social related behaviors such as mating, defensive burying

  7. Cosmic "Dig" Reveals Vestiges of the Milky Way's Building Blocks

    Science.gov (United States)

    2009-11-01

    Peering through the thick dust clouds of our galaxy's "bulge" (the myriads of stars surrounding its centre), and revealing an amazing amount of detail, a team of astronomers has unveiled an unusual mix of stars in the stellar grouping known as Terzan 5. Never observed anywhere in the bulge before, this peculiar "cocktail" of stars suggests that Terzan 5 is in fact one of the bulge's primordial building blocks, most likely the relic of a proto-galaxy that merged with the Milky Way during its very early days. "The history of the Milky Way is encoded in its oldest fragments, globular clusters and other systems of stars that have witnessed the entire evolution of our galaxy," says Francesco Ferraro from the University of Bologna, lead author of a paper appearing in this week's issue of the journal Nature. "Our study opens a new window on yet another piece of our galactic past." Like archaeologists, who dig through the dust piling up on top of the remains of past civilisations and unearth crucial pieces of the history of mankind, astronomers have been gazing through the thick layers of interstellar dust obscuring the bulge of the Milky Way and have unveiled an extraordinary cosmic relic. The target of the study is the star cluster Terzan 5. The new observations show that this object, unlike all but a few exceptional globular clusters, does not harbour stars which are all born at the same time - what astronomers call a "single population" of stars. Instead, the multitude of glowing stars in Terzan 5 formed in at least two different epochs, the earliest probably some 12 billion years ago and then again 6 billion years ago. "Only one globular cluster with such a complex history of star formation has been observed in the halo of the Milky Way: Omega Centauri," says team member Emanuele Dalessandro. "This is the first time we see this in the bulge." The galactic bulge is the most inaccessible region of our galaxy for astronomical observations: only infrared light can

  8. [Ovarian torsion revealing an ovarian cavernous hemangioma in a child].

    Science.gov (United States)

    M'pemba Loufoua-Lemay, A-B; Peko, J-F; Mbongo, J-A; Mokoko, J-C; Nzingoula, S

    2003-11-01

    The authors report one case of cavernous hemangioma of the left ovary, which was revealed by ovarian torsion. Such benign tumors of the blood vessels are rare in ovaries during childhood. This hemangioma was observed in a 13-year-old patient, who presented with abdominal and pelvic pain and vomiting. The pelvic mass was noted and sonography revealed a cystic tumor. An annexectomia was realized. Histology showed narcotized ovary cells, with an increased number of vascular channels composed of thin walled vessels, whose wall consisted of an endothelium. This aspect evoked a cavernous hemangioma of the ovary. PMID:14613693

  9. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

    Science.gov (United States)

    Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J.

    2015-01-01

    Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090

  10. Goodness-of-Fit for Revealed Preference Tests

    OpenAIRE

    Hal R. Varian

    1994-01-01

    I describe a goodness-of-fit measure for revealed preference tests. This index can be used to measure the degree to which an economic agent violates the model of utility maximization. I calculate the violation indices for a 38 consumers and find that the observed choice behavior is very close to optimizing behavior.

  11. When Values and Behaviors Conflict: Immigrant BSW Students' Experiences Revealed

    Science.gov (United States)

    Calderwood, Kimberly; Harper, Kim; Ball, Kellie; Liang, David

    2009-01-01

    This qualitative study reveals the discomfort seven immigrant bachelor of social work students reported experiencing when the behaviors expected of them as Canadian social workers conflicted with their fundamental family values. Behaviorally, participants had assimilated to Canadian and to social work cultures; however, the values they held from…

  12. [Ulcerated duodenitis revealing Henoch-Schönlein purpura].

    Science.gov (United States)

    Marting, A; Defrance, P; Wain, E; Van Severen, M; Deflandre, J

    2015-01-01

    Inflammation and duodenal ulcers can meet many etiologies. We report the case of a young adult with an ulcerated duodenitis revealing Henoch-Schönlein purpura. The abdominal symptoms preceded the emergence of the classical cutaneous signs of the disease. PMID:26376566

  13. MRI reveals reversible lesions resembling posterior reversible encephalopathy in porphyria

    International Nuclear Information System (INIS)

    We report a 20-year-old woman who had an attack of acute intermittent porphyria with seizures, hallucinations, autonomic and somatic neuropathy. T2-weighted MRI revealed multiple lesions which were no longer visible 3 months later. We suggest a similar mechanism to posterior reversible encephalopathy underlying cerebral symptoms in porphyria. (orig.)

  14. MRI reveals reversible lesions resembling posterior reversible encephalopathy in porphyria

    Energy Technology Data Exchange (ETDEWEB)

    Celik, M. [Huesrev Gerede c, 128/4 Tesvikiye, 80690 Istanbul (Turkey); Department of Neurology, Sisli Etfal Education and Research Hospital, Sisli Etfal S., Sisli, Istanbul (Turkey); Forta, H.; Babacan, G. [Department of Neurology, Sisli Etfal Education and Research Hospital, Sisli Etfal S., Sisli, Istanbul (Turkey); Dalkilic, Tuerker [Department of Neurosurgery, Sisli Etfal Education and Research Hospital, Sisli Etfal S., Sisli, Istanbul (Turkey)

    2002-10-01

    We report a 20-year-old woman who had an attack of acute intermittent porphyria with seizures, hallucinations, autonomic and somatic neuropathy. T2-weighted MRI revealed multiple lesions which were no longer visible 3 months later. We suggest a similar mechanism to posterior reversible encephalopathy underlying cerebral symptoms in porphyria. (orig.)

  15. UTV Expansion Pack: Special-Purpose Rank-Revealing Algorithms

    DEFF Research Database (Denmark)

    Fierro, Ricardo D.; Hansen, Per Christian

    2005-01-01

    This collection of Matlab 7.0 software supplements and complements the package UTV Tools from 1999, and includes implementations of special-purpose rank-revealing algorithms developed since the publication of the original package. We provide algorithms for computing and modifying symmetric rank...

  16. On galaxy spiral arms' nature as revealed by rotation frequencies

    NARCIS (Netherlands)

    Roca-Fabrega, Santi; Valenzuela, Octavio; Figueras, Francesca; Romero-Gomez, Merce; Velazquez, Hector; Antoja Castelltort, Teresa; Pichardo, Barbara

    2013-01-01

    High-resolution N-body simulations using different codes and initial condition techniques reveal two different behaviours for the rotation frequency of transient spiral arms like structures. Whereas unbarred discs present spiral arms nearly corotating with disc particles, strong barred models (bulge

  17. Nilaja Sun's "No Child"...: Revealing Teaching and Learning through Theater

    Science.gov (United States)

    Hetland, Lois

    2009-01-01

    This article presents an analysis of Nilaja Sun's one-woman play, "No Child" . . ., that applies the Studio Habits of Mind framework to reveal essential features of great teaching artistry and great teaching. The play conveys much about twenty-first century schools and the policies that control them; about respect, equity, justice, and the lack of…

  18. Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities.

    Science.gov (United States)

    Dini-Andreote, Francisco; Pylro, Victor Satler; Baldrian, Petr; van Elsas, Jan Dirk; Salles, Joana Falcão

    2016-08-01

    Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem. PMID:26824176

  19. SOHO reveals violent action on the quiet Sun

    Science.gov (United States)

    1996-05-01

    One instrument in SOHO avoids looking at the Sun, because it would be dazzled. Instead, SWAN surveys the sky all around and sees an ultraviolet glow from hydrogen atoms lit by the Sun. These atoms come on a breeze from the stars that blows through the Solar System. But the competing wind of charged particles from the Sun breaks the incoming atoms, so that they no longer emit their characteristic wavelength. The result is a hole in the pattern of emissions downstream from the Sun. The surviving emissions are brightest upstream, and far above the plane of the Sun's equator. The scientists conclude that the solar wind blowing from high-latitude regions of Sun is less strong, at least during the present quiet phase of the eleven-year cycle of activity. The Earth is also visible in the maps, because a cloud of hydrogen gas called the geocorona envelops it and glows in the ultraviolet. The geocorona would hamper observations of the interstellar glow by satellites close to the Earth. SOHO sees the geocorona from the outside, and will be able to monitor effects of solar activity on the Earth's outer atmosphere. "At the present time of a quiet Sun, our sky maps clearly indicate a situation of increased solar wind around the Sun's equator," says Jean-Loup Bertaux of the Service d'Aéronomie near Paris, who has prime responsibility for SWAN. "We are anxious to see what will happen when the Sun becomes stormier. Then we shall see important changes in the solar wind's impact on the interstellar gas, revealed by the changes in the sky maps. Meanwhile we use alternate days for special investigations, and at present we are tracking Comet Hyakutake as it approaches the Sun. When colleagues ask me why a solar spacecraft should look at comets, I remind them that the solar wind was discovered by studying comet tails." Sub-surface currents mapped SOHO is successfully probing the Sun's interior. It does so with several instruments that observe oscillations of the Sun's surface. They detect

  20. Autotriploid origin of Carassius auratus as revealed by chromosomal locus analysis.

    Science.gov (United States)

    Qin, Qinbo; Wang, Juan; Hu, Min; Huang, Shengnan; Liu, Shaojun

    2016-06-01

    In the Dongting water system, the Carassius auratus (Crucian carp) complex is characterized by the coexistence of diploid forms (2n=100, 2nCC) and polyploid forms. Chromosomal and karyotypic analyses have suggested that the polyploid C. auratus has a triploid (3n=150, 3nCC) and a tetraploid origin (4n=200), respectively. However, there is a lack of direct genetic evidence to support this conclusion. In this paper, analysis of the 5S rDNA chromosomal locus revealed that the 3nCC is of triploid origin. Analysis of the species-specific chromosomal centromere locus revealed that 3nCC individuals possess three sets of C. auratus-derived chromosomes. Our results provide direct cytogenetic evidence suggesting that individuals with 150 chromosomes are of autotriploid origin within the C. auratus complex. It marks an important contribution to the study of polyploidization and the evolution of vertebrates. PMID:27084707

  1. Nonnegative spline regression of incomplete tracing data reveals high resolution neural connectivity

    CERN Document Server

    Harris, Kameron Decker; Shea-Brown, Eric

    2016-01-01

    Whole-brain neural connectivity data are now available from viral tracing experiments, which reveal the connections between a source injection site and elsewhere in the brain. These hold the promise of revealing spatial patterns of connectivity throughout the mammalian brain. To achieve this goal, we seek to fit a weighted, nonnegative adjacency matrix among 100 {\\mu}m brain "voxels" using viral tracer data. Despite a multi-year experimental effort, the problem remains severely underdetermined: Injection sites provide incomplete coverage, and the number of voxels is orders of magnitude larger than the number of injections. Furthermore, projection data are missing within the injection site because local connections there are not separable from the injection signal. We use a novel machine-learning algorithm to meet these challenges and develop a spatially explicit, voxel-scale connectivity map of the mouse visual system. Our method combines three features: a matrix completion loss for missing data, a smoothing ...

  2. Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus

    International Nuclear Information System (INIS)

    The viral and virus-related structures of Rice dwarf virus have been visualized by cryo-electron microscopy and tomography revealing the viral infection and replication mechanisms. It is well known that viruses utilize the host cellular systems for their infection and replication processes. However, the molecular mechanisms underlying these processes are poorly understood for most viruses. To understand these molecular mechanisms, it is essential to observe the viral and virus-related structures and analyse their molecular interactions within a cellular context. Cryo-electron microscopy and tomography offer the potential to observe macromolecular structures and to analyse their molecular interactions within the cell. Here, using cryo-electron microscopy and tomography, the structures of Rice dwarf virus are reported within fully hydrated insect vector cells grown on electron microscopy grids towards revealing the viral infection and replication mechanisms

  3. Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, Naoyuki, E-mail: naomiya@nips.ac.jp [National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585 (Japan); Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Akita, Fusamichi [National Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666 (Japan); Graduate School of Natural Science and Technology, Faculty of Science, Okayama University, Okayama 700-8530 (Japan); Nakagawa, Atsushi [Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Murata, Kazuyoshi [National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585 (Japan); Omura, Toshihiro [National Agricultural Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666 (Japan); Iwasaki, Kenji, E-mail: naomiya@nips.ac.jp [Institute for Protein Research, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2013-11-01

    The viral and virus-related structures of Rice dwarf virus have been visualized by cryo-electron microscopy and tomography revealing the viral infection and replication mechanisms. It is well known that viruses utilize the host cellular systems for their infection and replication processes. However, the molecular mechanisms underlying these processes are poorly understood for most viruses. To understand these molecular mechanisms, it is essential to observe the viral and virus-related structures and analyse their molecular interactions within a cellular context. Cryo-electron microscopy and tomography offer the potential to observe macromolecular structures and to analyse their molecular interactions within the cell. Here, using cryo-electron microscopy and tomography, the structures of Rice dwarf virus are reported within fully hydrated insect vector cells grown on electron microscopy grids towards revealing the viral infection and replication mechanisms.

  4. Peripheral blood RNA gene expression profiling in illicit methcathinone users reveals effect on immune system

    Directory of Open Access Journals (Sweden)

    Katrin eSikk

    2011-08-01

    Full Text Available Methcathinone (ephedrone is relatively easily accessible for abuse. Its users develop an extrapyramidal syndrome and it is not known if this is caused by methcathinone itself, by side-ingredients (manganese, or both. In the present study we aimed to clarify molecular mechanisms underlying this condition. We analyzed whole genome gene expression patterns of peripheral blood from 20 methcathinone users and 20 matched controls. Gene expression profile data was analyzed by Bayesian modelling and functional annotation. In order to verify the genechip results we performed quantitative real-time (RT PCR in selected genes. 326 out of analyzed 28,869 genes showed statistically significant differential expression with FDR adjusted p-values below 0.05. Quantitative RT-PCR confirmed differential expression for the most of selected genes. Functional annotation and network analysis indicated that most of the genes were related to activation immunological disease, cellular movement and cardiovascular disease gene network (enrichment score 42. As HIV and HCV infections were confounding factors, we performed additional stratification of patients. A similar functional activation of the immunological disease pathway was evident when we compared patients according to the injection status (past versus current users, balanced for HIV and HCV infection. However, this difference was not large therefore the major effect was related to the HIV status of the patients. Mn-methcathinone abusers have blood transcriptional patterns mostly caused by their HIV and HCV infections.

  5. Comparative metagenomic profiling reveals lignocellulose degrading systems in microbial communities associated with wood-feeding insects

    Science.gov (United States)

    The Asian longhorned beetle (Anoplophora glabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. The biggest impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars locke...

  6. Survey of green building water systems reveals elevated water age and water quality concerns

    OpenAIRE

    Rhoads, William J.; Pruden, Amy; Edwards, Marc A.

    2015-01-01

    Widespread adoption of innovative water conservation strategies has potential unintended consequences for aesthetics and public health. A cross-section of green buildings were surveyed and compared to typical conventional buildings in terms of water retention time (i.e., water age), water chemistry, and levels of opportunistic pathogen genetic markers. Water age was estimated to be 2-6.7 months in an off-grid office, an average of 8 days in a Leadership in Environmental Engineering Design cer...

  7. Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome

    OpenAIRE

    Sohn, Yunkyu; Choi, Myung-Kyu; Ahn, Yong-Yeol; Lee, Junho; Jeong, Jaeseung

    2011-01-01

    The modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture. Here we use the modularity-based community detection method for directed, weighted networks to examine hierarchically organized modules in the complete wiring diagram (connectome) of Caenorhabditis elegans (C. elegans) and to investigate their topological properties. Incorporating bilateral symmetry of the network...

  8. Compelling evidence reveals that oral chronic infection and oral inflammation generate systemic consequences.

    Directory of Open Access Journals (Sweden)

    Adolfo Contreras

    2011-11-01

    Full Text Available The mouth is the gateway to our body. It represents ~10% of human body volume; however, important functions rely on the mouth: eating, degustation, exploring the world as a child, chewing, digestion,tasting, biting, breathing through the mouth, vomiting, kissing, smiling, speaking, nonverbal communication, sex appeal, and social relations also depend on having a healthy and functional mouth. The teeth, tongue, gums, nerves, muscles, ligaments, veins, arteries, bones, connective tissue, and epithelia are organized in the complex structural array that constitutes the mouth.The mouth establishes anatomical relationships with other essential organs like the pharynx, the esophagus, the nose, the face, the ears, the orbits and, perhaps most important, the brain. The physiologic mouth boundary with the body is by far more complex. Just to mentionthat saliva is an extremely important defensive body fluid, released into the mouth by which innate and acquired immune mechanisms effectively defend the host against foreign insults.

  9. Metagenome Analyses of Corroded Concrete Wastewater Pipe Biofilms Reveals a Complex Microbial System

    Science.gov (United States)

    Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe. Taxonomic and functio...

  10. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems

    OpenAIRE

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addi...

  11. Chain Dynamics in Solid Polymers and Polymerizing Systems as Revealed by Broadband Dielectric Spectroscopy

    Science.gov (United States)

    Williams, Graham

    2008-08-01

    A number of techniques are used to study the chain-dynamics of solid polymers, including those of dielectric relaxation [1-4], dynamic mechanical thermal analysis (DMTA) [1, 5], multinuclear NMR relaxations [6], quasi-elastic dynamic light scattering [7] and neutron scattering [8] (QELS & QENS) and transient fluorescence depolarization (TFD) [9]. Each technique has its own particular probe of the dynamics in a material. e.g. dielectric relaxation gives information on the angular motions of molecular chain-dipoles (for dipole relaxation) and the translational motions of ions (for f-dependent electrical conduction); NMR relaxations relate to the angular motions of chemical bonds; QELS relates to fluctuations in local refractive index; QENS to the time-dependent van Hove correlation function (suitably-defined) for proton-containing groups; TFD to the angular motions of fluorescent groups in a chain. Due to its relevance to practical applications of materials, DMTA is pre-eminent among the many physical techniques applied to solid polymers, but interpretations of behaviour in terms of molecular properties remain difficult since the direct link between an applied macroscopic stress and the molecular response of polymer chains in a bulk material remains an unsolved problem. Of the above techniques, Broadband Dielectric Spectroscopy (BDS) offers several advantages. (a) Materials may be studied in the frequency range 10-6 to 1010 Hz, over wide ranges of temperature and applied pressure, using commercially-available instrumentation. (b) Since the electrical capacitance of a film is inversely proportional its thickness, free-standing and supported films may be studied down to nm-thicknesses, giving e.g. information on the behaviour of the dynamic Tg as sample thickness approaches molecular dimensions. (c) Theoretical interpretations of dielectric relaxation and a.c. conduction are well-established in terms of Fourier transforms of molecular time correlation functions (TCFs) for motions of chain dipoles and ionic species. Large scale "Molecular dynamics" simulations have been used to calculate molecular TCFs, and hence the dielectric properties, of model bulk amorphous polymer materials [10, 11].

  12. Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma

    OpenAIRE

    Hayashi, Kentaro; Tabata, Sho; Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

    2015-01-01

    Cancer cells are highly variable and largely resistant to therapeutic intervention. Recently, the use of the tumor necrosis factor related apoptosis-inducing ligand (TRAIL) induced treatment is gaining momentum due to TRAIL’s ability to specifically target cancers with limited effect on normal cells. Nevertheless, several malignant cancer types still remain non-sensitive to TRAIL. Previously, we developed a dynamic computational model, based on perturbation-response differential equations app...

  13. Comparative systems biology reveals allelic variation modulating tocochromanol profiles in barley

    Science.gov (United States)

    Background: Tocochromanols are recognized for beneficial effects in plant stress response, seed storage longevity, and nutritional content. Efforts to elucidate specific bioactive forms and develop new crops with beneficial amounts and ratios have been hindered due to costly analytical methods. Obje...

  14. Functional genomics of tick thioester-containing proteins reveal the ancient origin of the complement system

    Czech Academy of Sciences Publication Activity Database

    Burešová, Veronika; Hajdušek, Ondřej; Franta, Zdeněk; Loosová, Gabriela; Grunclová, Lenka; Levashina, E.A.; Kopáček, Petr

    2011-01-01

    Roč. 3, č. 6 (2011), s. 623-630. ISSN 1662-811X R&D Projects: GA ČR GAP506/10/2136; GA MŠk(CZ) LC06009 Institutional research plan: CEZ:AV0Z60220518 Keywords : tick * thioester-containing proteins * complement Subject RIV: EC - Immunology Impact factor: 4.209, year: 2011

  15. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    DEFF Research Database (Denmark)

    Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria;

    2015-01-01

    Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide a...

  16. Hospitalized Children Reveal Health Systems Gaps in the Mother-Child HIV Care Cascade in Kenya.

    Science.gov (United States)

    Njuguna, Irene N; Wagner, Anjuli D; Cranmer, Lisa M; Otieno, Vincent O; Onyango, Judith A; Chebet, Daisy J; Okinyi, Helen M; Benki-Nugent, Sarah; Maleche-Obimbo, Elizabeth; Slyker, Jennifer A; John-Stewart, Grace C; Wamalwa, Dalton C

    2016-03-01

    To identify missed opportunities in HIV prevention, diagnosis, and linkage to care, we enrolled 183 hospitalized, HIV-infected, ART-naïve Kenyan children 0-12 years from four hospitals in Nairobi and Kisumu, and reviewed prevention of mother-to-child transmission of HIV (PMTCT), hospitalization, and HIV testing history. Median age was 1.8 years (IQR = 0.8, 4.5). Most mothers received HIV testing during pregnancy (77%). Among mothers tested, 60% and 40% reported HIV-negative and positive results, respectively; 33% of HIV-diagnosed mothers did not receive PMTCT antiretrovirals. First missed opportunities for pediatric diagnosis and linkage were due to failure to test mothers (23.1%), maternal HIV acquisition following initial negative test (45.7%), no early infant diagnosis (EID) or provider-initiated testing (PITC) (12.7%), late breastfeeding transmission (8.7%), failure to collect child HIV test results (1.2%), and no linkage to care following HIV diagnosis (8.7%). Among previously hospitalized children, 38% never received an HIV test. Strengthening initial and repeat maternal HIV testing and PITC are key interventions to prevent, detect, and treat pediatric HIV infections. PMID:27308805

  17. Glycan-Foraging Systems Reveal the Adaptation of Capnocytophaga canimorsus to the Dog Mouth

    OpenAIRE

    Renzi, Francesco; Manfredi, Pablo; Dol, Mélanie; Fu, Jian; Vincent, Stéphane; Cornelis, Guy Richard

    2015-01-01

    ABSTRACT Capnocytophaga canimorsus is known to form two kinds of cells on blood agar plates (coccoid and bacillary), evoking phase variation. When grown in coculture with animal cells these bacteria appeared only as bacilli, but in the presence of vancomycin they were round, indicating that coccoid shapes likely result from weakening of the peptidoglycan layer. Polysaccharide utilization locus 5 (PUL5) and sialidase mutant bacteria, unable to retrieve glycans from glycoproteins, grew less tha...

  18. Central nervous system PET-CT imaging reveals regional impairments in pediatric patients with Wolfram syndrome.

    Directory of Open Access Journals (Sweden)

    Agnieszka Zmyslowska

    Full Text Available Wolfram syndrome (WFS is inherited as an autosomal recessive disease with main clinical features of diabetes mellitus, optic atrophy, diabetes insipidus and deafness. However, various neurological defects may also be detected. The aim of this study was to evaluate aspects of brain structure and function using PET-CT (positron emission tomography and computed tomography and MRI (magnetic resonance imaging in pediatric patients with WFS. Regional changes in brain glucose metabolism were measured using standardized uptake values (SUVs based on images of (18F fluorodeoxyglucose (FDG uptake in 7 WFS patients aged 10.1-16.0 years (mean 12.9±2.4 and in 20 healthy children aged 3-17.9 years (mean 12.8±4.1. In all patients the diagnosis of WFS was confirmed by DNA sequencing of the WFS1 gene. Hierarchical clustering showed remarkable similarities of glucose uptake patterns among WFS patients and their differences from the control group. SUV data were subsequently standardized for age groups 13 years old to account for developmental differences. Reduced SUVs in WFS patients as compared to the control group for the bilateral brain regions such as occipital lobe (-1.24±1.20 vs. -0.13±1.05; p = 0.028 and cerebellum (-1.11±0.69 vs. -0.204±1.00; p = 0.036 were observed and the same tendency for cingulate (-1.13±1.05 vs. -0.15±1.12; p = 0.056, temporal lobe (-1.10±0.98 vs. -0.15±1.10; p = 0.057, parietal lobe (-1.06±1.20 vs. -0.08±1.08; p = 0.058, central region (-1.01±1.04 vs. -0.09±1.06; p = 0.060, basal ganglia (-1.05±0.74 vs. -0.20±1.07; p = 0.066 and mesial temporal lobe (-1.06±0.82 vs. -0.26±1.08; p = 0.087 was also noticed. After adjusting for multiple hypothesis testing, the differences in glucose uptake were non-significant. For the first time, regional differences in brain glucose metabolism among patients with WFS were shown using PET-CT imaging.

  19. A systems biology investigation of neurodegenerative dementia reveals a pivotal role of autophagy

    OpenAIRE

    Caberlotto, Laura; Nguyen, Thanh Phuong

    2014-01-01

    Background Neurodegenerative dementia comprises chronic and progressive illnesses with major clinical features represented by progressive and permanent loss of cognitive and mental performance, including impairment of memory and brain functions. Many different forms of neurodegenerative dementia exist, but they are all characterized by death of specific subpopulation of neurons and accumulation of proteins in the brain. We incorporated data from OMIM and primary molecular targets of drugs in ...

  20. Circumstellar material in the Vega inner system revealed by CHARA/FLUOR

    CERN Document Server

    Absil, O; Augereau, J C; Berger, D H; Brummelaar, T A; Folco, E; Foresto, V C; Kervella, P; McAlister, H A; Merand, A; Ridgway, S T; Sturmann, J; Sturmann, L; Turner, N H

    2006-01-01

    Only a handful of debris disks have been imaged up to now. Due to the need for high dynamic range and high angular resolution, very little is known about the inner planetary region, where small amounts of warm dust are expected to be found. We investigate the close neighbourhood of Vega with the help of infrared stellar interferometry and estimate the integrated K-band flux originating from the central 8 AU of the debris disk. We performed precise visibility measurements at both short (~30 m) and long (~150 m) baselines with the FLUOR beam-combiner installed at the CHARA Array (Mt Wilson, California) in order to separately resolve the emissions from the extended debris disk (short baselines) and from the stellar photosphere (long baselines). After revising Vega's K-band angular diameter (3.202+/-0.005 mas), we show that a significant deficit in squared visibility (1.88+/-0.34%) is detected at short baselines with respect to the best-fit uniform disk stellar model. This deficit can be either attributed to the ...

  1. Estimation of revealing methods of microstructure in duplex stainless steels

    International Nuclear Information System (INIS)

    Revealing of microstructure in duplex stainless steels by conventional chemical or electrochemical etching methods is relatively difficult as opposed to carbon steels. There are a many etching methods for duplex stainless steels, however electrolytic etching is really the best way to go. Electrochemical etching assures very good distinction of ferrite, austenite and secondary phases also etching of grain boundaries and twins, simultaneously warranting repeatability of process' circumstances. However, literature data do not deliver enough explicit parameters and conditions of electrolytic etching process, what in consequence can lead to indirect phenomenon during the process, such as pitting or etching twins. In frames of this work we have tested different methods of electrolytic etching of duplex stainless steel 1.4462-X2CrNiMoN 22.5.3 according to EURONORM (UNS S3108). This article has in view discussing of controversial matter of argument relating to revealing microstructure in duplex stainless steels on the ground of conducted investigations. (author)

  2. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

    DEFF Research Database (Denmark)

    Gerlinger, Marco; Rowan, Andrew J.; Horswell, Stuart; Larkin, James; Endesfelder, David; Gronroos, Eva; Martinez, Pierre; Matthews, Nicholas; Stewart, Aengus; Tarpey, Patrick; Varela, Ignacio; Phillimore, Benjamin; Begum, Sharmin; McDonald, Neil Q.; Butler, Adam; Jones, David; Raine, Keiran; Latimer, Calli; Santos, Claudio R.; Nohadani, Mahrokh; Eklund, Aron Charles; Spencer-Dene, Bradley; Clark, Graham; Pickering, Lisa; Stamp, Gordon; Gore, Martin; Szallasi, Zoltan Imre; Downward, Julian; Futreal, P. Andrew; Swanton, Charles

    2012-01-01

    BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples.METHODSTo examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy...... mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples...

  3. Revealing Topological Superconductivity in Extended Quantum Spin Hall Josephson Junctions

    OpenAIRE

    Lee, Shu-Ping; Michaeli, Karen; Alicea, Jason; Yacoby, Amir

    2014-01-01

    Quantum spin Hall-superconductor hybrids are promising sources of topological superconductivity and Majorana modes, particularly given recent progress on HgTe and InAs/GaSb. We propose a new method of revealing topological superconductivity in extended quantum spin Hall Josephson junctions supporting `fractional Josephson currents'. Specifically, we show that as one threads magnetic flux between the superconductors, the critical current traces an interference pattern featuring sharp fingerpri...

  4. Stated and revealed heterogeneous risk preferences in educational choice

    OpenAIRE

    Frank M. Fossen; Glocker, Daniela

    2014-01-01

    Stated survey measures of risk preferences are increasingly being used in the literature, and they have been compared to revealed risk aversion primarily by means of experiments such as lottery choice tasks. In this paper, we investigate educational choice, which involves the comparison of risky future income paths and therefore depends on risk and time preferences. In contrast to experimental settings, educational choice is one of the most important economic decisions taken by individuals, a...

  5. Interviewing young adolescent suspects: When to reveal incriminating information?

    OpenAIRE

    Jamie Lingwood; Ray Bull

    2013-01-01

    Recent research has demonstrated that the way in which interviewers reveal information/evidence tointerviewees/suspects can produce noticeable differences between truthful and deceptive verbalstatements. However, very little of this research has involved adolescents. In the present study, 12 to 14year old adolescents were asked to commit (n = 26) or not to commit (n = 26) a mock crime and atinterview to deny involvement in this crime. Prior to interview some information about each adolescent’...

  6. Monofractal nature of air temperature signals reveals their climate variability

    CERN Document Server

    Deliège, Adrien

    2014-01-01

    We use the discrete "wavelet transform microscope" to show that the surface air temperature signals of weather stations selected in Europe are monofractal. This study reveals that the information obtained in this way are richer than previous works studying long range correlations in meteorological stations. The approach presented here allows to bind the H\\"older exponents with the climate variability. We also establish that such a link does not exist with methods previously carried out.

  7. Epithelial structure revealed by chemical dissection and unembedded electron microscopy

    OpenAIRE

    Fey, E G; Capco, D G; Krochmalnic, G; Penman, S

    1984-01-01

    Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton w...

  8. HII 2407: A Low-Mass Eclipsing Binary Revealed by K2 Observations of the Pleiades

    CERN Document Server

    David, Trevor J; Hillenbrand, Lynne A; Cody, Ann Marie; Conroy, Kyle; Stassun, Keivan G; Pope, Benjamin; Aigrain, Suzanne; Gillen, Ed; Cameron, Andrew Collier; Barrado, David; Rebull, L M; Isaacson, Howard; Marcy, Geoffrey W; Zhang, Celia; Riddle, Reed L; Ziegler, Carl; Law, Nicholas M; Baranec, Christoph

    2015-01-01

    The star HII 2407 is a member of the relatively young Pleiades star cluster and was previously discovered to be a single-lined spectroscopic binary. It is newly identified here within $Kepler$/$K2$ photometric time series data as an eclipsing binary system. Mutual fitting of the radial velocity and photometric data leads to an orbital solution and constraints on fundamental stellar parameters. While the primary has arrived on the main sequence, the secondary is still pre-main-sequence and we compare our results for the $M/M_\\odot$ and $R/R_\\odot$ values with stellar evolutionary models. We also demonstrate that the system is likely to be tidally synchronized. Follow-up infrared spectroscopy is likely to reveal the lines of the secondary, allowing for dynamically measured masses and elevating the system to benchmark eclipsing binary status.

  9. Using metabarcoding to reveal and quantify plant-pollinator interactions.

    Science.gov (United States)

    Pornon, André; Escaravage, Nathalie; Burrus, Monique; Holota, Hélène; Khimoun, Aurélie; Mariette, Jérome; Pellizzari, Charlène; Iribar, Amaia; Etienne, Roselyne; Taberlet, Pierre; Vidal, Marie; Winterton, Peter; Zinger, Lucie; Andalo, Christophe

    2016-01-01

    Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole. PMID:27255732

  10. Contrast Agent Mass Spectrometry Imaging Reveals Tumor Heterogeneity.

    Science.gov (United States)

    Tata, Alessandra; Zheng, Jinzi; Ginsberg, Howard J; Jaffray, David A; Ifa, Demian R; Zarrine-Afsar, Arash

    2015-08-01

    Mapping intratumoral heterogeneity such as vasculature and margins is important during intraoperative applications. Desorption electrospray ionization mass spectrometry (DESI-MS) has demonstrated potential for intraoperative tumor imaging using validated MS profiles. The clinical translation of DESI-MS into a universal label-free imaging technique thus requires access to MS profiles characteristic to tumors and healthy tissues. Here, we developed contrast agent mass spectrometry imaging (CA-MSI) that utilizes a magnetic resonance imaging (MRI) contrast agent targeted to disease sites, as a label, to reveal tumor heterogeneity in the absence of known MS profiles. Human breast cancer tumors grown in mice were subjected to CA-MSI using Gadoteridol revealing tumor margins and vasculature from the localization of [Gadoteridol+K](+) and [Gadoteridol+Na](+) adducts, respectively. The localization of the [Gadoteridol+K](+) adduct as revealed through DESI-MS complements the in vivo MRI results. DESI-MS imaging is therefore possible for tumors for which no characteristic MS profiles are established. Further DESI-MS imaging of the flux of the contrast agent through mouse kidneys was performed indicating secretion of the intact label. PMID:26138213

  11. Land system science and sustainable development of the earth system

    DEFF Research Database (Denmark)

    Verburg, Peter H.; Crossman, Neville; Ellis, Erle C.;

    2015-01-01

    Land systems are the result of human interactions with the natural environment. Understanding the drivers, state, trends and impacts of different land systems on social and natural processes helps to reveal how changes in the land system affect the functioning of the socio-ecological system as a ...

  12. Vagoglossopharyngeal neuralgia revealed through predominant digestive vagal manifestations. Case report and literature review.

    Science.gov (United States)

    Antherieu, P; Vassal, F; Sindou, M

    2016-06-01

    Vagoglossopharyngeal neuralgia is a rare pathology whose atypical forms, dominated by syncopal manifestations, are still rarer. Although the territory of the vagus nerve involves, beyond the cardiovascular system, the respiratory and the digestive systems, there is no report in literature of atypical forms other than syncopal. Therefore, the authors were prompted to report the case of a patient whose vagoglossopharyngeal neuralgia was predominantly revealed by digestive symptoms. A 58-year-old patient presented with stereotypical severe digestive disturbances including nausea, vomiting and diarrhoea. High definition cranial MRI showed a neurovascular conflict between the posterior inferior cerebellar artery and the IXth and Xth nerves, on the right side. A microsurgical decompression was carried out which confirmed the vascular compression and successful transposition of the artery. One year after the surgery, the patient was free from all painful and digestive symptoms. A survey of the literature did not find any reference to digestive symptoms together with the neuralgia; only a syncopal type of cardiac symptoms related to the parasympathetic nervous system were described. The hypothesis was that the revealing digestive symptoms are linked to a similar parasympathetic mechanism, implying the visceral component of the Xth cranial nerve. PMID:27179388

  13. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

    Directory of Open Access Journals (Sweden)

    Phillip B Pope

    Full Text Available Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus. Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1. Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5 but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

  14. The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain

    OpenAIRE

    Sullivan, Nora L.; Septer, Alecia Noelle; Fields, Andrew T; Wenren, Larissa Man-Yin; Gibbs, Karine A.

    2013-01-01

    We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system for self recognition. This opportunistic pathogen contains a single, circular chromosome (3,846,754 bp). Comparisons between this genome and that of strain HI4320 reveal genetic variations corresponding to previously unknown physiological and self-recognition differences.

  15. The Complete Genome Sequence of Proteus mirabilis Strain BB2000 Reveals Differences from the P. mirabilis Reference Strain

    OpenAIRE

    Sullivan, Nora L.; Septer, Alecia N.; Fields, Andrew T; Wenren, Larissa M.; Gibbs, Karine A.

    2013-01-01

    We announce the complete genome sequence for Proteus mirabilis strain BB2000, a model system for self recognition. This opportunistic pathogen contains a single, circular chromosome (3,846,754 bp). Comparisons between this genome and that of strain HI4320 reveal genetic variations corresponding to previously unknown physiological and self-recognition differences.

  16. Crystal Structures and Molecular Dynamics Simulations of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion for Co-Substrate Binding

    OpenAIRE

    Hung, Chih-Hung; Hwang, Tzann-Shun; Chang, Yu-Yung; Luo, Huei-Ru; Wu, Szu-Pei; Hsu, Chun-Hua

    2013-01-01

    Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed great...

  17. Convergent Validity of Revealed and Stated Recreation Behavior with Quality Change: A Comparison of Multiple and Single Site Demands

    OpenAIRE

    John C. Whitehead; Daniel Phaneuf; Christopher F. Dumas; Jim Herstine; Jeffrey Hill; Bob Buerger

    2007-01-01

    We consider the convergent validity of several demand models using beach recreation data. Two models employ multiple site data: a count data demand system model and the Kuhn-Tucker demand system model. We explore the role of existing variation in beach width in explaining trip choices, and analyze a hypothetical 100 foot increase in beach width. We compare these models to a single equation model where we jointly estimate revealed and stated preference trip data, and focus on a hypothetical sc...

  18. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

    OpenAIRE

    Jinek, Martin; Jiang, Fuguo; Taylor, David W.; Sternberg, Samuel H.; Kaya, Emine; MA, ENBO; Anders, Carolin; Hauer, Michael; Zhou, Kaihong; Lin, Steven; Kaplan, Matias; Anthony T Iavarone; Charpentier, Emmanuelle; Nogales, Eva; Doudna, Jennifer A.

    2014-01-01

    Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all C...

  19. Controlled preparation of wet granular media reveals limits to lizard burial ability

    Science.gov (United States)

    Sharpe, Sarah S.; Kuckuk, Robyn; Goldman, Daniel I.

    2015-07-01

    Many animals move within ground composed of granular media (GM); the resistive properties of such substrates can depend on water content and compaction, but little is known about how such parameters affect locomotion or the physics of drag and penetration. Using apparatus to control compaction of GM, our recent studies of movement in dry GM have revealed locomotion strategies of specialized dry-sand-swimming reptiles. However, these animals represent a small fraction of the diversity and presumed burial strategies of fossorial reptilian fauna. Here we develop a system to create states of wet GM of varying moisture content and compaction in quantities sufficient to study the burial and subsurface locomotion of the Ocellated skink (C. ocellatus), a generalist lizard. X-ray imaging revealed that in wet and dry GM the lizard slowly buried (≈ 30 s) propagating a wave from head to tail, while moving in a start-stop motion. During forward movement, the head oscillated, and the forelimb on the convex side of the body propelled the animal. Although body kinematics and ‘slip’ were similar in both substrates, the burial depth was smaller in wet GM. Penetration and drag force experiments on smooth cylinders revealed that wet GM was ≈ 4× more resistive than dry GM. In total, our measurements indicate that while the rheology of the dry and wet GM differ substantially, the lizard's burial motor pattern is conserved across substrates, while its burial depth is largely constrained by environmental resistance.

  20. Gas Dynamics and Outflow in the Barred Starburst Galaxy NGC 1808 Revealed with ALMA

    CERN Document Server

    Salak, Dragan; Hatakeyama, Takuya; Miyamoto, Yusuke

    2016-01-01

    NGC 1808 is a nearby barred starburst galaxy with an outflow from the nuclear region. To study the inflow and outflow processes related to star formation and dynamical evolution of the galaxy, we have carried out \\(^{12}\\)CO (\\(J=1-0\\)) mapping observations of the central \\(r\\sim4\\) kpc of NGC 1808 using the Atacama Large Millimeter/submillimeter Array (ALMA). Four distinct components of molecular gas are revealed at high spatial resolution of 2\\arcsec (\\(\\sim100\\) pc): (1) a compact (\\(r<200\\) pc) circumnuclear disk (CND), (2) \\(r\\sim500\\) pc ring, (3) gas-rich galactic bar, and (4) spiral arms. Basic geometric and kinematic parameters are derived for the central 1-kpc region using tilted-ring modeling. The derived rotation curve reveals multiple mass components that include (1) a stellar bulge, (2) nuclear bar and molecular CND, and (3) unresolved massive (\\(\\sim10^7~M_\\sun\\)) core. Two systemic velocities, 998 km s\\(^{-1}\\) for the CND and 964 km s\\(^{-1}\\) for the 500-pc ring, are revealed, indicating ...

  1. Controlled preparation of wet granular media reveals limits to lizard burial ability.

    Science.gov (United States)

    Sharpe, Sarah S; Kuckuk, Robyn; Goldman, Daniel I

    2015-07-01

    Many animals move within ground composed of granular media (GM); the resistive properties of such substrates can depend on water content and compaction, but little is known about how such parameters affect locomotion or the physics of drag and penetration. Using apparatus to control compaction of GM, our recent studies of movement in dry GM have revealed locomotion strategies of specialized dry-sand-swimming reptiles. However, these animals represent a small fraction of the diversity and presumed burial strategies of fossorial reptilian fauna. Here we develop a system to create states of wet GM of varying moisture content and compaction in quantities sufficient to study the burial and subsurface locomotion of the Ocellated skink (C. ocellatus), a generalist lizard. X-ray imaging revealed that in wet and dry GM the lizard slowly buried (≈30 s) propagating a wave from head to tail, while moving in a start-stop motion. During forward movement, the head oscillated, and the forelimb on the convex side of the body propelled the animal. Although body kinematics and 'slip' were similar in both substrates, the burial depth was smaller in wet GM. Penetration and drag force experiments on smooth cylinders revealed that wet GM was ≈4× more resistive than dry GM. In total, our measurements indicate that while the rheology of the dry and wet GM differ substantially, the lizard's burial motor pattern is conserved across substrates, while its burial depth is largely constrained by environmental resistance. PMID:26109565

  2. Automatic decoding of facial movements reveals deceptive pain expressions

    OpenAIRE

    Bartlett, Marian Stewart; Littlewort, Gwen C.; Mark G. Frank; Lee, Kang

    2014-01-01

    In highly social species such as humans, faces have evolved to convey rich information for social interaction, including expressions of emotions and pain [1–3]. Two motor pathways control facial movement [4–7]. A subcortical extrapyramidal motor system drives spontaneous facial expressions of felt emotions. A cortical pyramidal motor system controls voluntary facial expressions. The pyramidal system enables humans to simulate facial expressions of emotions not actually experienced. Their simu...

  3. Many-objective optimization and visual analytics reveal key trade-offs for London's water supply

    Science.gov (United States)

    Matrosov, Evgenii S.; Huskova, Ivana; Kasprzyk, Joseph R.; Harou, Julien J.; Lambert, Chris; Reed, Patrick M.

    2015-12-01

    In this study, we link a water resource management simulator to multi-objective search to reveal the key trade-offs inherent in planning a real-world water resource system. We consider new supplies and demand management (conservation) options while seeking to elucidate the trade-offs between the best portfolios of schemes to satisfy projected water demands. Alternative system designs are evaluated using performance measures that minimize capital and operating costs and energy use while maximizing resilience, engineering and environmental metrics, subject to supply reliability constraints. Our analysis shows many-objective evolutionary optimization coupled with state-of-the art visual analytics can help planners discover more diverse water supply system designs and better understand their inherent trade-offs. The approach is used to explore future water supply options for the Thames water resource system (including London's water supply). New supply options include a new reservoir, water transfers, artificial recharge, wastewater reuse and brackish groundwater desalination. Demand management options include leakage reduction, compulsory metering and seasonal tariffs. The Thames system's Pareto approximate portfolios cluster into distinct groups of water supply options; for example implementing a pipe refurbishment program leads to higher capital costs but greater reliability. This study highlights that traditional least-cost reliability constrained design of water supply systems masks asset combinations whose benefits only become apparent when more planning objectives are considered.

  4. Interior Evolution of Ceres and Vesta Revealed by Dawn

    Science.gov (United States)

    Raymond, C. A.; Russell, C. T.; Bland, M. T.; Castillo, J. C.; De Sanctis, M. C.; Ermakov, A.; Jaumann, R.; Konopliv, A. S.; Marchi, S.; McCord, T. B.; McSween, H. Y., Jr.; Nathues, A.; Park, R. S.; Prettyman, T. H.; Toplis, M. J.; Zuber, M. T.

    2015-12-01

    Dawn's exploration of Vesta and Ceres has revealed their geophysical characteristics, informing the processes that shaped the bodies. Dawn has determined the average diameter of Ceres to be 940 km, smaller than the previously estimated 975 km [1]. This implies a density of 2160 kg/m3, indicating that Ceres is less differentiated than predicted [2]. Ceres' entire surface is cratered, implying the lack of a thick (10's of km) water ice layer at the surface. Variability in Ceres' crater morphology indicates that the near-surface layer has variable strength and rheology, likely due to heterogeneity in the near-surface mixture of rock, ice and salt. These observations may indicate that Ceres lost a significant amount of an original surface ice layer due to impact erosion. The lack of large impact basins on Ceres can be interpreted to be the result of viscous relaxation. These data provide insights into Ceres' thermal evolution and mechanical properties, which appear to be unique to this warm, icy body. In contrast to Ceres, Vesta formed very early and hot, resulting in a fully differentiated body. Dawn's exploration revealed geophysical and geochemical evidence for an iron-rich core and basaltic crust. However, unlike the pre-Dawn paradigm of Vesta's evolution, Dawn found that the crust and mantle of Vesta are less distinct than predicted by classical differentiation models. [1] Thomas, P. C., et al., Differentiation of the asteroid Ceres as revealed by its shape, Nature, 437, 224-226, 2005; [2] McCord et al., Ceres: Its Origin, Evolution and Structure and Dawn's Potential Contribution, Space Sci Rev
DOI 10.1007/s11214-010-9729-9, 2011.

  5. Genes but not genomes reveal bacterial domestication of Lactococcus lactis.

    Directory of Open Access Journals (Sweden)

    Delphine Passerini

    Full Text Available BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE. METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable

  6. Communicability reveals a transition to coordinated behavior in multiplex networks

    Science.gov (United States)

    Estrada, Ernesto; Gómez-Gardeñes, Jesús

    2014-04-01

    We analyze the flow of information in multiplex networks by means of the communicability function. First, we generalize this measure from its definition from simple graphs to multiplex networks. Then, we study its relevance for the analysis of real-world systems by studying a social multiplex where information flows using formal-informal channels and an air transportation system where the layers represent different air companies. Accordingly, the communicability, which is essential for the good performance of these complex systems, emerges at a systemic operation point in the multiplex where the performance of the layers operates in a coordinated way very differently from the state represented by a collection of unconnected networks.

  7. Communicability reveals a transition to coordinated behavior in multiplex networks

    CERN Document Server

    Estrada, Ernesto

    2013-01-01

    We analyse the flow of information in multiplex networks by means of the communicability function. First, we generalize this measure from its definition from simple graphs to multiplex networks. Then, we study its relevance for the analysis of real-world systems by studying a social multiplex where information flows using formal/informal channels and an air transportation system where the layers represent different air companies. Accordingly, the communicability, which is essential for the good performance of these complex systems, emerges at a systemic operation point in the multiplex where the performance of the layers operates in a coordinated way very differently from the state represented by a collection of unconnected networks.

  8. GBT Reveals Satellite of Milky Way in Retrograde Orbit

    Science.gov (United States)

    2003-05-01

    New observations with National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) suggest that what was once believed to be an intergalactic cloud of unknown distance and significance, is actually a previously unrecognized satellite galaxy of the Milky Way orbiting backward around the Galactic center. Path of Complex H Artist's rendition of the path of satellite galaxy Complex H (in red) in relation to the orbit of the Sun (in yellow) about the center of the Milky Way Galaxy. The outer layers of Complex H are being stripped away by its interaction with the Milky Way. The hydrogen atmosphere (in blue) is shown surrounding the visible portion (in white) of the Galaxy. CREDIT: Lockman, Smiley, Saxton; NRAO/AUI Jay Lockman of the National Radio Astronomy Observatory (NRAO) in Green Bank, West Virginia, discovered that this object, known as "Complex H," is crashing through the outermost parts of the Milky Way from an inclined, retrograde orbit. Lockman's findings will be published in the July 1 issue of the Astrophysical Journal, Letters. "Many astronomers assumed that Complex H was probably a distant neighbor of the Milky Way with some unusual velocity that defied explanation," said Lockman. "Since its motion appeared completely unrelated to Galactic rotation, astronomers simply lumped it in with other high velocity clouds that had strange and unpredictable trajectories." High velocity clouds are essentially what their name implies, fast-moving clouds of predominately neutral atomic hydrogen. They are often found at great distances from the disk of the Milky Way, and may be left over material from the formation of our Galaxy and other galaxies in our Local Group. Over time, these objects can become incorporated into larger galaxies, just as small asteroids left over from the formation of the solar system sometimes collide with the Earth. Earlier studies of Complex H were hindered because the cloud currently is passing almost exactly behind the outer disk of

  9. IVT-seq reveals extreme bias in RNA sequencing

    OpenAIRE

    Kavaklı, Halil; Lahens, Nicholas F.; Zhang, Ray; Hayer, Katharina; Black, Michael B.; Dueck, Hannah; Pizarro, Angel; Kim, Junhyong; Irizarry, Rafael; Thomas, Russell S.; Grant, Gregory R.; Hogenesch, John B.

    2014-01-01

    RESEARCH Open Access IVT-seq reveals extreme bias in RNA sequencing Nicholas F Lahens1, Ibrahim Halil Kavakli2,3, Ray Zhang1, Katharina Hayer4, Michael B Black5, Hannah Dueck6, Angel Pizarro7, Junhyong Kim6, Rafael Irizarry8, Russell S Thomas5, Gregory R Grant4,9 and John B Hogenesch1* Abstract Background: RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the prol...

  10. Planck revealed bulk motion of Centaurus A lobes

    CERN Document Server

    De Paolis, F; Nucita, A A; Ingrosso, G; Kashin, A L; Khachatryan, H G; Mirzoyan, S; Yegorian, G; Jetzer, Ph; Qadir, A; Vetrugno, D

    2015-01-01

    Planck data towards the active galaxy Centaurus A are analyzed in the 70, 100 and 143 GHz bands. We find a temperature asymmetry of the northern radio lobe with respect to the southern one that clearly extends at least up to 5 degrees from the Cen A center and diminishes towards the outer regions of the lobes. That transparent parameter - the temperature asymmetry - thus has to carry a principal information, i.e. indication on the line-of-sight bulk motion of the lobes, while the increase of that asymmetry at smaller radii reveals the differential dynamics of the lobes as expected at ejections from the center.

  11. Revealing and Characterizing Dark Excitons Through Coherent Multidimensional Spectroscopy

    CERN Document Server

    Tollerud, Jonathan O; Davis, Jeffrey A

    2016-01-01

    Dark excitons are of fundamental importance in a broad range of contexts, but are difficult to study using conventional optical spectroscopy due to their weak interaction with light. We show how coherent multidimensional spectroscopy can reveal and characterize dark states. Using this approach, we identify different types of dark excitons in InGaAs/GaAs quantum wells and determine details regarding lifetimes, homogeneous and inhomogeneous linewidths, broadening mechanisms and coupling strengths. The observations of coherent coupling between bright and dark excitons hint at a role for a multi-step process by which excitons in the barrier can relax into the quantum wells.

  12. How the ``Blues'' reveals the intimacy of music and physics

    Science.gov (United States)

    Gibson, J. Murray

    2013-03-01

    Little do most people know when they hear blues piano - and you'll hear some live in this talk - that physics permeates the style, as it does all of music. Why should you care? By deconstructing blues piano the intimacy of physics, mathematics and music will be revealed in its glory.[1] The exercise says something about how the brains of the music composer and of the listener must be intimately linked to the physical principles of acoustics. And it provides a great vehicle to explain physical phenomena to non-scientists - everything from quantum mechanics to protein structure.

  13. Recombination patterns reveal information about centromere location on linkage maps

    DEFF Research Database (Denmark)

    Limborg, Morten T.; McKinney, Garrett J.; Seeb, Lisa W.;

    2016-01-01

    , approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half....... mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  14. Data mining of VDJ genes reveals interesting clues.

    Science.gov (United States)

    Joshi, Rajani R; Gupta, Vinay K

    2006-01-01

    Hypervariability of the complementary determining regions in characteristic structure of Immunoglobulins and the distinct, cell-specific expressions of the genes coding for this important class of proteins pose intriguing problems in experimental and computational/informatics research requiring a special approach different from those for the other proteins. We present here an Average Linkage Hierarchical Clustering of the Homosapien VDJ genes and the Immunoglobulin polypeptides generated by them using special kind of data structures and correlation matrices in place of the microarray data. The results reveal interesting clues on the heterogeneity of exon - intron locations in these gene-families and its possible role in hypervariability of the Immunoglobulins. PMID:16842114

  15. Linear stability analysis reveals exclusion zone for sliding bed transport

    Directory of Open Access Journals (Sweden)

    Talmon Arnold M.

    2015-06-01

    Full Text Available A bend or any another pipe component disturbs solids transport in pipes. Longitudinal pressure profiles downstream of such a component may show a stationary transient harmonic wave, as revealed by a recent settling slurry laboratory experiment. Therefore the fundamental transient response of the two-layer model for fully stratified flow is investigated as a first approach. A linear stability analysis of the sliding bed configuration is conducted. No stationary transient harmonic waves are found in this analysis, but adaptation lengths for exponential recovery are quantified. An example calculation is given for a 0.1 m diameter pipeline.

  16. Indentation Tests Reveal Geometry-Regulated Stiffening of Nanotube Junctions.

    Science.gov (United States)

    Ozden, Sehmus; Yang, Yang; Tiwary, Chandra Sekhar; Bhowmick, Sanjit; Asif, Syed; Penev, Evgeni S; Yakobson, Boris I; Ajayan, Pulickel M

    2016-01-13

    Here we report a unique method to locally determine the mechanical response of individual covalent junctions between carbon nanotubes (CNTs), in various configurations such as "X", "Y", and "Λ"-like. The setup is based on in situ indentation using a picoindenter integrated within a scanning electron microscope. This allows for precise mapping between junction geometry and mechanical behavior and uncovers geometry-regulated junction stiffening. Molecular dynamics simulations reveal that the dominant contribution to the nanoindentation response is due to the CNT walls stretching at the junction. Targeted synthesis of desired junction geometries can therefore provide a "structural alphabet" for construction of macroscopic CNT networks with tunable mechanical response. PMID:26618517

  17. Windows PowerShell desired state configuration revealed

    CERN Document Server

    Chaganti, Ravikanth

    2014-01-01

    Desired State Configuration (DSC) is a powerful new configuration management platform that makes it easier than ever to perform cross-platform configuration management of your infrastructure, whether on-premise or in the cloud. DSC provides the management platform and Application Programming Interface (API) that can be used with any programming language. Windows PowerShell Desired State Configuration Revealed will take you through this new technology from start to finish and demonstrates the DSC interfaces through Windows PowerShell. DSC allows you to manage target devices by simply declarin

  18. Revealing the Energetics and Structure of AGN Jets

    CERN Document Server

    Perlman, E S; Biretta, J A; Perlman, Eric S.; Marshall, Herman L.; Biretta, John A.

    2001-01-01

    Until very recently, few constraints existed on the physics of jets, even though they represent the first known evidence of mass outflow in AGN. This has begun to change with HST and Chandra observations, which allow us to observe short-lived, dynamic features, and compare their spectra and morphology to those of longer-lived particles seen in the radio. We examine HST and Chandra observations of M87 and 3C273 which reveal that these two prototype objects seem radically different.

  19. "Euclidean Revealed Preferences: Testing the Spatial Voting Model"

    OpenAIRE

    Marc Henry; Ismael Mourifie

    2011-01-01

    In the spatial model of voting, voters choose the candidate closest to them in the ideological space. Recent work by (Degan and Merlo 2009) shows that it is falsifiable on the basis of individual voting data in multiple elections. We show how to tackle the fact that the model only partially identifies the distribution of voting profiles and we give a formal revealed preference test of the spatial voting model in 3 national elections in the US, and strongly reject the spatial model in all case...

  20. Malar Bone Metastasis Revealing a Papillary Thyroid Carcinoma

    Directory of Open Access Journals (Sweden)

    Ihsen Slim

    2012-01-01

    Full Text Available Papillary thyroid carcinoma is the most common form of differentiated thyroid carcinoma. It is generally confined to the neck with or without spread to regional lymph nodes. Metastatic thyroid carcinomas are uncommon and mainly include lung and bone. Metastases involving oral and maxillofacial region are extremely rare. We described a case of malar metastasis revealing a follicular variant of papillary thyroid carcinoma, presenting with pain and swelling of the left cheek in a 67-years-old female patient with an unspecified histological left lobo-isthmectomy medical history. To our knowledge, this is the first recorded instance of a malar metastasis from a follicular variant of papillary thyroid carcinoma.

  1. Cryptic diversity of African tigerfish (genus Hydrocynus reveals palaeogeographic signatures of linked neogene geotectonic events.

    Directory of Open Access Journals (Sweden)

    Sarah A M Goodier

    Full Text Available The geobiotic history of landscapes can exhibit controls by tectonics over biotic evolution. This causal relationship positions ecologically specialized species as biotic indicators to decipher details of landscape evolution. Phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, including fishes, can reveal key events of drainage evolution, notably where geochronological resolution is insufficient. Where geochronological resolution is insufficient, phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, notably fishes, can reveal key events of drainage evolution. This study evaluates paleo-environmental causes of mitochondrial DNA (mtDNA based phylogeographic records of tigerfishes, genus Hydrocynus, in order to reconstruct their evolutionary history in relation to landscape evolution across Africa. Strong geographical structuring in a cytochrome b (cyt-b gene phylogeny confirms the established morphological diversity of Hydrocynus and reveals the existence of five previously unknown lineages, with Hydrocynus tanzaniae sister to a clade comprising three previously unknown lineages (Groups B, C and D and H. vittatus. The dated phylogeny constrains the principal cladogenic events that have structured Hydrocynus diversity from the late Miocene to the Plio-Pleistocene (ca. 0-16 Ma. Phylogeographic tests reveal that the diversity and distribution of Hydrocynus reflects a complex history of vicariance and dispersals, whereby range expansions in particular species testify to changes to drainage basins. Principal divergence events in Hydrocynus have interfaced closely with evolving drainage systems across tropical Africa. Tigerfish evolution is attributed to dominant control by pulses of geotectonism across the African plate. Phylogenetic relationships and divergence estimates among the ten mtDNA lineages illustrates where and when local

  2. Cryptic diversity of African tigerfish (genus Hydrocynus) reveals palaeogeographic signatures of linked neogene geotectonic events.

    Science.gov (United States)

    Goodier, Sarah A M; Cotterill, Fenton P D; O'Ryan, Colleen; Skelton, Paul H; de Wit, Maarten J

    2011-01-01

    The geobiotic history of landscapes can exhibit controls by tectonics over biotic evolution. This causal relationship positions ecologically specialized species as biotic indicators to decipher details of landscape evolution. Phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, including fishes, can reveal key events of drainage evolution, notably where geochronological resolution is insufficient. Where geochronological resolution is insufficient, phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, notably fishes, can reveal key events of drainage evolution. This study evaluates paleo-environmental causes of mitochondrial DNA (mtDNA) based phylogeographic records of tigerfishes, genus Hydrocynus, in order to reconstruct their evolutionary history in relation to landscape evolution across Africa. Strong geographical structuring in a cytochrome b (cyt-b) gene phylogeny confirms the established morphological diversity of Hydrocynus and reveals the existence of five previously unknown lineages, with Hydrocynus tanzaniae sister to a clade comprising three previously unknown lineages (Groups B, C and D) and H. vittatus. The dated phylogeny constrains the principal cladogenic events that have structured Hydrocynus diversity from the late Miocene to the Plio-Pleistocene (ca. 0-16 Ma). Phylogeographic tests reveal that the diversity and distribution of Hydrocynus reflects a complex history of vicariance and dispersals, whereby range expansions in particular species testify to changes to drainage basins. Principal divergence events in Hydrocynus have interfaced closely with evolving drainage systems across tropical Africa. Tigerfish evolution is attributed to dominant control by pulses of geotectonism across the African plate. Phylogenetic relationships and divergence estimates among the ten mtDNA lineages illustrates where and when local tectonic events

  3. Forming different planetary systems

    Institute of Scientific and Technical Information of China (English)

    Ji-Lin Zhou; Ji-Wei Xie; Hui-Gen Liu; Hui Zhang; Yi-Sui Sun

    2012-01-01

    With the increasing number of detected exoplanet samples,the statistical properties of planetary systems have become much clearer.In this review,we summarize the major statistical results that have been revealed mainly by radial velocity and transiting observations,and try to interpret them within the scope of the classical core-accretion scenario of planet formation,especially in the formation of different orbital architectures for planetary systems around main sequence stars.Based on the different possible formation routes for different planet systems,we tentatively classify them into three major catalogs:hot Jupiter systems,standard systems and distant giant planet systems.The standard systems can be further categorized into three sub-types under different circumstances:solar-like systems,hot Super-Earth systems,and subgiant planet systems.We also review the theory of planet detection and formation in binary systems as well as planets in star clusters.

  4. Revealing quantum correlation by negativity of the Wigner function

    Science.gov (United States)

    Taghiabadi, Razieh; Akhtarshenas, Seyed Javad; Sarbishaei, Mohsen

    2016-05-01

    We analyze two two-mode continuous variable separable states with the same marginal states. We adopt the definition of classicality in the form of well-defined positive Wigner function describing the state and find that although the states possess positive local Wigner functions, they exhibit negative Wigner functions for the global states. Using the negativity of Wigner function as an indicator of nonclassicality, we show that despite these states possess different negativities of the Wigner function, they do not reveal this difference as phase space nonclassicalities such as negativity of the Mandel Q parameter or quadrature squeezing. We then concentrate on quantum correlation of these states and show that quantum discord and local quantum uncertainty, as two well-defined measures of quantum correlation, manifest the difference between negativity of the Wigner functions. The non-Gaussianity of these states is also examined and show that the difference in behavior of their non-Gaussianity is the same as the difference between negativity of their Wigner functions. We also investigate the influence of correlation rank criterion and find that when the states can be produced locally from classical states, the Wigner functions cannot reveal their quantum correlations.

  5. Interviewing young adolescent suspects: When to reveal incriminating information?

    Directory of Open Access Journals (Sweden)

    Jamie Lingwood

    2013-07-01

    Full Text Available Recent research has demonstrated that the way in which interviewers reveal information/evidence tointerviewees/suspects can produce noticeable differences between truthful and deceptive verbalstatements. However, very little of this research has involved adolescents. In the present study, 12 to 14year old adolescents were asked to commit (n = 26 or not to commit (n = 26 a mock crime and atinterview to deny involvement in this crime. Prior to interview some information about each adolescent’sbehaviour was made available to the interviewer but this was not enough to enable determination ofwhether he or she had committed the crime. The interviewer revealed such information either at thebeginning of the interview (the ‘traditional method’, at the end of the interview (as pioneered by the ‘SUE’technique, or gradually. The interviews were analysed for interviewees’ ‘evidence omissions’ and‘statement-evidence contradictions’. As predicted, liars omitted more crime-related information/detailsand their statements were significantly more inconsistent with the information/evidence known to/disclosed by the interviewer. The timing of the interviewer’s evidence revelation had a significant effect onliars’ mentioning during their free recall of some of this information and on the total number of detailsmentioned in free recall.

  6. Aberrant activity in degenerated retinas revealed by electrical imaging

    Directory of Open Access Journals (Sweden)

    Günther eZeck

    2016-02-01

    Full Text Available In this review I present and discuss the current understanding of aberrant electrical activity found in the ganglion cell layer (GCL of rod-degenerated (rd mouse retinas. The reported electrophysiological properties revealed by electrical imaging using high-density microelectrode arrays can be subdivided between spiking activity originating from retinal ganglion cells (RGCs and local field potentials reflecting strong trans-membrane currents within the GCL. RGCs in rod-degenerated retinas show increased and rhythmic spiking compared to age-matched wild-type retinas. Fundamental spiking frequencies range from 5 to 15 Hz in various mouse models. The rhythmic RGC spiking is driven by a presynaptic network comprising AII amacrine and bipolar cells. In the healthy retina this rhythm-generating circuit is inhibited by photoreceptor input. A unique physiological feature of rd retinas is rhythmic local field potentials (LFP manifested as spatially-restricted low-frequency (5–15 Hz voltage changes. Their spatiotemporal characterization revealed propagation and correlation with RGC spiking. LFPs rely on gap-junctional coupling and are shaped by glycinergic and by GABAergic transmission. The aberrant RGC spiking and LFPs provide a simple readout of the functionality of the remaining retinal circuitry which can be used in the development of improved vision restoration strategies.

  7. Revealing evolved massive stars with Spitzer, WISE and SALT

    CERN Document Server

    Kniazev, A

    2016-01-01

    We present the results of optical spectroscopic observations of 54 candidate evolved massive stars revealed through the detection of mid-infrared nebulae of various shapes surrounding them with the {\\it Spitzer Space Telescope} and {\\it Wide-field Infrared Survey Explorer}. These observations, carried out with the Southern African Large Telescope (SALT) in 2010-2015, led to the discovery of about two dozens emission-line stars, of which 15 stars we classify as candidate luminous blue variables (cLBVs). Spectroscopic and photometric monitoring revealed significant changes in the spectra and brightness of four newly identified cLBVs, meaning that they are new members of the class of bona fide LBVs. We present an updated list of the Galactic bona fide LBVs. Currently, this list contains eighteen stars, of which more than 70 per cent are associated with circumstellar nebulae. We also discovered a very rare [WN] star - the central star of the planetary nebula Abell 48, and a WN3 star in a close, eccentric binary s...

  8. Blue whale earplug reveals lifetime contaminant exposure and hormone profiles.

    Science.gov (United States)

    Trumble, Stephen J; Robinson, Eleanor M; Berman-Kowalewski, Michelle; Potter, Charles W; Usenko, Sascha

    2013-10-15

    Lifetime contaminant and hormonal profiles have been reconstructed for an individual male blue whale (Balaenoptera musculus, Linnaeus 1758) using the earplug as a natural aging matrix that is also capable of archiving and preserving lipophilic compounds. These unprecedented lifetime profiles (i.e., birth to death) were reconstructed with a 6-mo resolution for a wide range of analytes including cortisol (stress hormone), testosterone (developmental hormone), organic contaminants (e.g., pesticides and flame retardants), and mercury. Cortisol lifetime profiles revealed a doubling of cortisol levels over baseline. Testosterone profiles suggest this male blue whale reached sexual maturity at approximately 10 y of age, which corresponds well with and improves on previous estimates. Early periods of the reconstructed contaminant profiles for pesticides (such as dichlorodiphenyltrichloroethanes and chlordanes), polychlorinated biphenyls, and polybrominated diphenyl ethers demonstrate significant maternal transfer occurred at 0-12 mo. The total lifetime organic contaminant burden measured between the earplug (sum of contaminants in laminae layers) and blubber samples from the same organism were similar. Total mercury profiles revealed reduced maternal transfer and two distinct pulse events compared with organic contaminants. The use of a whale earplug to reconstruct lifetime chemical profiles will allow for a more comprehensive examination of stress, development, and contaminant exposure, as well as improve the assessment of contaminant use/emission, environmental noise, ship traffic, and climate change on these important marine sentinels. PMID:24043814

  9. Revealing alteration of membrane structures during ischema using impedance spectroscopy

    Directory of Open Access Journals (Sweden)

    Mihaela Gheorghiu

    2002-11-01

    Full Text Available Alterations of membrane structure and function are essential characteristics of cells undergoing ischemia. Noninvasive monitoring of tissue alterations during ischemia and the estimation of the reversibility domain (corresponding to organ capability to fully recover its functions after shifting back to normal blood perfusion are important for biomedical applications allowing better time management during surgical interventions, especially in organ transplantation. Due to it’s capability to reveal inhomogeneities, as well as it’s noninvasive character, impedance spectroscopy was used for continuous monitoring of the progression of excised tissue samples during ischemia. We have developed a fast, noninvasive, automated method for quantitative analysis of impedance spectra of tissue samples, capable of revealing, through characteristic parameters (dispersion amplitudes, time constants and distribution parameters membrane based microscopic processes like the closure ofgap-junctions (a characteristic of the early alterations of ischemic tissues in the reversibility phase. Microscopic and equivalent circuit modeling was used to probe the effect of closure of cell connections and of changes in electrical properties of cell constituents on impedance spectra. We have developed a normalizing procedure emphasizing the pattern of ischemic alterations and enabling the comparison of different data sets.

  10. The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

    Directory of Open Access Journals (Sweden)

    Fernando Dini Andreote

    Full Text Available Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04 in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

  11. Functionalities of expressed messenger RNAs revealed from mutant phenotypes.

    Science.gov (United States)

    Liao, Ben-Yang; Weng, Meng-Pin

    2016-07-01

    Total messenger RNAs mRNAs that are produced from a given gene under a certain set of conditions include both functional and nonfunctional transcripts. The high prevalence of nonfunctional mRNAs that have been detected in cells has raised questions regarding the functional implications of mRNA expression patterns and divergences. Phenotypes that result from the mutagenesis of protein-coding genes have provided the most straightforward descriptions of gene functions, and such data obtained from model organisms have facilitated investigations of the functionalities of expressed mRNAs. Mutant phenotype data from mouse tissues have revealed various attributes of functional mRNAs, including tissue-specificity, strength of expression, and evolutionary conservation. In addition, the role that mRNA expression evolution plays in driving morphological evolution has been revealed from studies designed to exploit morphological and physiological phenotypes of mouse mutants. Investigations into yeast essential genes (defined by an absence of colony growth after gene deletion) have further described gene regulatory strategies that reduce protein expression noise by mediating the rates of transcription and translation. In addition to the functional significance of expressed mRNAs as described in the abovementioned findings, the functionalities of other type of RNAs (i.e., noncoding RNAs) remain to be characterized with systematic mutations and phenotyping of the DNA regions that encode these RNA molecules. WIREs RNA 2016, 7:416-427. doi: 10.1002/wrna.1329 For further resources related to this article, please visit the WIREs website. PMID:26748449

  12. Social Investment for Sustainability of Groundwater: A Revealed Preference Approach

    Directory of Open Access Journals (Sweden)

    Edna Tusak Loehman

    2014-08-01

    Full Text Available Groundwater is a form of natural capital that is valued for the goods it provides, including ecosystem health, water quality, and water consumption. Degradation of groundwater could be alleviated through social investment such as for water reuse and desalination to reduce the need for withdrawals from groundwater. This paper develops a participatory planning process—based on combining revealed preference with economic optimization—to choose a desired future for sustaining groundwater. Generation of potential groundwater futures is based on an optimal control model with investment and withdrawal from groundwater as control variables. In this model, groundwater stock and aquatic health are included as inter-temporal public goods. The social discount rate expressing time preference—an important parameter that drives optimization—is revealed through the participatory planning process. To implement the chosen future, a new method of inter-temporal pricing is presented to finance investment and supply costs. Furthermore, it is shown that the desired social outcome could be achieved by a form of privatization in which the pricing method, the appropriate discount rate, and the planning period are contractually specified.

  13. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics.

    Science.gov (United States)

    Shankaran, Mahalakshmi; King, Chelsea L; Angel, Thomas E; Holmes, William E; Li, Kelvin W; Colangelo, Marc; Price, John C; Turner, Scott M; Bell, Christopher; Hamilton, Karyn L; Miller, Benjamin F; Hellerstein, Marc K

    2016-01-01

    Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders. PMID:26657858

  14. Network Physiology reveals relations between network topology and physiological function

    CERN Document Server

    Bashan, Amir; Kantelhardt, Jan W; Havlin, Shlomo; Ivanov, Plamen Ch; 10.1038/ncomms1705

    2012-01-01

    The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and quantifying dynamical networks of diverse systems with different types of interactions is a challenge. Here, we develop a framework to probe interactions among diverse systems, and we identify a physiologic network. We find that each physiologic state is characterized by a specific network structure, demonstrating a robust interplay between network topology and function. Across physiologic states the network undergoes topological transitions associated with fast reorganization of physiologic interactions on time scales of a few minutes, indicating high network flexibility in response to perturbations. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.

  15. Nemesis Autonomous Test System

    Science.gov (United States)

    Barltrop, Kevin J.; Lee, Cin-Young; Horvath, Gregory A,; Clement, Bradley J.

    2012-01-01

    A generalized framework has been developed for systems validation that can be applied to both traditional and autonomous systems. The framework consists of an automated test case generation and execution system called Nemesis that rapidly and thoroughly identifies flaws or vulnerabilities within a system. By applying genetic optimization and goal-seeking algorithms on the test equipment side, a "war game" is conducted between a system and its complementary nemesis. The end result of the war games is a collection of scenarios that reveals any undesirable behaviors of the system under test. The software provides a reusable framework to evolve test scenarios using genetic algorithms using an operation model of the system under test. It can automatically generate and execute test cases that reveal flaws in behaviorally complex systems. Genetic algorithms focus the exploration of tests on the set of test cases that most effectively reveals the flaws and vulnerabilities of the system under test. It leverages advances in state- and model-based engineering, which are essential in defining the behavior of autonomous systems. It also uses goal networks to describe test scenarios.

  16. Genetic tracing reveals a stereotyped sensory map in the olfactory cortex

    Science.gov (United States)

    Zou, Zhihua; Horowitz, Lisa F.; Montmayeur, Jean-Pierre; Snapper, Scott; Buck, Linda B.

    2001-11-01

    The olfactory system translates myriad chemical structures into diverse odour perceptions. To gain insight into how this is accomplished, we prepared mice that coexpressed a transneuronal tracer with only one of about 1,000 different odorant receptors. The tracer travelled from nasal neurons expressing that receptor to the olfactory bulb and then to the olfactory cortex, allowing visualization of cortical neurons that receive input from a particular odorant receptor. These studies revealed a stereotyped sensory map in the olfactory cortex in which signals from a particular receptor are targeted to specific clusters of neurons. Inputs from different receptors overlap spatially and could be combined in single neurons, potentially allowing for an integration of the components of an odorant's combinatorial receptor code. Signals from the same receptor are targeted to multiple olfactory cortical areas, permitting the parallel, and perhaps differential, processing of inputs from a single receptor before delivery to the neocortex and limbic system.

  17. Marine spawning sites of perch Perca fluviatilis revealed by oviduct-inserted acoustic transmitters

    DEFF Research Database (Denmark)

    Skovrind, Mikkel; Christensen, Emil A.F.; Carl, Henrik;

    2013-01-01

    In the 1970s, a flood-protection system dramatically changed a large part of the coastal environment of Køge Bugt, a bay in the western Baltic Sea, from open coast to a brackish lagoon habitat. An anadromous stock of European perch Perca fluviatilis seems to have benefitted from this change, but...... details about their spawning behavior remain unknown. We used oviductinserted acoustic transmitters to reveal the pre-spawning behavior and spawning sites of this population. Thirteen female perch were caught in the lower stream basin of St. Vejle Å, and were tagged with acoustic transmitters inserted...... through the oviduct. The fish were tracked from March 2 to May 24, 2012 with both passive and active telemetry systems. The pre-spawning behavior involved short trips between the stream and adjacent lagoons. Twelve of the 13 transmitters (92%) were expulsed during spawning, providing for the first time a...

  18. Conditional gene deletion reveals functional redundancy of GABAB receptors in peripheral nociceptors in vivo

    Directory of Open Access Journals (Sweden)

    Bettler Bernhard

    2009-11-01

    Full Text Available Abstract Background γ-aminobutyric acid (GABA is an important inhibitory neurotransmitter which mainly mediates its effects on neurons via ionotropic (GABAA and metabotropic (GABAB receptors. GABAB receptors are widely expressed in the central and the peripheral nervous system. Although there is evidence for a key function of GABAB receptors in the modulation of pain, the relative contribution of peripherally- versus centrally-expressed GABAB receptors is unclear. Results In order to elucidate the functional relevance of GABAB receptors expressed in peripheral nociceptive neurons in pain modulation we generated and analyzed conditional mouse mutants lacking functional GABAB(1 subunit specifically in nociceptors, preserving expression in the spinal cord and brain (SNS-GABAB(1-/- mice. Lack of the GABAB(1 subunit precludes the assembly of functional GABAB receptor. We analyzed SNS-GABAB(1-/- mice and their control littermates in several models of acute and neuropathic pain. Electrophysiological studies on peripheral afferents revealed higher firing frequencies in SNS-GABAB(1-/- mice compared to corresponding control littermates. However no differences were seen in basal nociceptive sensitivity between these groups. The development of neuropathic and chronic inflammatory pain was similar across the two genotypes. The duration of nocifensive responses evoked by intraplantar formalin injection was prolonged in the SNS-GABAB(1-/- animals as compared to their control littermates. Pharmacological experiments revealed that systemic baclofen-induced inhibition of formalin-induced nociceptive behaviors was not dependent upon GABAB(1 expression in nociceptors. Conclusion This study addressed contribution of GABAB receptors expressed on primary afferent nociceptive fibers to the modulation of pain. We observed that neither the development of acute and chronic pain nor the analgesic effects of a systematically-delivered GABAB agonist was significantly

  19. 2-D Convection and Electrodynamic Features of Substorms Revealed by Multiple Radar Observations (Invited)

    Science.gov (United States)

    Zou, S.

    2010-12-01

    Substorms are one of the fundamental elements of geomagnetic activity, which involve complex magnetosphere-ionosphere coupling processes. In this work, we aim to better understand the evolution of high latitude ionospheric convection and the relevant current systems associated with substorms, with emphasis on these features near the nightside Harang reversal region. Three different types of radars, including the Super Dual Auroral Radar Network (SuperDARN) coherent-scatter radars, the new advanced modular incoherent-scatter radar at Poker Flat (PFISR), and the Sondrestrom ISR, have been utilized. Observations from these radars, together with those from complementary instruments, including satellites and other ground-based instruments, have enabled fundamental new understanding of the ionospheric electrodynamic properties associated with substorms. In this presentation, I focus on electrodynamics near the nightside Harang reversal region. Observations from the SuperDARN and the PFISR radars revealed that auroral activity at substorm onset is located near the center of the Harang reversal, which represents a key feature of magnetospheric and ionospheric convection and is part of the Region 2 system. The observations also show nightside convection flows exhibit repeatable, distinct variations at different locations relative to the substorm-related auroral activity. Taking advantage of the simultaneous flow and ionization measurements from PFISR, a current closure relation has been found between the Region 2 and the substorm field-aligned current systems. By synthesizing these observations, a 2-D comprehensive view of the nightside ionospheric electrodynamical features, including electrical equipotentials, flows and FACs, and their evolution associated with substorms has been constructed, which has revealed a strong coupling between the substorm and the Region 2 current systems. This study sheds new light on substorm-related magnetosphere-ionosphere coupling and

  20. Secret Weapon of "Flesh-Eating Bugs" Revealed

    Institute of Scientific and Technical Information of China (English)

    David Osumi-Sutherland; 秦小岑

    2004-01-01

    @@ Bacteria can use our own clot①-busting system to spread around the body,according to US researchers. They hope their findings will be used to design drugs or vaccines② to prevent certain types of infection becoming fatal.

  1. Comparative genomics reveals insights into avian genome evolution and adaptation

    DEFF Research Database (Denmark)

    Zhang, Guojie; Li, Cai; Li, Qiye;

    2014-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size......, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this...... pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits....

  2. The genome of Tetranychus urticae reveals herbivorous pest adaptations

    Science.gov (United States)

    Grbić, Miodrag; Van Leeuwen, Thomas; Clark, Richard M.; Rombauts, Stephane; Rouzé, Pierre; Grbić, Vojislava; Osborne, Edward J.; Dermauw, Wannes; Ngoc, Phuong Cao Thi; Ortego, Félix; Hernández-Crespo, Pedro; Diaz, Isabel; Martinez, Manuel; Navajas, Maria; Sucena, Élio; Magalhães, Sara; Nagy, Lisa; Pace, Ryan M.; Djuranović, Sergej; Smagghe, Guy; Iga, Masatoshi; Christiaens, Olivier; Veenstra, Jan A.; Ewer, John; Villalobos, Rodrigo Mancilla; Hutter, Jeffrey L.; Hudson, Stephen D.; Velez, Marisela; Yi, Soojin V.; Zeng, Jia; Pires-daSilva, Andre; Roch, Fernando; Cazaux, Marc; Navarro, Marie; Zhurov, Vladimir; Acevedo, Gustavo; Bjelica, Anica; Fawcett, Jeffrey A.; Bonnet, Eric; Martens, Cindy; Baele, Guy; Wissler, Lothar; Sanchez-Rodriguez, Aminael; Tirry, Luc; Blais, Catherine; Demeestere, Kristof; Henz, Stefan R.; Gregory, T. Ryan; Mathieu, Johannes; Verdon, Lou; Farinelli, Laurent; Schmutz, Jeremy; Lindquist, Erika; Feyereisen, René; Van de Peer, Yves

    2016-01-01

    The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant–herbivore interactions, and provides unique opportunities for developing novel plant protection strategies. PMID:22113690

  3. Gastrin release: Antrum microdialysis reveals a complex neural control

    DEFF Research Database (Denmark)

    Ericsson, P; Håkanson, R; Rehfeld, Jens F.;

    2010-01-01

    vagus has not only a prompt stimulatory but also a slow inhibitory effect on gastrin release. 2) Although vagal denervation did not affect the gastrin response to anacidity, the TTX experiments revealed that both food-evoked and anacidity-evoked gastrin release depends on neural input.......We used microdialysis to monitor local gastrin release in response to food, acid blockade and acute vagal excitation. For the first time, gastrin release has been monitored continuously in intact conscious rats in a physiologically relevant experimental setting in a fashion that minimizes...... serum regardless of the prandial state. The rats were conscious during microdialysis except when subjected to electrical vagal stimulation. Acid blockade (omeprazole treatment of freely fed rats for 4 days), or bilateral sectioning of the abdominal vagal trunks (fasted, 3 days post-op.), raised the...

  4. Deciphering CAPTCHAs: what a Turing test reveals about human cognition.

    Directory of Open Access Journals (Sweden)

    Thomas Hannagan

    Full Text Available Turning Turing's logic on its head, we used widespread letter-based Turing Tests found on the internet (CAPTCHAs to shed light on human cognition. We examined the basis of the human ability to solve CAPTCHAs, where machines fail. We asked whether this is due to our use of slow-acting inferential processes that would not be available to machines, or whether fast-acting automatic orthographic processing in humans has superior robustness to shape variations. A masked priming lexical decision experiment revealed efficient processing of CAPTCHA words in conditions that rule out the use of slow inferential processing. This shows that the human superiority in solving CAPTCHAs builds on a high degree of invariance to location and continuous transforms, which is achieved during the very early stages of visual word recognition in skilled readers.

  5. Mitochondrial specialization revealed by single muscle fiber proteomics

    DEFF Research Database (Denmark)

    Schiaffino, S; Reggiani, C; Kostrominova, T Y;

    2015-01-01

    to buffering the H2 O2 produced by the respiratory chain. Nicotinamide nucleotide transhydrogenase (NNT), the other major mito-chondrial enzyme involved in NADPH generation, is also more abundant in type 1 fibers. We suggest that the continuously active type 1 fibers are endowed with a more efficient......We have developed a highly sensitive mass spectrometry-based proteomic workflow to examine the proteome of single muscle fibers. This study revealed significant differences in the mitochondrial proteome of the four major fiber types present in mouse skeletal muscle. Here, we focus on Krebs cycle...... enzymes and in particular on the differential distribution of the two mitochondrial isocitrate dehydrogenases, IDH2 and IDH3. Type 1/slow fibers contain high levels of IDH2 and relatively low levels of IDH3, whereas fast 2X and 2B fibers show an opposite expression pattern. The findings suggest that in...

  6. Thermodynamic R-diagrams reveal solid-like fluid states

    International Nuclear Information System (INIS)

    We evaluate the thermodynamic curvature R for fluid argon, hydrogen, carbon dioxide, and water. For these fluids, R is mostly negative, but we also find significant regimes of positive R, which we interpret as indicating solid-like fluid properties. Regimes of positive R are present in all four fluids at very high pressure. Water has, in addition, a narrow slab of positive R in the stable liquid phase near its triple point. Also, water is the only fluid we found having R decrease on cooling into the metastable liquid phase, consistent with a possible second critical point. - Highlights: • Thermodynamic curvature is evaluated for argon, hydrogen, carbon dioxide, and water. • Thermodynamic curvature reveals solid-like states in liquids, including water. • Thermodynamic curvature is a thermodynamic measure of interactions

  7. Early allelic selection in maize as revealed by ancient DNA.

    Science.gov (United States)

    Jaenicke-Després, Viviane; Buckler, Ed S; Smith, Bruce D; Gilbert, M Thomas P; Cooper, Alan; Doebley, John; Pääbo, Svante

    2003-11-14

    Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete. PMID:14615538

  8. Ternary structure reveals mechanism of a membrane diacylglycerol kinase

    Science.gov (United States)

    Li, Dianfan; Stansfeld, Phillip J.; Sansom, Mark S. P.; Keogh, Aaron; Vogeley, Lutz; Howe, Nicole; Lyons, Joseph A.; Aragao, David; Fromme, Petra; Fromme, Raimund; Basu, Shibom; Grotjohann, Ingo; Kupitz, Christopher; Rendek, Kimberley; Weierstall, Uwe; Zatsepin, Nadia A.; Cherezov, Vadim; Liu, Wei; Bandaru, Sateesh; English, Niall J.; Gati, Cornelius; Barty, Anton; Yefanov, Oleksandr; Chapman, Henry N.; Diederichs, Kay; Messerschmidt, Marc; Boutet, Sébastien; Williams, Garth J.; Marvin Seibert, M.; Caffrey, Martin

    2015-12-01

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.

  9. Metabolomics reveals metabolic biomarkers of Crohn's disease

    Energy Technology Data Exchange (ETDEWEB)

    Jansson, J.K.; Willing, B.; Lucio, M.; Fekete, A.; Dicksved, J.; Halfvarson, J.; Tysk, C.; Schmitt-Kopplin, P.

    2009-06-01

    The causes and etiology of Crohn's disease (CD) are currently unknown although both host genetics and environmental factors play a role. Here we used non-targeted metabolic profiling to determine the contribution of metabolites produced by the gut microbiota towards disease status of the host. Ion Cyclotron Resonance Fourier Transform Mass Spectrometry (ICR-FT/MS) was used to discern the masses of thousands of metabolites in fecal samples collected from 17 identical twin pairs, including healthy individuals and those with CD. Pathways with differentiating metabolites included those involved in the metabolism and or synthesis of amino acids, fatty acids, bile acids and arachidonic acid. Several metabolites were positively or negatively correlated to the disease phenotype and to specific microbes previously characterized in the same samples. Our data reveal novel differentiating metabolites for CD that may provide diagnostic biomarkers and/or monitoring tools as well as insight into potential targets for disease therapy and prevention.

  10. Revealed Comparative Advantage and Competitiveness in Chinese Agricultural Sectors

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    This paper examined the competitiveness of Chinese agricultural products, in relation to the rest of the world, based on the index of revealed comparative advantage, using lots of data during period of 1980 to 2000. The index is useful in identifying the demarcation between comparative advantage and comparative disadvantage, though a problem exits when using it. China is shown to have a comparative advantage in a range of agricultural products, including edible vegetables and tea. This complements the findings of those studies that have used price and cost based on approaches in identifying competitiveness in agricultural products. Results indicated that the RCA values had been weakening over the 21-year period. These have vastly different implication for the future reform in China's agriculture.

  11. Experience and Interpretation: Emotion as Revealed in Narration

    Directory of Open Access Journals (Sweden)

    Annikki Kaivola-Bregenhøj

    2008-12-01

    Full Text Available I discuss in this article some key narratives of women I interviewed in Ingria 1992–1993. The narratives of those women were about dramatic stages of their lives during the World War II. The main themes of the life stories were forced transfers and deportation suffered by the Ingrian Finns. I examine with some examples how various paralinguistic devices, such as speech tempo, emotional outbursts or silence, were tied in with the verbalisation of experiences. The three factors I discuss here are woven into the narratives of the women I interviewed. The first factor is “impassioned narrating”, which shows how a narrator reveals how she is reliving the event, she told about. The second factor is weeping and we may ask how the tears affect the narrator. The third factor is silence and reticence. In retrospect I have thought about the therapeutic effect of speaking, forgetting and remaining silent.

  12. Transcriptomic variation in a coral reveals pathways of clonal organisation

    DEFF Research Database (Denmark)

    K Bay, Line; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard;

    2009-01-01

    A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base......) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with...... perimeter of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or...

  13. Physical Principles of Skeletal Minerals Revealed with Spectromicroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Pupa [U of Wisconsin-Madison

    2009-08-05

    Skeletal elements of marine and terrestrial organisms have the most fascinating nano-to-macro-structures, attracting the attention of physicists, biologists, chemists, and materials scientists. Using X-PEEM spectromicroscopy we revealed some of the fundamental mechanisms leading to the formation of these biominerals. Specifically, we addressed the following questions and provided the answers: 1Q) How do teeth, bones, and echinoderm and mollusk shells acquire their unusual, curved and complex morphology, if they are composed of single crystals? 1A) Via amorphous precursor phases; 2Q) How does crystallinity propagate through the amorophous precursor phases in sea urchin spicules and teeth? 2A) By secondary nucleation, following random walk patterns; 3Q) How does iridescent mother-of-pearl become ordered? 3A) Gradually, through a kinetic mechanisms in which fastest growing single-crystals win the competition for space, thus end up being approximately co-oriented.

  14. Structural characterization of human heparanase reveals insights into substrate recognition.

    Science.gov (United States)

    Wu, Liang; Viola, Cristina M; Brzozowski, Andrzej M; Davies, Gideon J

    2015-12-01

    Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis. Here we present crystal structures of human HPSE at 1.6-Å to 1.9-Å resolution that reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. We used oligosaccharide complexes to map the substrate-binding and sulfate-recognition motifs. These data shed light on the structure and interactions of a key enzyme involved in ECM maintenance and provide a starting point for the design of HPSE inhibitors for use as biochemical tools and anticancer therapeutics. PMID:26575439

  15. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

    Science.gov (United States)

    Mieczkowski, Jakub; Cook, April; Bowman, Sarah K; Mueller, Britta; Alver, Burak H; Kundu, Sharmistha; Deaton, Aimee M; Urban, Jennifer A; Larschan, Erica; Park, Peter J; Kingston, Robert E; Tolstorukov, Michael Y

    2016-01-01

    Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation. PMID:27151365

  16. Internal structure of sponge glass fiber revealed by ptychographic nanotomography.

    Science.gov (United States)

    Birkbak, Mie E; Guizar-Sicairos, Manuel; Holler, Mirko; Birkedal, Henrik

    2016-04-01

    Sponge glass spicules have solicited great interest due to their mechanical and optical properties. Herein we use ptychographic nanotomography to obtain detailed insights into the internal structure of an anchor spicule from the Venus flower basket. The obtained dataset has 90nm resolution in 3D and provides quantitative determination of the electron density. The data reveal significant variations in electron density across the spicule. The central organic filament is found to be slightly but significantly displaced from the spicule central axis. Analysis of the electron density affords an estimate of a protein volume fraction in the organic filament of about 70%. In the highly mineralized part of the spicule, the electron density is seen to display circular symmetry and be neigh independent of position along the spicule long axis. Variations in the electron density beyond those included in current models of spicule mechanics are observed. PMID:26853498

  17. Heat islands over Mumbai as revealed by autorecorded thermograph data

    Indian Academy of Sciences (India)

    A K Srivastava; James Voogt; S R Kshirsagar; Kavita Srivastava

    2016-02-01

    This study examined hourly temperature data of two locations of Mumbai metropolitan city. One data point (Coloba, Mumbai) is in centre of the city and the other one (Santacruz, Mumbai) is at the airport. The study finds that there were many occasions when night-time hourly temperatures over the city centre were considerably higher than that of the airport, even though temperature at the time of sunset at both the places was nearly same. In this study, the occasions, when hourly night-time temperature over city was more than that of the airport by objectively defined threshold value (3.0°C in this study) for most of the hours in the night, were termed as heat island events. Analysis of the study reveals that these events are mostly confined to November–February months. The study also found that frequency of such events has doubled in recent two decades in comparison to the earlier two decades.

  18. Silicon-wafer-surface damage revealed by surface photovoltage measurements

    International Nuclear Information System (INIS)

    Anomalous results of surface photovoltage (SPV) measurements on Si wafers are shown to be associated with a damaged region beneath the illuminated surface of the wafer being measured. The anomaly is a concave-upward curvature of the I0(α-1) plot with an r2 value, derived from linear regression analysis, less than the normally observed minimum value (approx.0.98). Removal of the damaged region by an appropriate etching procedure allows subsequent SPV measurements whose results are substantially free of the previously observed anomaly. The qualitative character of the anomaly can be reproduced by a simple theoretical model in which only one effect of the damage is considered; this effect is a diminished quantum efficiency for hole-electron pair generation by photon absorption in the damaged region. The results suggest the use of SPV measurements as a test procedure for revealing the presence of surface damage in Si wafers

  19. Silicon-wafer-surface damage revealed by surface photovoltage measurements

    Science.gov (United States)

    Goodman, Alvin M.

    1982-11-01

    Anomalous results of surface photovoltage (SPV) measurements on Si wafers are shown to be associated with a damaged region beneath the illuminated surface of the wafer being measured. The anomaly is a concave-upward curvature of the I0(α-1) plot with an r2 value, derived from linear regression analysis, less than the normally observed minimum value (˜0.98). Removal of the damaged region by an appropriate etching procedure allows subsequent SPV measurements whose results are substantially free of the previously observed anomaly. The qualitative character of the anomaly can be reproduced by a simple theoretical model in which only one effect of the damage is considered; this effect is a diminished quantum efficiency for hole-electron pair generation by photon absorption in the damaged region. The results suggest the use of SPV measurements as a test procedure for revealing the presence of surface damage in Si wafers.

  20. Conformational changes in DNA gyrase revealed by limited proteolysis

    DEFF Research Database (Denmark)

    Kampranis, S C; Maxwell, A

    1998-01-01

    We have used limited proteolysis to identify conformational changes in DNA gyrase. Gyrase exhibits a proteolytic fingerprint dominated by two fragments, one of approximately 62 kDa, deriving from the A protein, and another of approximately 25 kDa from the B protein. Quinolone binding to the enzyme......-DNA complex induces a conformational change which is reflected in the protection of the C-terminal 47-kDa domain of the B protein. An active site mutant (Tyr122 to Ser in the A protein) that binds quinolones but cannot cleave DNA still gives the quinolone proteolytic pattern, while stabilization of a cleaved......-DNA intermediate by calcium ions does not reveal any protection, suggesting that the quinolone-induced conformational change is different from an "open-gate" state of the enzyme. A quinolone-resistant mutant of gyrase fails to give the characteristic quinolone-associated proteolytic signature. The ATP...

  1. Revealing the structure of the world airline network

    CERN Document Server

    Verma, Trivik; Herrmann, Hans J

    2014-01-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their ...

  2. Computed tomography angiography reveals the crime instrument - case report

    International Nuclear Information System (INIS)

    Background: The development of multislice CT technology enabled imaging of post-traumatic brain lesions with isotropic resolution, which led to unexpected results in the presented case Case Report: An unconscious, 49-year-old male with a suspected trauma underwent a routine CT examination of the head, which revealed an unusual intracerebral bleeding and therefore was followed by CT angiography (CTA). The thorough analysis of CTA source scans led to the detection of the bleeding cause. Conclusions: The presented case showed that a careful analysis of a CT scan allows not only to define the extent of pathological lesions in the intracranial space but it also helps to detect the crime instrument, which is of medico-legal significance. (authors)

  3. Inheritance Patterns in Citation Networks Reveal Scientific Memes

    Science.gov (United States)

    Kuhn, Tobias; Perc, Matjaž; Helbing, Dirk

    2014-10-01

    Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

  4. Demand Model Combining Stated And Revealed Preference Data

    Directory of Open Access Journals (Sweden)

    Luciana Londero Brandli

    2007-10-01

    Full Text Available The revealed and stated preference methods have been contributing a lot for the development of the econometric literature in the attempt of determining the variables that influence the individual decision in a choice process. This article combines preference data, with the objective of obtaining the advantages of the complementarity of the forces and frankness of both types of data. The approach involves the estimate of a model only with RP data, only with SP data and combining RP and SP data. The application is in the housing market, where it is observed, through the literature, that most of the papers of the consumer's choice has restricted the only one approaches. The utility functions obtained show the relative importance of the attributes, the tendency of behavior through the signs and its significance statistical. The results analysis of the models indicates differences and similarities about the attribute’s behavior.

  5. Early MAVEN Deep Dip campaign reveals thermosphere and ionosphere variability.

    Science.gov (United States)

    Bougher, S; Jakosky, B; Halekas, J; Grebowsky, J; Luhmann, J; Mahaffy, P; Connerney, J; Eparvier, F; Ergun, R; Larson, D; McFadden, J; Mitchell, D; Schneider, N; Zurek, R; Mazelle, C; Andersson, L; Andrews, D; Baird, D; Baker, D N; Bell, J M; Benna, M; Brain, D; Chaffin, M; Chamberlin, P; Chaufray, J-Y; Clarke, J; Collinson, G; Combi, M; Crary, F; Cravens, T; Crismani, M; Curry, S; Curtis, D; Deighan, J; Delory, G; Dewey, R; DiBraccio, G; Dong, C; Dong, Y; Dunn, P; Elrod, M; England, S; Eriksson, A; Espley, J; Evans, S; Fang, X; Fillingim, M; Fortier, K; Fowler, C M; Fox, J; Gröller, H; Guzewich, S; Hara, T; Harada, Y; Holsclaw, G; Jain, S K; Jolitz, R; Leblanc, F; Lee, C O; Lee, Y; Lefevre, F; Lillis, R; Livi, R; Lo, D; Ma, Y; Mayyasi, M; McClintock, W; McEnulty, T; Modolo, R; Montmessin, F; Morooka, M; Nagy, A; Olsen, K; Peterson, W; Rahmati, A; Ruhunusiri, S; Russell, C T; Sakai, S; Sauvaud, J-A; Seki, K; Steckiewicz, M; Stevens, M; Stewart, A I F; Stiepen, A; Stone, S; Tenishev, V; Thiemann, E; Tolson, R; Toublanc, D; Vogt, M; Weber, T; Withers, P; Woods, T; Yelle, R

    2015-11-01

    The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability. PMID:26542579

  6. Divergence of multimodular polyketide synthases revealed by a didomain structure.

    Science.gov (United States)

    Zheng, Jianting; Gay, Darren C; Demeler, Borries; White, Mark A; Keatinge-Clay, Adrian T

    2012-07-01

    The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues. PMID:22634636

  7. Hybridization Reveals the Evolving Genomic Architecture of Speciation

    Directory of Open Access Journals (Sweden)

    Marcus R. Kronforst

    2013-11-01

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

  8. [Hodgkin disease revealed by a nephrotic syndrome: A case report].

    Science.gov (United States)

    Cheptou, M; Pichault, V; Campagni, R; Vodoff, M-V; Fischbach, M; Paillard, C

    2015-12-01

    Pediatric nephrotic syndrome (NS) is most often idiopathic or primary but in rare cases, it can be secondary to neoplasia. We report on a case of steroid-resistant NS revealing as a paraneoplastic syndrome of Hodgkin disease (HD) in a 12-year-old boy. The onset of the NS can be earlier, later, or simultaneous to the HD. Treatment of the lymphoma allows the disappearance of the NS. In the case we observed, the diagnosis of HD was delayed because HD presented with an isolated, hilar adenopathy in the absence of retroperitoneal or peripheral locations. In children aged 10 years or more presenting with NS, steroid-resistant or otherwise, a possible paraneoplastic origin such as Hodgkin lymphoma should always be taken into consideration and eventually eliminated. PMID:26598043

  9. Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

    Directory of Open Access Journals (Sweden)

    Penelope K Lindeque

    Full Text Available BACKGROUND: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. METHODOLOGY/PRINCIPLE FINDINGS: Plankton net hauls (200 µm were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. CONCLUSIONS: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may

  10. A Network Based Methodology to Reveal Patterns in Knowledge Transfer

    Directory of Open Access Journals (Sweden)

    Orlando López-Cruz

    2015-12-01

    Full Text Available This paper motivates, presents and demonstrates in use a methodology based in complex network analysis to support research aimed at identification of sources in the process of knowledge transfer at the interorganizational level. The importance of this methodology is that it states a unified model to reveal knowledge sharing patterns and to compare results from multiple researches on data from different periods of time and different sectors of the economy. This methodology does not address the underlying statistical processes. To do this, national statistics departments (NSD provide documents and tools at their websites. But this proposal provides a guide to model information inferences gathered from data processing revealing links between sources and recipients of knowledge being transferred and that the recipient detects as main source to new knowledge creation. Some national statistics departments set as objective for these surveys the characterization of innovation dynamics in firms and to analyze the use of public support instruments. From this characterization scholars conduct different researches. Measures of dimensions of the network composed by manufacturing firms and other organizations conform the base to inquiry the structure that emerges from taking ideas from other organizations to incept innovations. These two sets of data are actors of a two- mode-network. The link between two actors (network nodes, one acting as the source of the idea. The second one acting as the destination comes from organizations or events organized by organizations that “provide” ideas to other group of firms. The resulting demonstrated design satisfies the objective of being a methodological model to identify sources in knowledge transfer of knowledge effectively used in innovation.

  11. Eye movement monitoring reveals differential influences of emotion on memory

    Directory of Open Access Journals (Sweden)

    Lily Riggs

    2010-11-01

    Full Text Available Research shows that memory for emotional aspects of an event may be enhanced at the cost of impaired memory for surrounding peripheral details. However, this has only been assessed directly via verbal reports which reveal the outcome of a long stream of processing but cannot shed light on how/when emotion may affect the retrieval process. In the present experiment, eye movement monitoring was used as an indirect measure of memory as it can reveal aspects of online memory processing. For example, do emotions modulate the nature of memory representations or the speed with which such memories can be accessed? Participants viewed central negative and neutral scenes surrounded by three neutral objects and after a brief delay, memory was assessed indirectly via eye movement monitoring and then directly via verbal reports. Consistent with the previous literature, emotion enhanced central and impaired peripheral memory as indexed by eye movement scanning and verbal reports. This suggests that eye movement scanning may contribute and/or is related to conscious access of memory. However, the central/peripheral tradeoff effect was not observed in an early measure of eye movement behavior, i.e. participants were faster to orient to a critical region of change in the periphery irrespective of whether it was previously studied in a negative or neutral context. These findings demonstrate emotion’s differential influences on different aspects of retrieval. In particular, emotion appears to affect the detail within, and/or the evaluation of, stored memory representations, but it may not affect the initial access to those representations.

  12. Four not six: Revealing culturally common facial expressions of emotion.

    Science.gov (United States)

    Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

    2016-06-01

    As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record PMID:27077757

  13. Antibody protection reveals extended epitopes on the human TSH receptor.

    Directory of Open Access Journals (Sweden)

    Rauf Latif

    Full Text Available Stimulating, and some blocking, antibodies to the TSH receptor (TSHR have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD. However, successful crystallization of TSHR residues 22-260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1-412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity.

  14. Antibody protection reveals extended epitopes on the human TSH receptor.

    Science.gov (United States)

    Latif, Rauf; Teixeira, Avelino; Michalek, Krzysztof; Ali, M Rejwan; Schlesinger, Max; Baliram, Ramkumarie; Morshed, Syed A; Davies, Terry F

    2012-01-01

    Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22-260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1-412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity. PMID:22957097

  15. Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions

    Directory of Open Access Journals (Sweden)

    Marin de Mas Igor

    2011-10-01

    Full Text Available Abstract Background Stable isotope tracers are used to assess metabolic flux profiles in living cells. The existing methods of measurement average out the isotopic isomer distribution in metabolites throughout the cell, whereas the knowledge of compartmental organization of analyzed pathways is crucial for the evaluation of true fluxes. That is why we accepted a challenge to create a software tool that allows deciphering the compartmentation of metabolites based on the analysis of average isotopic isomer distribution. Results The software Isodyn, which simulates the dynamics of isotopic isomer distribution in central metabolic pathways, was supplemented by algorithms facilitating the transition between various analyzed metabolic schemes, and by the tools for model discrimination. It simulated 13C isotope distributions in glucose, lactate, glutamate and glycogen, measured by mass spectrometry after incubation of hepatocytes in the presence of only labeled glucose or glucose and lactate together (with label either in glucose or lactate. The simulations assumed either a single intracellular hexose phosphate pool, or also channeling of hexose phosphates resulting in a different isotopic composition of glycogen. Model discrimination test was applied to check the consistency of both models with experimental data. Metabolic flux profiles, evaluated with the accepted model that assumes channeling, revealed the range of changes in metabolic fluxes in liver cells. Conclusions The analysis of compartmentation of metabolic networks based on the measured 13C distribution was included in Isodyn as a routine procedure. The advantage of this implementation is that, being a part of evaluation of metabolic fluxes, it does not require additional experiments to study metabolic compartmentation. The analysis of experimental data revealed that the distribution of measured 13C-labeled glucose metabolites is inconsistent with the idea of perfect mixing of hexose

  16. [Munchhausen syndrome by proxy revealed by falsely toxic methotrexate levels].

    Science.gov (United States)

    Charfi, Rim; Trabelsi, Sameh; Salouage, Issam; Gaïes, Emna; Jebabli, Nadia; Lakhal, Mohamed; Klouz, Anis

    2012-01-01

    Methotrexate is an antifolate drug used intravenously at high-dose in acute lymphocytic leukemia (ALL). Therapeutic drug monitoring is required to identify patients at risk of developing toxicity and to control folinic acid rescue. We report a case of Münchausen syndrome by proxy revealed by high and persistent falsely toxic methotrexate plasmatic levels. A 12 year-old child was treated with chemotherapy including methotrexate every 70 days for an ALL. The last methotrexate plasmatic level was 0.15 μmol/L at the 72th hour of the infusion. Then, he was treated by oral rout low-dose methotrexate. Ten days after methotrexate infusion, the patient consulted for asthenia, vomiting and presented a mucositis. Methotrexate plasmatic level was 2323 μmol/L. Renal function was normal. All drugs' intake was stopped. Folinic acid rescue was instituted. Even though there was no clinical sign of toxicity, therapeutic drug monitoring showed persistent high methotrexate plasmatic levels. Investigations eliminated measurement errors and pharmacokinetic problems. A deliberate methotrexate addition in each child blood sample brought by the mother was highly suspected. We confirmed this hypothesis by measuring methotrexate plasmatic levels in three samples: one brought by the mother, the second brought by the child's doctor and the last collected in our laboratory. Methotrexate plasmatic levels were respectively over 10,000 μmol/L (first sample) and lower than 0.02 μmol/L (the two others). The diagnosis of Munchausen's syndrome by proxy revealed by falsely toxic methotrexate plasmatic levels was made and the mother was addressed to the psychiatric department. PMID:22484536

  17. Revealing novel quantum phases in quantum antiferromagnets on random lattices

    Directory of Open Access Journals (Sweden)

    R. Yu

    2009-01-01

    Full Text Available Quantum magnets represent an ideal playground for the controlled realization of novel quantum phases and of quantum phase transitions. The Hamiltonian of the system can be indeed manipulated by applying a magnetic field or pressure on the sample. When doping the system with non-magnetic impurities, novel inhomogeneous phases emerge from the interplay between geometric randomness and quantum fluctuations. In this paper we review our recent work on quantum phase transitions and novel quantum phases realized in disordered quantum magnets. The system inhomogeneity is found to strongly affect phase transitions by changing their universality class, giving the transition a novel, quantum percolative nature. Such transitions connect conventionally ordered phases to unconventional, quantum disordered ones - quantum Griffiths phases, magnetic Bose glass phases - exhibiting gapless spectra associated with low-energy localized excitations.

  18. Electrochemical etching of sharp tips for STM reveals singularity

    DEFF Research Database (Denmark)

    Quaade, Ulrich; Oddershede, Lene

    2002-01-01

    towards and away from a particular singular point in time, exactly the time at which the wire breaks. The obtained scaling exponents coincide with exponents reported from other singular dynamical systems. The results also provide knowledge of how to control STM tip properties on the nano-scale.......Electrochemical etching of metal wires is widely used to produce atomically sharp tips for use in scanning tunneling microscopy (STM). In this letter we uncover the existence of a finite-time singularity in the process: Several of the physical parameters describing the system exhibit scaling...

  19. Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae.

    Science.gov (United States)

    Huang, Jiun-Yan; Huang, Chi-Wei; Kao, Kuo-Ching; Lai, Pik-Yin

    2013-04-10

    Biological systems are often organized spatially and temporally by multi-scale functional subsystems (modules). A specific subcellular process often corresponds to a subsystem composed of some of these interconnected modules. Accurate identification of system-level modularity organization from the large scale networks can provide valuable information on subsystem models of subcellular processes or physiological phenomena. Computational identification of functional modules from the large scale network is the key approach to solve the complexity of modularity in the past decade, but the overlapping and multi-scale nature of modules often renders unsatisfactory results in these methods. Most current methods for modularity detection are optimization-based and suffered from the drawback of size resolution limit. It is difficult to trace the origin of the unsatisfactory results, which may be due to poor data, inappropriate objective function selection or simply resulted from natural evolution, and hence no system-level accurate modular models for subcellular processes can be offered. Motivated by the idea of evolution with robustness and adaption as guiding principles, we propose a novel approach that can identify significant multi-scale overlapping modules that are sufficiently accurate at the system and subsystem levels, giving biological insights for subcellular processes. The success of our evolution strategy method is demonstrated by applying to the yeast protein-protein interaction network. Functional subsystems of important physiological phenomena can be revealed. In particular, the cell cycle controlling network is selected for detailed discussion. The cell cycle subcellular processes in yeast can be successfully dissected into functional modules of cell cycle control, cell size check point, spindle assembly checkpoint, and DNA damage check point in G2/M and S phases. The interconnections between check points and cell cycle control modules provide clues on the

  20. What Plurals and Compounds Reveal about Constraints in Word Formation

    Science.gov (United States)

    Jaensch, Carol; Heyer, Vera; Gordon, Peter; Clahsen, Harald

    2014-01-01

    Morphological systems are constrained in how they interact with each other. One case that has been widely studied in the psycholinguistic literature is the avoidance of plurals inside compounds (e.g. *"rats eater" vs. "rat eater") in English and other languages, the so-called "plurals-in-compounds effect." Several…