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Sample records for brachyspira hyodysenteriae reveals

  1. Multiresistentie van Brachyspira hyodysenteriae in Nederland

    NARCIS (Netherlands)

    Duinhof, T.F.; Dierikx, C.M.; Bergen, van M.A.P.; Koene, M.G.J.; Mevius, D.J.; Veldman, K.T.; Winne, de R.; Beers, van H.

    2008-01-01

    This case study describes the isolation of a multiresistant strain of Brachyspira hyodysenteriae in April 2007 in a Dutch sow herd with recurrent diarrhoea. Examination of faecal samples taken from 7-month-old breeding gilts with diarrhoea revealed the presence of resistance against tiamulin,

  2. Antimicrobial susceptibility of Brachyspira hyodysenteriae in Switzerland.

    Science.gov (United States)

    Kirchgässner, C; Schmitt, S; Borgström, A; Wittenbrink, M M

    2016-06-01

    Brachyspira (B.) hyodysenteriae is the causative agent of swine dysentery (SD), a severe mucohaemorrhagic diarrheal disease in pigs worldwide. So far, the antimicrobial susceptibility patterns of B. hyodysenteriae in Switzerland have not been investigated. Therefore, a panel of 30 porcine B. hyodysenteriae isolates were tested against 6 antimicrobial agents by using the VetMIC Brachy panel, a broth microdilution test. Tiamulin and valnemulin showed high antimicrobial activity inhibiting all isolates at low concentrations. The susceptibility testing of doxycycline revealed values from ≤0.25 μg/ ml (47%) to 2 μg/ml (10%). The MIC values of lincomycin ranged between ≤0.5 μg/ml (30%) and 32 μg/ml (43%). For tylosin, 57% of the isolates could not be inhibited at the highest concentration of ≥128 μg/ml. The MIC values for tylvalosin were between ≤0.25 μg/ml (10%) and 8 μg/ml (20%). These findings reveal Switzerland's favourable situation compared to other European countries. Above all, tiamulin and valnemulin are still effective antimicrobial agents and can be further used for the treatment of SD.

  3. Susceptibility to pleuromutilins in Brachyspira (Serpulina) hyodysenteriae.

    Science.gov (United States)

    Karlsson, M; Gunnarsson, A; Franklin, A

    2001-06-01

    The pleuromutilins are the only antimicrobial agents with sufficient minimum inhibitory concentration (MIC) values left to treat swine dysentery in Sweden. Other antimicrobials are either not approved for use against swine dysentery or only partly active against Brachyspira hyodysenteriae. To date, in Sweden two pleuromutilins, tiamulin and valnemulin, are authorized for use in pigs. This study includes a comparison between MICs of tiamulin and valnemulin for Swedish field isolates of B. hyodysenteriae, as determined by broth dilution. For different isolates the MIC of tiamulin was between 0 and 8 times higher than that of valnemulin. No resistance to pleuromutilins was recorded (tiamulin MIC range 0.031-2 microg/ml, valnemulin MIC range valnemulin; the MIC increased from 0.25 to more than 64 microg/ml. The valnemulin MIC for one B. hyodysenteriae strain increased from 0.031 microg/ml to 32 microg/ml. Valnemulin MIC was not determined for the B. hyodysenteriae strain that only went through 29 passages. The valnemulin MIC of the other B. pilosicoli strain increased from 0.031 to 4 microg/ml.

  4. [Multiresistant Brachyspira hyodysenteriae in a Dutch sow herd].

    Science.gov (United States)

    Duinhof, T F; Dierikx, C M; Koene, M G J; van Bergen, M A P; Mevius, D J; Veldman, K T; van Beers-Schreurs, H M G; de Winne, R T J A

    This case study describes the isolation ofa multiresistant strain ofBrachyspira hyodysenteriae in April 2007 in a Dutch sow herd with recurrent diarrhoea. Examination of faecal samples taken from 7-month-old breeding gilts with diarrhoea revealed the presence of resistance against tiamulin, lincomycin, tylosin, doxycycline, and tylvalosin (the active substance in Aivlosin) in four of five samples. Tiamulin resistance has not been reported in The Netherlands before. The repeated use of tiamulin on the affected farm was assumed to be the main cause of the development of resistance to the drug. The farmer was advised to adopt a medication strategy and to implement management practices that would prevent an ongoing cycle of infection on the farm. It is important that the Dutch swine industry appreciates that tiamulin-resistant strains of B. hyodysenteriae may be found on other farms as well. The appropriate and prudent use of antibiotics is essential in order to prevent the development of resistance against the last option left to cure B. hyodysenteriae infections: valnemulin.

  5. Antimicrobial susceptibility of porcine brachyspira hyodysenteriae isolates from Switzerland

    OpenAIRE

    Kirchgässner, Constanze

    2016-01-01

    The anaerobic spirochaete Brachyspira (B.) hyodysenteriae is the causative agent of swine dysentery (SD), a severe mucohaemorrhagic diarrheal disease in pigs worldwide. Currently, no data for antimicrobial susceptibility of B. hyodysenteriae from Switzerland are available and though antimicrobial treatment is the main therapy, no standardised methods for antimicrobial susceptibility testing are established. Therefore, a broth microdilution test was performed for 30 Swiss porcine field isolate...

  6. Characterisation of multiresistant Brachyspira hyodysenteriae isolates from Czech pig farms.

    Science.gov (United States)

    Sperling, D; Smola, J; Cízek, A

    2011-02-26

    The aim of the present study was to evaluate the importance of clonal spread of Brachyspira hyodysenteriae resistant to pleuromutilins (tiamulin, valnemulin) on farms in the Czech Republic. Agar dilution method and macrorestriction fragment profile analysis by pulsed field gel electrophoresis were used to characterise 35 B hyodysenteriae isolates that were obtained from clinical cases of swine dysentery on 32 farms between 2000 and 2005. Most isolates showed multiple resistances to tiamulin, valnemulin, tylosin and lincomycin. A total of six pulsotypes were detected in these multiresistant isolates. An analysis of epidemiological data showed that multiresistant B hyodysenteriae isolates were more often detected on fattening farms (59 per cent), compared with farms with other types of production. Furthermore, it was found that multiresistant B hyodysenteriae clones were most frequently selected on farms with endemic incidence of swine dysentery. This finding was confirmed by the characterisation of 21 B hyodysenteriae isolates obtained from three large-scale operations in seven consecutive years.

  7. Antimicrobial susceptibility of Brachyspira hyodysenteriae isolated from 21 Polish farms.

    Science.gov (United States)

    Zmudzki, J; Szczotka, A; Nowak, A; Strzelecka, H; Grzesiak, A; Pejsak, Z

    2012-01-01

    Swine dysentery (SD) is a common disease among pigs worldwide, which contributes to major production losses. Antimicrobial susceptibility testing of B. hyodysenteriae, the etiological agent of SD, is mainly performed by the agar dilution method. This method has certain limitations due to difficulties in interpretation of results. The aim of this study was the analysis of antimicrobial susceptibility of Brachyspira hyodysenteriae (B. hyodysenteriae) Polish field isolates by broth microdilution procedure. The study was performed on 21 isolates of B. hyodysenteriae, collected between January 2006 to December 2010 from cases of swine dysentery. VetMIC Brachyspira panels with antimicrobial agents (tiamulin, valnemulin, doxycycline, lincomycin, tylosin and ampicillin) were used for susceptibility testing of B. hyodysenteriae. The minimal inhibitory concentration (MIC) was determined by the broth dilution procedure. The lowest antimicrobial activity was demonstrated for tylosin and lincomycin, with inhibition of bacterial growth using concentrations > 128 microg/ml and 32 microg/ml, respectively. In the case of doxycycline, the MIC values were valnemulin) used in treatment of swine dysentery. Further studies are necessary to evaluate a possible slow decrease in susceptibility to tiamulin and valnemulin of B. hyodysenteriae strains in Poland.

  8. Minimum inhibitory concentration of Brazilian Brachyspira hyodysenteriae strains

    Directory of Open Access Journals (Sweden)

    Amanda G.S. Daniel

    Full Text Available ABSTRACT: The objectives of this study were to characterize Brachyspira hyodysenteriae isolates and to evaluate the antimicrobial susceptibility patterns of strains obtained from pigs in Brazil based on the minimal inhibitory concentration test (MIC. The MIC was performed for 22 B. hyodysenteriae isolates obtained from 2011 to 2013 using the following antimicrobial drugs: tylosin, tiamulin, valnemulin, doxycycline, lincomycin and tylvalosin. Outbreaks of swine dysentery were diagnosed based on clinical presentation, bacterial isolation, gross and microscopic lesions, duplex PCR for B. hyodysenteriae and B. pilosicoli and nox gene sequencing. All obtained MIC values were consistently higher or equal to the microbiological cut-off described in the literature. The MIC 90 values for the tested drugs were 8μg/ml for doxycycline, >4μg/ml for valnemulin, 8μg/ml for tiamulin, 32μg/ml for tylvalosin, >64μg/ml for lincomycin and >128μg/ml for tylosin. These results largely corroborate those reported in the literature. Tiamulin, doxycycline and tylvalosin showed the lowest MIC results. All of the samples subjected to phylogenetic analysis based on the nox gene sequence exhibited similar results, showing 100% identity to B. hyodysenteriae. This is the first study describing the MIC pattern of B. hyodysenteriae isolated in Brazil.

  9. Antimicrobial susceptibility of porcine Brachyspira hyodysenteriae and Brachyspira pilosicoli isolated in Sweden between 1990 and 2010.

    Science.gov (United States)

    Pringle, Märit; Landén, Annica; Unnerstad, Helle Ericsson; Molander, Benedicta; Bengtsson, Björn

    2012-09-21

    The anaerobic spirochetes Brachyspira hyodysenteriae and Brachyspira pilosicoli cause diarrheal diseases in pigs. Their fastidious nature has hampered standardization of methods for antimicrobial susceptibility testing. For monitoring of antimicrobial susceptibility wild type cutoff values are needed to define where the wild type distribution of MICs ends and no approved cutoffs are available for Brachyspira spp. In this study antimicrobial susceptibility data for both species (in total 906 isolates) were compiled and analyzed and wild type cut off values for B. hyodysenteriae proposed. The MICs of tiamulin, valnemulin, tylosin, tylvalosin, doxycycline and lincomycin were determined by broth dilution in brain heart infusion broth supplemented with 10% fetal calf serum. The compiled MICs from the broth dilution tests of the B. hyodysenteriae type strain, B78T (ATCC® 27164T), showed that the method yields reproducible results. In an international perspective the frequencies of isolates with decreased antimicrobial susceptibility were low among both B. hyodysenteriae and B. pilosicoli. However, in B. pilosicoli a constant level of 10-15% isolates with tiamulin MICs >4 μg/ml was detected between 2002 and 2010 and in B. hyodysenteriae a gradual increase in tiamulin MICs was seen between 1990 and 2003 although this increase has ceased during the last years. The wild type cutoff values proposed for B. hyodysenteriae are: tiamulin >0.25 μg/ml, valnemulin >0.125 μg/ml, tylosin >16 μg/ml, tylvalosin >1 μg/ml, lincomycin >1 μg/ml and doxycycline >0.5 μg/ml. The broth dilution method used in this study has over the years generated tightly grouped MIC populations for the field isolates and reproducible results for the control strain B78T and is therefore a suitable antimicrobial susceptibility test method for monitoring of Brachyspira spp. Here we propose wild type cutoff values for six antimicrobial agents for B. hyodysenteriae tested by broth dilution based on MIC

  10. Antimicrobial susceptibility of porcine Brachyspira hyodysenteriae and Brachyspira pilosicoli isolated in Sweden between 1990 and 2010

    Directory of Open Access Journals (Sweden)

    Pringle Märit

    2012-09-01

    Full Text Available Abstract Background The anaerobic spirochetes Brachyspira hyodysenteriae and Brachyspira pilosicoli cause diarrheal diseases in pigs. Their fastidious nature has hampered standardization of methods for antimicrobial susceptibility testing. For monitoring of antimicrobial susceptibility wild type cutoff values are needed to define where the wild type distribution of MICs ends and no approved cutoffs are available for Brachyspira spp. In this study antimicrobial susceptibility data for both species (in total 906 isolates were compiled and analyzed and wild type cut off values for B. hyodysenteriae proposed. Methods The MICs of tiamulin, valnemulin, tylosin, tylvalosin, doxycycline and lincomycin were determined by broth dilution in brain heart infusion broth supplemented with 10% fetal calf serum. Results The compiled MICs from the broth dilution tests of the B. hyodysenteriae type strain, B78T (ATCC® 27164T, showed that the method yields reproducible results. In an international perspective the frequencies of isolates with decreased antimicrobial susceptibility were low among both B. hyodysenteriae and B. pilosicoli. However, in B. pilosicoli a constant level of 10-15% isolates with tiamulin MICs >4 μg/ml was detected between 2002 and 2010 and in B. hyodysenteriae a gradual increase in tiamulin MICs was seen between 1990 and 2003 although this increase has ceased during the last years. The wild type cutoff values proposed for B. hyodysenteriae are: tiamulin >0.25 μg/ml, valnemulin >0.125 μg/ml, tylosin >16 μg/ml, tylvalosin >1 μg/ml, lincomycin >1 μg/ml and doxycycline >0.5 μg/ml. Conclusions The broth dilution method used in this study has over the years generated tightly grouped MIC populations for the field isolates and reproducible results for the control strain B78T and is therefore a suitable antimicrobial susceptibility test method for monitoring of Brachyspira spp. Here we propose wild type cutoff values for six antimicrobial

  11. Identification of a Divided Genome for VSH-1, the Prophage-Like Gene Transfer Agent of Brachyspira hyodysenteriae

    Science.gov (United States)

    The Brachyspira hyodysenteriae B204 genome sequence revealed three VSH-1 tail genes hvp31, hvp60, and hvp37, in a 3.6 kb cluster. The location and transcription direction of these genes relative to the previously described VSH-1 16.3 kb gene operon indicate that the gene transfer agent VSH-1 has a ...

  12. Trends towards Lower Antimicrobial Susceptibility and Characterization of Acquired Resistance among Clinical Isolates of Brachyspira hyodysenteriae in Spain

    DEFF Research Database (Denmark)

    Hidalgo, Alvaro; Carvajal, Ana; Vester, Birte

    2011-01-01

    The antimicrobial susceptibility of clinical isolates of Brachyspira hyodysenteriae in Spain was monitored, and the underlying molecular mechanisms of resistance were investigated. MICs of tylosin, tiamulin, valnemulin, lincomycin, and tylvalosin were determined for 87 B. hyodysenteriae isolates ...

  13. Quality-control ranges for antimicrobial susceptibility testing by broth dilution of the Brachyspira hyodysenteriae type strain (ATCC 27164(T))

    DEFF Research Database (Denmark)

    Pringle, M.; Aarestrup, Frank Møller; Bergsjø, B.

    2006-01-01

    There are no approved standards for antimicrobial susceptibility testing of the fastidious spirochete Brachyspira hyodysenteriae. An interlaboratory study was performed to establish MIC quality control ranges for six antimicrobial agents for the type strain of B. hyodysenteriae using broth diluti...

  14. The in vitro effect of Garden Thyme (Thymus vulgaris L.) extract on Brachyspira hyodysenteriae.

    Science.gov (United States)

    Kutasi, József; Jakab, László; Jurkovich, Viktor; Rafai, Pál

    2016-12-01

    Filtrates of a water extract of commercially available garden thyme (Thymus vulgaris L.) were used for studying its possible bactericidal effect on Brachyspira hyodysenteriae, the causative agent of swine dysentery, by agar-diffusion technique. Five of the six studied Brachyspira strains have proven to be sensitive and one moderately sensitive in the in vitro tests. It was concluded that water extract of garden thyme possesses inhibitory effects against B. hyodysenteriae. In vivo experiments are needed to check the validity of this conclusion.

  15. Antimicrobial susceptibility testing of Spanish field isolates of Brachyspira hyodysenteriae.

    Science.gov (United States)

    Hidalgo, A; Carvajal, A; García-Feliz, C; Osorio, J; Rubio, P

    2009-08-01

    This study is the first conducted in Spain to evaluate antimicrobial susceptibility of field isolates of Brachyspira hyodysenteriae. One hundred and eight isolates of the bacterium, recovered from different Spanish swine farms between 2000 and 2007, were investigated. The minimum inhibitory concentrations (MIC) of erythromycin, tylosin, tiamulin, valnemulin, clindamycin and lincomycin were determined using a broth microdilution technique. Most of the isolates showed poor susceptibility to erythromycin (MIC(90)>256 microg/ml), tylosin (MIC(90)>256 microg/ml), clindamycin (MIC(90)>4 microg/ml) and lincomycin (MIC(90)=128 microg/ml). Reduced susceptibility to tiamulin and valnemulin was observed with a MIC>2 microg/ml in 17.6% and 7.41% of the B. hyodysenteriae isolates, respectively. Moreover, a survival analysis permitted the detection of an increasing trend in the MIC values for almost all the antimicrobials used in the treatment of swine dysentery when comparing recent isolates (from 2006 to 2007) with those recovered in earlier years (between 2000 and 2004).

  16. In vitro antimicrobial susceptibility of Brachyspira hyodysenteriae strains isolated in Japan from 1985 to 2009.

    Science.gov (United States)

    Ohya, Tatsuo; Sueyoshi, Masuo

    2010-12-01

    The antimicrobial susceptibilities of 72 Brachyspira hyodysenteriae isolates collected from clinical cases of swine dysentery (SD) in 11 prefectures in Japan between 1985 and 2009 were investigated by an agar dilution method using five antimicrobial agents. There is a tendency of Japanese field isolates of B. hyodysenteriae to acquire resistance to the main antimicrobials used in SD treatment such as tiamulin, valnemulin, and efrotomycin. A responsible approach for selection and use of antimicrobial agents is required for SD treatment.

  17. The use of culture, pooled samples and PCR for identification of herds infected with Brachyspira hyodysenteriae.

    Science.gov (United States)

    Fellström, C; Zimmerman, U; Aspan, A; Gunnarsson, A

    2001-06-01

    The sensitivity of culturing Brachyspira hyodysenteriae was determined after sampling with swabs from porcine fecal specimens inoculated with tenfold dilutions of a field strain of these microbes. After storage of swabs, Brachyspira hyodysenteriae was recovered throughout the first 3 weeks after inoculation from feces with more than 140 cells/g. Viable spirochetes could still be recovered after up to 83 days of storage from feces, with 1.4 x 10(6) cells or more per gram. Culture for Brachyspira spp. was performed on 285 rectal swabs, which were pooled in batches of five. The number of pooled samples positive for B. hyodysenteriae corresponded with the sum results of individual analysis of the corresponding collections of five samples. A PCR system based on the tlyA gene of B. hyodysenteriae was developed and tested on primary cultures of pooled samples. The results of the PCR assay showed a 97% correlation with the culture results. The prevalence of Brachyspira spp. was determined in five swine herds and found to be highest among breeding gilts and boars aged 13-16 weeks and among 6-12-week-old weaned pigs. In contrast, Brachyspira spp. were only rarely found in sows, which may reflect the development of immunity by adult pigs to all species of the genus.

  18. Concentração inibitória mínima de cepas Brachyspira hyodysenteriae brasileiras

    OpenAIRE

    Amanda G.S. Daniel; José P.H. Sato; Gabardo,Michelle P.; Resende, Talita P.; Barcellos,David E.S.N. de; Pereira, Carlos E.R.; Vannucci,Fábio A.; Guedes,Roberto M.C.

    2017-01-01

    ABSTRACT: The objectives of this study were to characterize Brachyspira hyodysenteriae isolates and to evaluate the antimicrobial susceptibility patterns of strains obtained from pigs in Brazil based on the minimal inhibitory concentration test (MIC). The MIC was performed for 22 B. hyodysenteriae isolates obtained from 2011 to 2013 using the following antimicrobial drugs: tylosin, tiamulin, valnemulin, doxycycline, lincomycin and tylvalosin. Outbreaks of swine dysentery were diagnosed based ...

  19. Mechanisms of antibacterial action of Quinoxaline 1,4-di-N-oxides against Clostridium perfringens and Brachyspira hyodysenteriae

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    Fanfan Xu

    2016-12-01

    Full Text Available Quinoxaline 1,4-di-N-oxides (QdNOs are a class of bioreductive compounds, however their antibacterial mechanisms are still unclarified. The aim of this study was to assess the ability of two representative QdNO drugs, cyadox (CYA and olaquindox (OLA, to produce reactive oxide species (ROS in Gram-positive anaerobe Clostridium perfringens CVCC1125 and Gram-negative anaerobe Brachyspira hyodysenteriae B204. In addition, the effects of QdNOs on the integrity of bacterial cell walls and membranes as well as the morphological alterations and DNA oxidative damage in C. perfringens and B. hyodysenteriae were analyzed. It was demonstrated that under anaerobic conditions, QdNOs were metabolized into the reduced products which did not show any antibacterial activity. A significant dose-related increase of intracellular ROS level and intracellular hydroxyl radicals were evident in bacteria exposed to QdNOs. The result of biochemical assay showed that the cell walls and membranes of the bacteria treated with QdNOs were damaged. After exposure to 1/2MIC to 4MIC of CYA and OLA, C. perfringens and B. hyodysenteriae became elongated and filamentous. Morphological observation with scanning and transmission electron microscopes revealed rupture, loss of cytoplasmic material and cell lysis in QdNO-treated bacteria, indicating serious damage of cells. There was an increase of 8-OHdG in the two strains treated by QdNOs, but it was lower in Gram-positive than in Gram-negative bacteria. Agarose gel electrophoresis showed the degradation of chromosomal DNA in both of the two anaerobes treated by QdNOs. The results suggest that QdNOs may kill C. perfringens and B. hyodysenteriae via the generation of ROS and hydroxyl radicals from the bacterial metabolism of QdNOs, which cause oxidative damage in bacteria under anaerobic conditions.

  20. Presence and mechanisms of acquired antimicrobial resistance in Belgian Brachyspira hyodysenteriae isolates belonging to different clonal complexes.

    Science.gov (United States)

    Mahu, M; Pasmans, F; Vranckx, K; De Pauw, N; Vande Maele, L; Vyt, Philip; Vandersmissen, Tamara; Martel, A; Haesebrouck, F; Boyen, F

    2017-08-01

    Swine dysentery (SD) is an economically important disease for which antimicrobial treatment still occupies an important place to control outbreaks. However, acquired antimicrobial resistance is increasingly observed in Brachyspira hyodysenteriae. In this study, the Minimal Inhibitory Concentrations (MIC) of six antimicrobial compounds for 30 recent Belgian B. hyodysenteriae isolates were determined using a broth microdilution method. In addition, relevant regions of the 16S rRNA, 23S rRNA and the L3 protein encoding genes were sequenced to reveal mutations associated with acquired resistance. Finally, a phylogeny was reconstructed using minimal spanning tree analysis of multi locus sequence typing of the isolates. For lincomycin, doxycycline, tylosin and tylvalosin, at least 70% of the isolates did not belong to the wild-type population and were considered to have acquired resistance. For valnemulin and tiamulin, this was over 50%. In all isolates with acquired resistance to doxycycline, the G1058C mutation was present in their 16S rRNA gene. All isolates showing acquired resistance to lincomycin and both macrolides displayed the A2058T mutation in their 23S rRNA gene. Other mutations in this gene and the N148S mutation in the L3 protein were present in both wild-type isolates and isolates considered to have acquired resistance. Multi locus sequence analysis revealed a previously undescribed clonal complex, with 4 novel sequence types in which the majority of isolates showed acquired resistance to all tested antimicrobial products. In conclusion, acquired antimicrobial resistance is widespread among Belgian B. hyodysenteriae isolates. The emergence of multi-resistant clonal complexes can pose a threat to swine industry. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Decreased susceptibility to tiamulin and valnemulin among Czech isolates of Brachyspira hyodysenteriae.

    Science.gov (United States)

    Lobová, Dana; Smola, Jiri; Cizek, Alois

    2004-04-01

    The agar dilution method was used to investigate the sensitivity to pleuromutilins of 100 isolates of Brachyspira hyodysenteriae isolated from 63 pig farms between 1997 and 2001. In the period under investigation, MICs to both tiamulin and valnemulin increased, with differences between the periods 1997-98 and 1999-2001 being statistically significant (P valnemulin). Between 1997 and 2001, the MIC50 and MIC90 of tiamulin increased from 0.062 and 0.25 microg ml, respectively, to 1.0 and 4.0 microg ml. Valnemulin MIC50 and MIC90 were valnemulin demonstrated in this study reflect the intensity of pleuromutilin use in the treatment of swine dysentery in the Czech Republic.

  2. Antimicrobial susceptibility testing of Australian isolates of Brachyspira hyodysenteriae using a new broth dilution method.

    Science.gov (United States)

    Karlsson, Märit; Oxberry, Sophy L; Hampson, David J

    2002-01-03

    The antimicrobial susceptibilities of 76 field isolates of Brachyspira hyodysenteriae from different states of Australia were tested in a newly developed broth dilution procedure. The antimicrobial agents used were tiamulin, valnemulin, tylosin, erythromycin, lincomycin and clindamycin. The results from the broth dilution susceptibility testing of 39 of the isolates were compared with results obtained for the same isolates using the agar dilution method. Amongst the isolates tested by broth dilution, 17 were from three farms and had been collected over a number of years. Their pulsed field gel electrophoresis pattern previously had been determined. The broth dilution technique was simple to use, less labor intensive than agar dilution, and gave clear end points. The results obtained using the two methods generally corresponded well, although in a few cases the MIC obtained by broth dilution were lower than those with agar dilution. For the 76 isolates tested by broth dilution, the MIC(90) (mg/l) was: tiamulin, 1; valnemulin, 0.5; tylosin>256; erythromycin>256; lincomycin, 64 and clindamycin, 16. Only minor differences in susceptibility patterns were found amongst isolates from different Australian states. Over all the isolates, and also amongst the isolates obtained from different years on the three farms, there was no trend for the susceptibility of the isolates to alter with time.

  3. Characterization of Brachyspira hyodysenteriae isolates from Italy by multilocus sequence typing and multiple locus variable number tandem repeat analysis.

    Science.gov (United States)

    Gasparrini, S; Alborali, G L; Pitozzi, A; Guarneri, F; Giacomini, E; Baldo, V; Scali, F; Lazzaro, M; Boniotti, M B

    2017-08-01

    To evaluate and compare the capabilities of multilocus sequence typing (MLST) and multiple locus variable number tandem repeat analysis (MLVA) techniques to characterize Brachyspira hyodysenteriae isolates and to investigate the relationship between pleuromutilin resistance and genetic variability. MLST genotyping was performed on 180 B. hyodysenteriae isolates, and the results were evaluated considering profiles from 108 other strains previously reported in the database. In total, 37 sequence types were obtained. The MLVA approach completely characterized 172 strains and grouped the isolates into 22 different profiles. The combination of MLST and MLVA showed a slight increase in the discriminatory power, identifying 33 joint profiles. An antibiotic resistance analysis showed a reduction in the susceptibility to pleuromutilins over time, and a weak association between susceptibility to valnemulin and inclusion in clonal complex 4. MLST and MLVA are reliable methods for characterizing B. hyodysenteriae strains and they have comparable discriminatory power. The genotyping of B. hyodysenteriae isolates and a database of all the genetic profiles collected during the diagnostic activities could support traditional epidemiological investigations in identifying infection sources and routes of transmission among herds, and in developing more effective control measures. © 2017 The Society for Applied Microbiology.

  4. In vitro susceptibility of 21 antimicrobial agents to 37 isolates of Brachyspira hyodysenteriae isolated from pigs in Okinawa Prefecture.

    Science.gov (United States)

    Uezato, Kayo; Kinjo, Eiki; Adachi, Yoshikazu

    2004-03-01

    The in vitro susceptibilities to 21 antimicrobial agents, of 37 isolates of Brachyspira (B.) hyodysenteriae isolated from pigs in Okinawa meat center and a pig farm in Okinawa Prefecture, Japan, were determined by the agar dilution method. Carbadox was the most active of all the agents tested against the isolates (MIC: valnemulin with MICs ranging from

  5. Drug-susceptibility of isolates of Brachyspira hyodysenteriae isolated from colonic mucosal specimens of pigs collected from slaughter houses in Japan in 2009.

    Science.gov (United States)

    Kajiwara, Keita; Kozawa, Midori; Kanazawa, Takuya; Uetsuka, Kouji; Nakajima, Hiromi; Adachi, Yoshikazu

    2016-03-01

    Twenty nine isolates identified as Brachyspira hyodysenteriae were most susceptible to carbadox and metronidazole, whereas they were resistant to macrolides. The isolates showed intermediate susceptibility to tiamulin, lincomycin, penicillin G, ampicillin, chloramphenicol, tetracycline, enrofloxacin and valnemulin, with MIC50 values ranging from 0.39 to 3.13.

  6. Drug-susceptibility of isolates of Brachyspira hyodysenteriae isolated from colonic mucosal specimens of pigs collected from slaughter houses in Japan in 2009

    OpenAIRE

    KAJIWARA, Keita; KOZAWA, Midori; Kanazawa, Takuya; UETSUKA, Kouji; Nakajima, Hiromi; Adachi, Yoshikazu

    2015-01-01

    Twenty nine isolates identified as Brachyspira hyodysenteriae were most susceptible to carbadox and metronidazole, whereas they were resistant to macrolides. The isolates showed intermediate susceptibility to tiamulin, lincomycin, penicillin G, ampicillin, chloramphenicol, tetracycline, enrofloxacin and valnemulin, with MIC50 values ranging from 0.39 to 3.13.

  7. Comparison of methods for antimicrobial susceptibility testing and MIC values for pleuromutilin drugs for Brachyspira hyodysenteriae isolated in Germany.

    Science.gov (United States)

    Rohde, Judith; Kessler, Martina; Baums, Christoph G; Amtsberg, Gunter

    2004-08-19

    In Germany treatment of swine dysentery is hampered by Brachyspira hyodysenteriae strains showing elevated MIC values to the few antibiotics licensed. Therefore, susceptibility testing of clinical isolates is an important service to the swine practitioner. This study compares the established agar dilution procedure for antimicrobial susceptibility testing of this fastidious anaerobe to the broth microdilution test newly developed [Anim. Health Res. 2 (2001) 59; Vet. Microbiol. 84 (2002) 123; J. Clin. Microbiol. 41 (2003) 2596]. A total of 221 isolates were examined twice with either test procedure using tiamulin and valnemulin as antibiotics. Both methods gave reproducible results, and the MIC values for the reference strains B. hyodysenteriae B204 and Staphylococcus aureus ATCC 29213 corresponded to previously published data. However, the results for individual strains differed significantly for both tests (P < 0.001) with MIC values being on average one dilution step lower in the broth dilution method. The 221 strains used for comparing test procedures were isolated between 1989 and 2001. An additional 102 strains isolated in 2002 were tested only with the broth dilution procedure. A significant rise in the average MIC value for both pleuromutilins could be demonstrated when comparing earlier isolates to those from 2000 to 2001 (P < 0.05), while in 2002 the average MIC significantly decreased when compared to the value in 2000 (P < 0.05). However, strains with MIC values for tiamulin as high as 8 microg/ml (broth dilution) could still be isolated.

  8. Trends towards Lower Antimicrobial Susceptibility and Characterization of Acquired Resistance among Clinical Isolates of Brachyspira hyodysenteriae in Spain ▿

    Science.gov (United States)

    Hidalgo, Álvaro; Carvajal, Ana; Vester, Birte; Pringle, Märit; Naharro, Germán; Rubio, Pedro

    2011-01-01

    The antimicrobial susceptibility of clinical isolates of Brachyspira hyodysenteriae in Spain was monitored, and the underlying molecular mechanisms of resistance were investigated. MICs of tylosin, tiamulin, valnemulin, lincomycin, and tylvalosin were determined for 87 B. hyodysenteriae isolates recovered from 2008 to 2009 by broth dilution. Domain V of the 23S rRNA gene and the ribosomal protein L3 gene were sequenced in 20 isolates for which the tiamulin MIC was ≥4 μg/ml, presenting decreased susceptibility, and in 18 tiamulin-susceptible isolates (MIC ≤ 0.125 μg/ml), and all isolates were typed by multiple-locus variable-number tandem repeats analysis. A comparison with antimicrobial susceptibility data from 2000 to 2007 showed an increase in pleuromutilin resistance over time, doubling the number of isolates with decreased susceptibility to tiamulin. No alteration in susceptibility was detected for lincomycin, and the MIC of tylosin remained high (MIC50 > 128 μg/ml). The decreased susceptibility to tylosin and lincomycin can be explained by mutations at position A2058 of the 23S rRNA gene (Escherichia coli numbering). A2058T was the predominant mutation, but A2058G also was found together with a change of the neighboring base pair at positions 2057 to 2611. The role of additional point mutations in the vicinity of the peptidyl transferase center and mutations in the L3 at amino acids 148 and 149 and their possible involvement in antimicrobial susceptibility are considered. An association between G2032A and high levels of tiamulin and lincomycin MICs was found, suggesting an increasing importance of this mutation in antimicrobial resistance of clinical isolates of B. hyodysenteriae. PMID:21555771

  9. Sequence types and pleuromutilin susceptibility of Brachyspira hyodysenteriae isolates from Italian pigs with swine dysentery: 2003-2012.

    Science.gov (United States)

    Rugna, G; Bonilauri, P; Carra, E; Bergamini, F; Luppi, A; Gherpelli, Y; Magistrali, C F; Nigrelli, A; Alborali, G L; Martelli, P; La, T; Hampson, D J; Merialdi, G

    2015-01-01

    Swine dysentery is a mucohaemorrhagic colitis of pigs caused by infection with Brachyspira hyodysenteriae. The disease can be controlled by treatment with antimicrobial agents, with the pleuromutilins tiamulin and valnemulin being widely used. In recent years, the occurrence of B. hyodysenteriae with reduced susceptibility to these drugs has been increasing. The aim of this study was to determine temporal changes in genetic groups and pleuromutilin susceptibility amongst B. hyodysenteriae isolates from Italy. Multilocus sequence typing (MLST) was performed on 108 isolates recovered from 87 farms in different regions of Italy from 2003 to 2012, and their minimum inhibitory concentrations (MICs) for tiamulin and valnemulin were determined. Logistic regression was performed to assess associations between susceptibility to the two antimicrobial agents and genetic group, year and region of isolation. The isolates were allocated to 23 sequence types (STs), with five clonal clusters (Ccs) and seven singletons. More than 50% of isolates were resistant to both pleuromutilins (MIC >2.0 µg/mL for tiamulin and >1.0 µg/mL for valnemulin). All 10 isolates in ST 83 were resistant; these were first isolated in 2011 and came from nine farms, suggesting recent widespread dissemination of a resistant strain. Significant associations were found between the proportion of pleuromutilin susceptible isolates and the genetic group and year of isolation. Although resistant isolates were found in all Ccs, isolates in Ccs 2 and 7 were over five times more likely to be susceptible than those in the other Ccs. A significant trend in the reduction of susceptibility over time also was observed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Trends towards lower antimicrobial susceptibility and characterization of acquired resistance among clinical isolates of Brachyspira hyodysenteriae in Spain.

    Science.gov (United States)

    Hidalgo, Álvaro; Carvajal, Ana; Vester, Birte; Pringle, Märit; Naharro, Germán; Rubio, Pedro

    2011-07-01

    The antimicrobial susceptibility of clinical isolates of Brachyspira hyodysenteriae in Spain was monitored, and the underlying molecular mechanisms of resistance were investigated. MICs of tylosin, tiamulin, valnemulin, lincomycin, and tylvalosin were determined for 87 B. hyodysenteriae isolates recovered from 2008 to 2009 by broth dilution. Domain V of the 23S rRNA gene and the ribosomal protein L3 gene were sequenced in 20 isolates for which the tiamulin MIC was ≥ 4 μg/ml, presenting decreased susceptibility, and in 18 tiamulin-susceptible isolates (MIC ≤ 0.125 μg/ml), and all isolates were typed by multiple-locus variable-number tandem repeats analysis. A comparison with antimicrobial susceptibility data from 2000 to 2007 showed an increase in pleuromutilin resistance over time, doubling the number of isolates with decreased susceptibility to tiamulin. No alteration in susceptibility was detected for lincomycin, and the MIC of tylosin remained high (MIC(50) > 128 μg/ml). The decreased susceptibility to tylosin and lincomycin can be explained by mutations at position A2058 of the 23S rRNA gene (Escherichia coli numbering). A2058T was the predominant mutation, but A2058G also was found together with a change of the neighboring base pair at positions 2057 to 2611. The role of additional point mutations in the vicinity of the peptidyl transferase center and mutations in the L3 at amino acids 148 and 149 and their possible involvement in antimicrobial susceptibility are considered. An association between G2032A and high levels of tiamulin and lincomycin MICs was found, suggesting an increasing importance of this mutation in antimicrobial resistance of clinical isolates of B. hyodysenteriae.

  11. Comparison of Brachyspira hyodysenteriae Isolates Recovered from Pigs in Apparently Healthy Multiplier Herds with Isolates from Herds with Swine Dysentery.

    Directory of Open Access Journals (Sweden)

    Tom La

    Full Text Available Swine dysentery (SD is a mucohaemorrhagic colitis of grower/finisher pigs classically resulting from infection by the anaerobic intestinal spirochaete Brachyspira hyodysenteriae. This study aimed to determine whether B. hyodysenteriae isolates from pigs in three healthy German multiplier herds supplying gilts to other farms differed from isolates from nine German production herds with SD. Isolates were subjected to whole genomic sequencing, and in silico multilocus sequence typing showed that those from the three multiplier herds were of previously undescribed sequence types (ST132, ST133 and ST134, with all isolates from the same herd having the same ST. All isolates were examined for the presence of 332 genes encoding predicted virulence or virulence lifestyle associated factors, and these were well conserved. Isolates from one multiplier herd were atypical in being weakly haemolytic: they had 10 amino acid substitutions in the haemolysin III protein and five in the haemolysin activation protein compared to reference strain WA1, and had a disruption in the promoter site of the hlyA gene. These changes likely contribute to the weakly haemolytic phenotype and putative lack of virulence. These same isolates also had nine base pair insertions in the iron metabolism genes bitB and bitC and lacked five of six plasmid genes that previously have been associated with colonisation. Other overall differences between isolates from the different herds were in genes from three of five outer membrane proteins, which were not found in all the isolates, and in members of a block of six plasmid genes. Isolates from three herds with SD had all six plasmid genes, while isolates lacking some of these genes were found in the three healthy herds-but also in isolates from six herds with SD. Other differences in genes of unknown function or in gene expression may contribute to variation in virulence; alternatively, superior husbandry and better general health may have

  12. Comparison of Lesion Severity, Distribution, and Colonic Mucin Expression in Pigs With Acute Swine Dysentery Following Oral Inoculation With “Brachyspira hampsonii” or Brachyspira hyodysenteriae

    National Research Council Canada - National Science Library

    Wilberts, B. L; Arruda, P. H; Kinyon, J. M; Madson, D. M; Frana, T. S; Burrough, E. R

    2014-01-01

    ...) clade II or a classic strain of B. hyodysenteriae (B204; n = 10) to compare gross and microscopic lesions and alterations in colonic mucin expression in pigs with clinical disease versus controls (n = 6...

  13. Changes in the expression of galanin and galanin receptors in the wall of the colon in pigs experimentally infected with Brachyspira hyodysenteriae

    Directory of Open Access Journals (Sweden)

    Wąsowicz Krzysztof

    2014-03-01

    Full Text Available The expression of galanin (GAL and its three receptors (GalR1, GalR2, and GalR3 were studied with real-time PCR in the colonic wall of pigs suffering from experimental colitis caused by the infection with Brachyspira hyodysenteriae. The expression was studied in the muscular membrane, mucosa/submucosa layer, and in lymphocytes isolated from mucosa/submucosa. The expression levels were normalized to glyceraldehyde-6-phosphate dehydrogenase (GAPDH expression and compared to expression levels in control animals. GAL expression was found in all three studied compartments of the colonic wall. A significant decrease in GAL expression level was found in the mucosa/submucosa and in isolated lymphocytes, whereas the decrease was much less profound in the muscular membrane. In the case of galanin receptors their expression was found in all studied compartments of the colonic wall, however at different levels, as compared to GAPDH expression. The decrease of galanin receptors expression was found in all studied compartments of the colonic wall of the sick animals.

  14. Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.

    Science.gov (United States)

    Mushtaq, Mamoona; Zubair, Saima; Råsbäck, Therese; Bongcam-Rudloff, Erik; Jansson, Désirée S

    2015-10-12

    The genus Brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. In a previous study a group of strongly haemolytic isolates from pigs and mallards was provisionally described as a new species within genus Brachyspira, "B. suanatina", and enteropathogenic properties were demonstrated in a porcine challenge model. In the current study characterization of B. suanatina was performed on the basis of cell morphology, growth characteristics, enzyme profiles, DNA-DNA hybridization (DDH) and whole genome comparisons. The draft genome sequence of B. suanatina strain AN4859/03 was determined and compared with the available genomes of all valid species of Brachyspira. According to morphological traits, growth characteristics and enzymatic profiles, B. suanatina was similar to the type strain of B. hyodysenteriae, but using the recommended threshold value of 70% similarity by DDH it did not belong to any of the recognized Brachyspira species (range 16-64% similarity). This was further supported by average nucleotide identity values. Phylogenetic analysis performed using housekeeping genes and core genomes of all valid Brachyspira sp. and "B. hampsonii" revealed that B. suanatina and B. intermedia formed a clade distinct from B. hyodysenteriae. By comparing the genomes of the three closely related species B. intermedia, B. hyodysenteriae and B. suanatina similar profiles of general genomic features and distribution of genes in different functional categories were obtained. However, the genome size of B. hyodysenteriae was smallest among the species, suggesting the possibility of reductive evolution in the divergence of this species. A bacteriophage region and a putative plasmid sequence were also found in the genome of B. suanatina strain AN4859/03. The results of our study suggest that despite being similar to B. hyodysenteriae phenotypically, B. suanatina should be regarded as a separate species based on its genetic

  15. Antimicrobial Susceptibility Patterns of Brachyspira Species Isolated from Swine Herds in the United States

    OpenAIRE

    Mirajkar, Nandita S.; Davies, Peter R.; Gebhart, Connie J.

    2016-01-01

    Outbreaks of swine dysentery, caused by Brachyspira hyodysenteriae and the recently discovered “Brachyspira hampsonii,” have reoccurred in North American swine herds since the late 2000s. Additionally, multiple Brachyspira species have been increasingly isolated by North American diagnostic laboratories. In Europe, the reliance on antimicrobial therapy for control of swine dysentery has been followed by reports of antimicrobial resistance over time. The objectives of our study were to determi...

  16. Isolation and antimicrobial susceptibility of Brachyspira species from feces of layer chickens in Germany.

    Science.gov (United States)

    Herbst, Werner; Willems, Hermann; Heuser, Jörg; Ewers, Christa

    2017-11-03

    Anaerobic spirochetes of the genus Brachyspira are important pathogens causing swine dysentery (Brachyspira [B.] hyodysenteriae) and porcine intestinal spirochetosis (B. pilosicoli, PIS). In addition, avian intestinal spirochetosis (AIS) is caused by B. pilosicoli, B. intermedia and B. alvinipulli. Despite the economic impact of AIS, the disease has not received appropriate attention in Germany. This study was aimed at identifying Brachyspira spp. in Germany and determining their antimicrobial susceptibility. From 2009 to 2013, a total of 71 fecal swabs were obtained from clinically healthy layer hens from eight different commercial flocks. Brachyspira spp. culture was performed in trypticase soybean agar added with 5% sheep blood. Species determination was conducted by PCRs targeting the NADH-gen and the 16S rDNA or by nox-gene sequencing. Antimicrobial susceptibility to macrolides, lincosamides and pleuromutilins was tested by a microdilution assay. Brachyspira spp. were isolated from 40 (56.3%) swabs distributed over all eight flocks. In 26 cases, the following species were determined by PCR: B. pilosicoli (n = 16), B. intermedia (2), B. innocens (3), B. murdochii (1), mixtures of B. pilosicoli/B. intermedia (2), B. innocens/B. intermedia (1), B. innocens/B. murdochii (1). Remaining isolates were characterized by nox-gene sequencing as B. "pulli" (n = 9), B. alvinipulli (3), B. intermedia (1) and as not identifiable (1). Antimicrobial susceptibility testing of 37 isolates revealed minimal inhibitory concentrations 90 (MIC90) of > 128 mg/l (tylosin), 64 mg/l (lincomycin), 8 mg/l (tiamulin) and 4 mg/l (valnemulin), respectively. Comparing to breakpoints applied to pigs, these values lie within the range of resistance. The demonstration of different Brachyspira spp., particularly B. pilosicoli, intermedia and alvinipulli in commercial layers, indicates the need of further research to assess their potential role in causing AIS in German poultry flocks. The

  17. Antimicrobial Susceptibility Patterns of Brachyspira Species Isolated from Swine Herds in the United States.

    Science.gov (United States)

    Mirajkar, Nandita S; Davies, Peter R; Gebhart, Connie J

    2016-08-01

    Outbreaks of swine dysentery, caused by Brachyspira hyodysenteriae and the recently discovered "Brachyspira hampsonii," have reoccurred in North American swine herds since the late 2000s. Additionally, multiple Brachyspira species have been increasingly isolated by North American diagnostic laboratories. In Europe, the reliance on antimicrobial therapy for control of swine dysentery has been followed by reports of antimicrobial resistance over time. The objectives of our study were to determine the antimicrobial susceptibility trends of four Brachyspira species originating from U.S. swine herds and to investigate their associations with the bacterial species, genotypes, and epidemiological origins of the isolates. We evaluated the susceptibility of B. hyodysenteriae, B. hampsonii, Brachyspira pilosicoli, and Brachyspira murdochii to tiamulin, valnemulin, doxycycline, lincomycin, and tylosin by broth microdilution and that to carbadox by agar dilution. In general, Brachyspira species showed high susceptibility to tiamulin, valnemulin, and carbadox, heterogeneous susceptibility to doxycycline, and low susceptibility to lincomycin and tylosin. A trend of decreasing antimicrobial susceptibility by species was observed (B. hampsonii > B. hyodysenteriae > B. murdochii > B. pilosicoli). In general, Brachyspira isolates from the United States were more susceptible to these antimicrobials than were isolates from other countries. Decreased antimicrobial susceptibility was associated with the genotype, stage of production, and production system from which the isolate originated, which highlights the roles of biosecurity and husbandry in disease prevention and control. Finally, this study also highlights the urgent need for Clinical and Laboratory Standards Institute-approved clinical breakpoints for Brachyspira species, to facilitate informed therapeutic and control strategies. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  18. Species characterization and minimum inhibitory concentration patterns of Brachyspira species isolates from swine with clinical disease.

    Science.gov (United States)

    Clothier, Kristin A; Kinyon, Joann M; Frana, Timothy S; Naberhaus, Nadine; Bower, Leslie; Strait, Erin L; Schwartz, Kent

    2011-11-01

    Typhlocolitis and dysentery due to Brachyspira hyodysenteriae infection represent an economically important disease syndrome in growing pigs. Largely disappearing from U.S. swine herds in the late 1990 s and early 2000s, Brachyspira-associated disease and bacterial isolation from swine with clinical disease has increased in the last several years, and non-B. hyodysenteriae isolates are commonly identified. Antimicrobial resistance has been demonstrated in Brachyspira spp. isolates from Europe and Asia, and may be the reason for the resurgence in U.S. herds. Seventy-nine clinical isolates identified at the Iowa State University Veterinary Diagnostic Lab were tested with multiple polymerase chain reaction assays to establish species identity, and evaluated for minimum inhibitory concentrations (MICs) using an agar dilution method against lincomycin, gentamicin, valnemulin, tiamulin, salinomycin, and carbadox. Only 38.0% of isolates could be confirmed as the known pathogens B. hyodysenteriae (30.4%) or Brachyspira pilosicoli (7.6%). Twenty of the 79 isolates (25.3%) were identified as Brachyspira murdochii, and 13.9% could not be identified to species. The MIC values were consistently high against lincomycin and moderately high against gentamicin. The remaining antimicrobials had MICs that were at the low end of the test ranges. Brachyspira murdochii and Brachyspira spp. had significantly greater MIC values against several of these drugs than other Brachyspira spp. examined. The increased incidence of these less definitively characterized Brachyspira species with increased MIC values to commonly prescribed antimicrobials may, at least in part, explain the increased prevalence and severity of this disease complex in recent years. Further research is necessary to understand these changes.

  19. Comparison of agar dilution and antibiotic gradient strip test with broth microdilution for susceptibility testing of swine Brachyspira species.

    Science.gov (United States)

    Mirajkar, Nandita S; Gebhart, Connie J

    2016-03-01

    Production-limiting diseases in swine caused by Brachyspira are characterized by mucohemorrhagic diarrhea (B. hyodysenteriae and "B. hampsonii") or mild colitis (B. pilosicoli), while B. murdochii is often isolated from healthy pigs. Emergence of novel pathogenic Brachyspira species and strains with reduced susceptibility to commonly used antimicrobials has reinforced the need for standardized susceptibility testing. Two methods are currently used for Brachyspira susceptibility testing: agar dilution (AD) and broth microdilution (BMD). However, these tests have primarily been used for B. hyodysenteriae and rarely for B. pilosicoli. Information on the use of commercial susceptibility testing products such as antibiotic gradient strips is lacking. Our main objective was to validate and compare the susceptibility results, measured as the minimum inhibitory concentration (MIC), of 6 antimicrobials for 4 Brachyspira species (B. hyodysenteriae, "B. hampsonii", B. pilosicoli, and B. murdochii) by BMD and AD (tiamulin, valnemulin, lincomycin, tylosin, and carbadox) or antibiotic gradient strip (doxycycline) methods. In general, the results of a high percentage of all 4 Brachyspira species differed by ±1 log2 dilution or less by BMD and AD for tiamulin, valnemulin, lincomycin, and tylosin, and by BMD and antibiotic gradient strip for doxycycline. The carbadox MICs obtained by BMD were 1-5 doubling dilutions different than those obtained by AD. BMD for Brachyspira was quicker to perform with less ambiguous interpretation of results when compared with AD and antibiotic gradient strip methods, and the results confirm the utility of BMD in routine diagnostics. © 2016 The Author(s).

  20. Reproduction of mucohaemorrhagic diarrhea and colitis indistinguishable from swine dysentery following experimental inoculation with "Brachyspira hampsonii" strain 30446.

    Directory of Open Access Journals (Sweden)

    Joseph E Rubin

    Full Text Available BACKGROUND: Mucohaemorrhagic diarrhea caused by Brachyspira hyodysenteriae, swine dysentery, is a severe production limiting disease of swine. Recently, pigs in western Canada with clinical signs indistinguishable from swine dysentery were observed. Despite the presence of spirochetes on fecal smears, recognized Brachyspira spp. including B. hyodysenteriae could not be identified. A phylogenetically distinct Brachyspira, called "B. hampsonii" strain 30446, however was isolated. The purpose of this study was to experimentally reproduce mucohaemorrhagic colitis and characterize strain 30446 shedding following inoculation. METHODS AND FINDINGS: Eighteen 13-week-old pigs were randomly assigned to inoculation (n = 12 or control (n = 6 groups in each of two trials. In trial 1, pigs were inoculated with a tissue homogenate collected from clinically affected field cases. In trial 2, pigs were inoculated with a pure broth culture of strain 30446. In both trials, mucohaemorrhagic diarrhea was significantly more common in inoculated pigs than controls, all of which remained healthy. In animals with mucohaemorrhagic diarrhea, significantly more spirochetes were observed on Gram stained fecal smears, and higher numbers of strain 30446 genome equivalents were detected by quantitative PCR (qPCR. Strain 30446 was cultured from colon and/or feces of all affected but no control animals at necropsy. CONCLUSIONS: "Brachyspira hampsonii" strain 30446 causes mucohaemorrhagic diarrhea in pigs following a 4-9 day incubation period. Fecal shedding was detectable by day 4 post inoculation, and rarely preceded the onset of mucoid or haemorrhagic diarrhea by more than 2 days. Culture and 30446-specific qPCR are reliable methods of detection of this organism in feces and tissues of diarrheic pigs. The emergence of a novel Brachyspira spp., such as "B. hampsonii", creates diagnostic challenges including higher risk of false negative diagnostic tests. We therefore

  1. Reproduction of Mucohaemorrhagic Diarrhea and Colitis Indistinguishable from Swine Dysentery following Experimental Inoculation with “Brachyspira hampsonii” Strain 30446

    Science.gov (United States)

    Rubin, Joseph E.; Costa, Matheus O.; Hill, Janet E.; Kittrell, Heather E.; Fernando, Champika; Huang, Yanyun; O’Connor, Brendan; Harding, John C. S.

    2013-01-01

    Background Mucohaemorrhagic diarrhea caused by Brachyspira hyodysenteriae, swine dysentery, is a severe production limiting disease of swine. Recently, pigs in western Canada with clinical signs indistinguishable from swine dysentery were observed. Despite the presence of spirochetes on fecal smears, recognized Brachyspira spp. including B. hyodysenteriae could not be identified. A phylogenetically distinct Brachyspira, called “B. hampsonii” strain 30446, however was isolated. The purpose of this study was to experimentally reproduce mucohaemorrhagic colitis and characterize strain 30446 shedding following inoculation. Methods and Findings Eighteen 13-week-old pigs were randomly assigned to inoculation (n = 12) or control (n = 6) groups in each of two trials. In trial 1, pigs were inoculated with a tissue homogenate collected from clinically affected field cases. In trial 2, pigs were inoculated with a pure broth culture of strain 30446. In both trials, mucohaemorrhagic diarrhea was significantly more common in inoculated pigs than controls, all of which remained healthy. In animals with mucohaemorrhagic diarrhea, significantly more spirochetes were observed on Gram stained fecal smears, and higher numbers of strain 30446 genome equivalents were detected by quantitative PCR (qPCR). Strain 30446 was cultured from colon and/or feces of all affected but no control animals at necropsy. Conclusions “Brachyspira hampsonii” strain 30446 causes mucohaemorrhagic diarrhea in pigs following a 4–9 day incubation period. Fecal shedding was detectable by day 4 post inoculation, and rarely preceded the onset of mucoid or haemorrhagic diarrhea by more than 2 days. Culture and 30446-specific qPCR are reliable methods of detection of this organism in feces and tissues of diarrheic pigs. The emergence of a novel Brachyspira spp., such as “B. hampsonii”, creates diagnostic challenges including higher risk of false negative diagnostic tests. We therefore recommend

  2. Reproduction of mucohaemorrhagic diarrhea and colitis indistinguishable from swine dysentery following experimental inoculation with "Brachyspira hampsonii" strain 30446.

    Science.gov (United States)

    Rubin, Joseph E; Costa, Matheus O; Hill, Janet E; Kittrell, Heather E; Fernando, Champika; Huang, Yanyun; O'Connor, Brendan; Harding, John C S

    2013-01-01

    Mucohaemorrhagic diarrhea caused by Brachyspira hyodysenteriae, swine dysentery, is a severe production limiting disease of swine. Recently, pigs in western Canada with clinical signs indistinguishable from swine dysentery were observed. Despite the presence of spirochetes on fecal smears, recognized Brachyspira spp. including B. hyodysenteriae could not be identified. A phylogenetically distinct Brachyspira, called "B. hampsonii" strain 30446, however was isolated. The purpose of this study was to experimentally reproduce mucohaemorrhagic colitis and characterize strain 30446 shedding following inoculation. Eighteen 13-week-old pigs were randomly assigned to inoculation (n = 12) or control (n = 6) groups in each of two trials. In trial 1, pigs were inoculated with a tissue homogenate collected from clinically affected field cases. In trial 2, pigs were inoculated with a pure broth culture of strain 30446. In both trials, mucohaemorrhagic diarrhea was significantly more common in inoculated pigs than controls, all of which remained healthy. In animals with mucohaemorrhagic diarrhea, significantly more spirochetes were observed on Gram stained fecal smears, and higher numbers of strain 30446 genome equivalents were detected by quantitative PCR (qPCR). Strain 30446 was cultured from colon and/or feces of all affected but no control animals at necropsy. "Brachyspira hampsonii" strain 30446 causes mucohaemorrhagic diarrhea in pigs following a 4-9 day incubation period. Fecal shedding was detectable by day 4 post inoculation, and rarely preceded the onset of mucoid or haemorrhagic diarrhea by more than 2 days. Culture and 30446-specific qPCR are reliable methods of detection of this organism in feces and tissues of diarrheic pigs. The emergence of a novel Brachyspira spp., such as "B. hampsonii", creates diagnostic challenges including higher risk of false negative diagnostic tests. We therefore recommend diagnostic laboratories routinely use Brachyspira culture

  3. Bestimmung der Antibiotikaempfindlichkeit bei Brachyspira spp.-Stämmen von deutschen Mastschweinen aus den Jahren 2003 - 2005

    OpenAIRE

    Schlez, Karen

    2011-01-01

    Die Schweinedysenterie hat nach wie vor grosse Bedeutung für die Schweineproduktion. Neben prophylaktischen Massnahmen steht die antibiotische Therapie im Vordergrund. Für den Therapieerfolg spielt die Antibiotikaempfindlichkeit des Erregers Brachyspira (B.) hyodysenteriae gegenüber den eingesetzten Chemotherapeutika eine entscheidende Rolle. Die Bestimmung der Antibiotikaempfindlichkeit von Brachyspiren, die vorab aus deutschen Schweinebeständen isoliert und anschließend im La...

  4. MALDI-TOF MS analysis of human and animal Brachyspira species and benefits of database extension.

    Science.gov (United States)

    Calderaro, Adriana; Piccolo, Giovanna; Montecchini, Sara; Buttrini, Mirko; Gorrini, Chiara; Rossi, Sabina; Arcangeletti, Maria Cristina; De Conto, Flora; Medici, Maria Cristina; Chezzi, Carlo

    2013-01-14

    Spirochaetes belonging to the genus Brachyspira are anaerobic bacteria that colonize the large intestine of humans and animals, mainly pigs. The main species are namely, B. hyodysenteriae, the etiological agent of swine dysentery, B. pilosicoli, a zoonotic agent causing colonic spirochaetosis both in humans and different animal species, B. aalborgi, exclusively infecting humans causing colonic spirochaetosis, B. intermedia, a potential animal pathogen, B. innocens and B. murdochii, generally commensal of pigs, and B. alvinipulli, found in egg laying hens with diarrhea. In this study, for the first time, MALDI-TOF MS was applied on Brachyspira strains of human and animal origins, supplementing the existing database, limited to the species B. murdochii only, with spirochaetal protein profiles and demonstrating its usefulness in the rapid, cheap and reliable identification of Brachyspira strains at the species level, overcoming the problems previously encountered in the identification of these spirochaetes when using biochemical and genetic-based methods. Moreover, a dendrogram based on protein profiles of the different spirochaetal species was generated reflecting their host spectrum, showing in the same branch the only two species able to infect humans (B. aalborgi and B. pilosicoli) and in the other branch the spirochaetes infecting exclusively animals. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Phenotypic and molecular characterization of Brachyspira spp. isolated from laying hens in different housing systems.

    Science.gov (United States)

    Jansson, D S; Fellström, C; Råsbäck, T; Vågsholm, I; Gunnarsson, A; Ingermaa, F; Johansson, K-E

    2008-08-25

    Several species of intestinal spirochaetes, Brachyspira (B.) alvinipulli, B. intermedia and B. pilosicoli, may cause reduced egg production and faecal staining of eggshells in chickens. The aim of this study was to characterize potentially pathogenic and presumably non-pathogenic Brachyspira spp. from commercial laying hens. Selective culture, phenotyping, PCR and 16S rRNA gene sequencing were used and clinical data were collected. Phenotypic profiles were obtained for 489 isolates and 351 isolates obtained after subculture, and 30 isolates were selected for molecular characterization. Seven isolates were positive by a B. intermedia-specific PCR based on the nox gene, and two were positive in a B. hyodysenteriae-specific 23S rRNA gene based PCR. By comparative phylogenetic analysis in combination with PCR and phenotyping, seven isolates were identified as B. intermedia, eight isolates as B. innocens, five as B. murdochii, and three isolates each as B. alvinipulli and "B. pulli". The remaining four isolates could not be assigned to any presently recognized species. Co-infection with several species or genetic variants of Brachyspira spp. were detected in some flocks and samples, suggesting a high level of diversity. Organic flocks with access to outdoor areas were at higher risk (RR=2.3; 95% CI 1.5-3.6) for being colonized than chickens in other housing systems. No significant differences between colonized and non-colonized flocks were found regarding clinical parameters, i.e. mortality, egg production, faecally contaminated eggshells, and wet litter. Our results show that a combination of traditional laboratory diagnostics, molecular tests and phylogeny is needed for identification of Brachyspira sp. from chickens.

  6. Brachyspira murdochii colitis in pigs

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Christensen, A. S.; Boye, Mette

    2010-01-01

    The weakly beta-hemolytic porcine spirochete Brachyspira murdochii is considered a normal intestinal commensal. In the present study, however, a field case of B murdochii–associated catarrhal colitis was identified in a pig, as characterized by extensive spirochetal colonization of the surface...... epithelium. Experimentally, 8 weaned pigs were challenged with the B murdochii isolate, reproducing catarrhal colitis in 2 animals. By applying fluorescent in situ hybridization using a species-specific oligonucleotide probe targeting 23S rRNA, B murdochii organisms were found in high numbers and were...... closely associated with the surface epithelium in the pigs with catarrhal colitis. The results indicate that, when present in high numbers, B murdochii is low pathogenic for pigs....

  7. Improved selective medium for the isolation of Treponema hyodysenteriae.

    OpenAIRE

    Kunkle, R A; Kinyon, J M

    1988-01-01

    An agar medium with improved selection for Treponema hyodysenteriae was developed. Cultures of T. hyodysenteriae and T. innocens, feces from 11 clinically normal pigs, and colonic contents from 6 pigs with gross lesions consistent with swine dysentery were diluted in phosphate-buffered saline and plated on Trypticase soy agar (BBL Microbiology Systems, Cockeysville, Md.) with 5% citrated bovine blood (TSA), TSA with 400 micrograms of spectinomycin per ml (TSA-S400), TSA-S400 with 25 microgram...

  8. Antimicrobial susceptibility pattern of Brachyspira intermedia isolates from European layers.

    Science.gov (United States)

    Verlinden, Marc; Boyen, Filip; Pasmans, Frank; Garmyn, An; Haesebrouck, Freddy; Martel, An

    2011-09-01

    A broth microdilution method was used to determine the antimicrobial susceptibility of 20 Brachyspira intermedia isolates obtained from different layer flocks in Belgium and The Netherlands between 2008 and 2010. The antimicrobial agents used were tylosin, tilmicosin, tiamulin, valnemulin, doxycycline, and lincomycin. The minimal inhibitory concentration (MIC) distribution patterns of tylosin, tilmicosin, lincomycin, and doxycycline were bimodal, demonstrating acquired resistance against doxycycline in three strains, against the macrolides in two strains, and against lincomycin in one strain. The MICs of tiamulin and valnemulin showed a monomodal distribution, but with tailing toward the higher MIC values, possibly suggesting low-level acquired resistance in six isolates. Sequencing revealed a G1058C mutation in the 16S rRNA gene in all doxycycline-resistant strains. The strain resistant to tylosin, tilmicosin, and lincomycin had an A2058T mutation in the 23S rRNA gene.

  9. First identification of "Brachyspira hampsonii" in wild European waterfowl.

    Directory of Open Access Journals (Sweden)

    Francisco Javier Martínez-Lobo

    Full Text Available Anseriformes deserve special attention in the epidemiology of Brachyspira spp. because diverse Anseriformes species have been described to act as highly efficient carriers of several Brachyspira spp. that can also infect livestock. The aim of this study was to investigate the prevalence and diversity of Brachyspira spp. in waterfowl that winter in Spain. Brachyspira spp. were isolated from 51 of the 205 faecal samples collected from graylag geese and mallards in the Villafáfila Lagoons Nature Reserve (Northwestern Spain. The Brachyspira species identified through phenotyping, PCR and sequencing of the nox gene were B. pilosicoli (5.9%, B. alvinipulli (11.8%, "B. hampsonii" (19.6%, B. murdochii (23.5% and B. innocens (39.2%. The most relevant finding of this study is the description of "B. hampsonii" in specimens from birds for the first time. Phylogenetic analysis of the nox gene sequences grouped all of the obtained "B. hampsonii" isolates into a cluster with Brachyspira strains previously identified by others as "B. hampsonii" and separated from other Brachyspira spp. isolates and reference strains. Additionally, this cluster was related to clades that grouped B. murdochii and B. innocens isolates. The identification of "B. hampsonii" was also achieved in 8 of the 10 isolates by sequencing the16S rRNA gene and tlyA gene. Regardless of the species identified, no antimicrobial resistance was observed in any of the enteropathogenic isolates recovered. This is the first description of "B. hampsonii" in European waterfowl, which might represent hosts that serve as natural reservoirs of this Brachyspira species. This finding indicates that this spirochete is not limited to North America, and its presence in wild birds in Europe poses a risk of transmission to livestock.

  10. Tiamulin resistance in porcine Brachyspira pilosicoli isolates.

    Science.gov (United States)

    Pringle, M; Landén, A; Franklin, A

    2006-02-01

    There are few studies on antimicrobial susceptibility of Brachyspira pilosicoli, therefore this study was performed to investigate the situation among isolates from pigs. The tiamulin and tylosin susceptibility was determined by broth dilution for 93 and 86 porcine B. pilosicoli isolates, respectively. The isolates came from clinical samples taken in Swedish pig herds during the years 2002 and 2003. The tylosin minimal inhibitory concentration (MIC) was >16 microg/ml for 50% (n=43) of the isolates tested. A tiamulin MIC >2 microg/ml was obtained for 14% (n=13) of the isolates and these were also tested against doxycycline, salinomycin, valnemulin, lincomycin and aivlosin. For these isolates the susceptibility to salinomycin and doxycycline was high but the MICs for aivlosin varied. The relationship between the 13 tiamulin resistant isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Among the 13 isolates 10 different PFGE patterns were identified.

  11. Brachyspira pilosicoli-induced avian intestinal spirochaetosis

    Directory of Open Access Journals (Sweden)

    Caroline I. Le Roy

    2015-12-01

    Full Text Available Avian intestinal spirochaetosis (AIS is a common disease occurring in poultry that can be caused by Brachyspira pilosicoli, a Gram-negative bacterium of the order Spirochaetes. During AIS, this opportunistic pathogen colonises the lower gastrointestinal (GI tract of poultry (principally, the ileum, caeca, and colon, which can cause symptoms such as diarrhoea, reduced growth rate, and reduced egg production and quality. Due to the large increase of bacterial resistance to antibiotic treatment, the European Union banned in 2006 the prophylactic use of antibiotics as growth promoters in livestock. Consequently, the number of outbreaks of AIS has dramatically increased in the UK resulting in significant economic losses. This review summarises the current knowledge about AIS infection caused by B. pilosicoli and discusses various treatments and prevention strategies to control AIS.

  12. Association of Serpulina hyodysenteriae with the colonic mucosa in experimental swine dysentery studied by fluorescent in situ hybridization

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Møller, Kristian

    1998-01-01

    The localization of Serpulina hyodysenteriae in experimental swine dysentery was studied by fluorescent in situ hybridization (FISH) using an oligonucleotide probe targeting the 23S rRNA of S. hyodysenteriae. Nine 8-week-old pigs were challenged. Seven of the pigs were intragastrically dosed with 1......x10(9) cfu S. hyodysenteriae for 3 consecutive days, whereas two pigs were infected by contact. Six non-challenged pigs served as negative controls. The challenged pigs developed clinical swine dysentery from 8 to 14 days postinfection with typical gross lesions. By FISH S. hyodysenteriae cells...... in the adjacent lamina propria. The distribution of spirochaetes in the mucosa provides further evidence that S. hyodysenteriae is intimately associated with the mucus layer and the epithelium in a random pattern. Furthermore, the results demonstrate the applicability of FISH for specific detection of S...

  13. In vitro sensitivity of poultry Brachyspira isolates to essential oil components and in vivo reduction of Brachyspira intermedia in rearing pullets with cinnamaldehyde feed supplementation

    OpenAIRE

    Verlinden, Marc; Pasmans, Frank; Mahu, Maxime; Vande Maele, Lien; De Pauw, Nele; YANG Zhen; Haesebrouck, Freddy; Martel, An

    2013-01-01

    Cecal enteritis due to Brachyspira infections tends to be chronic in laying hens. Limited availability of antimicrobial drugs for use in laying hens emphasizes the need for alternative control measures. A broth microdilution method was used to determine the antimicrobial susceptibility of 20 Brachyspira intermedia field isolates from laying hen flocks to components of essential oils (EO). Minimal inhibitory concentration (MIC) distributions, obtained for eight EO components, were all monomoda...

  14. Risk factors for intestinal pathogens in Danish finishing pig herds

    DEFF Research Database (Denmark)

    Stege, H.; Jensen, Tim Kåre; Møller, Kristian

    2001-01-01

    The objective of this investigation was to identify risk factors for infection with the intestinal bacteria: Lawsonia intracellularis, Brachyspira hyodysenteriae, Serpulina intermedia, Brachyspira innocens, Brachyspira pilosicoli and swine-pathogenic Escherichia coli (serogroups O138, O139, O141...

  15. In vitro sensitivity of poultry Brachyspira intermedia isolates to essential oil components and in vivo reduction of Brachyspira intermedia in rearing pullets with cinnamaldehyde feed supplementation.

    Science.gov (United States)

    Verlinden, M; Pasmans, F; Mahu, M; Vande Maele, L; De Pauw, N; Yang, Z; Haesebrouck, F; Martel, A

    2013-05-01

    Cecal enteritis due to Brachyspira infections tends to be chronic in laying hens. Limited availability of antimicrobial drugs for use in laying hens emphasizes the need for alternative control measures. A broth microdilution method was used to determine the antimicrobial susceptibility of 20 Brachyspira intermedia field isolates from laying hen flocks to components of essential oils (EO). Minimal inhibitory concentration (MIC) distributions, obtained for 8 EO components, were all monomodal. Cinnamaldehyde had the lowest MIC values (40 to 80 mg/L), followed by nerolidol, capsaicin, carvacrol, and thymol (80 to 320 mg/L), eugenol (160 to 640 mg/L), and linalool (320 to 1,280 mg/L). The MIC ranges of piperine were mostly above the test range of 1,280 mg/L. In an in vivo experiment, coated trans-cinnamaldehyde was supplemented to the feed of rearing pullets. A completely randomized experimental design with 4 treatments and 3 replicates each (replicate = group of seven 1-d-old laying hen chickens) was applied. The negative and positive controls received a conventional feed during the whole trial. The positive controls were orally inoculated on 3 consecutive days (d 22, 23, and 24) with 1 mL of 1.0 × 10(8) cfu/mL of a B. intermedia field isolate. Two treatment groups (preventive and curative), identically inoculated, received the coated trans-cinnamaldehyde-supplemented feed (500 mg/kg of trans-cinnamaldehyde), the preventive group from d 1, the curative from d 25. On d 32, ceca were collected for bacteriologic Brachyspira enumeration. The mean enumeration of Brachyspira cells was decreased (P feed supplemented with coated trans-cinnamaldehyde. Further studies are necessary to investigate the mode of action of the coated trans-cinnamaldehyde in reducing Brachyspira colonization of the ceca.

  16. Scanning electron microscopy and fluorescent in situ hybridization of experimental Brachyspira (Serpulina) pilosicoli infection in growing pigs

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Møller, Kristian; Boye, Mette

    2000-01-01

    Two groups of six 8-week-old pigs were challenged with 1X10(9) cfu Brachyspira (Serpulina) pilosicoli or Serpulina intermedia daily for 3 consecutive days to study the pathology of porcine colonic spirochetosis by scanning electron microscopy (SEM) and fluorescent in situ hybridization (FISH...... of the S. intermedia-inoculated pigs and the control pigs appeared normal. SEM examination of B. pilosicoli-infected pigs revealed degenerated epithelial cells and spirochetal colonization of the colonic mucosa in four pigs. By FISH, B. pilosicoli cells were found colonizing and invading the surface...... mucosa of four pigs by FISH. The results provide further evidence that B. pilosicoli is associated with colitis in pigs, although the gross lesions are mild. The spirochete is capable of colonizing the large intestine, inducing mucosal damage, invasion of the crypt and surface epithelium, and focal...

  17. Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).

    Science.gov (United States)

    Jansson, Désirée S; Pringle, Märit

    2011-08-01

    In vitro antimicrobial susceptibility to tylosin, valnemulin, tiamulin, doxycycline, lincomycin and ampicillin was investigated by broth dilution in 48 Brachyspira spp. isolates from commercial laying hens (n=30) and free-living wild mallards (Anas platyrhynchos) (n=18). Presumed pathogens (Brachyspira alvinipulli, Brachyspira intermedia, Brachyspira pilosicoli), commensals (Brachyspira murdochii, Brachyspira innocens, "Brachyspira pulli"), and isolates of undetermined species affiliation were included. The laying hens had not been exposed to therapeutic levels of antimicrobials for at least 50 weeks before sampling, and low levels of environmental antimicrobial exposure were presumed in mallards. No isolates with decreased susceptibility to tylosin, valnemulin, tiamulin or doxycycline were found. Decreased susceptibility to lincomycin (minimum inhibitory concentration 16 µg/ml) was detected in two isolates (Brachyspira sp.) from laying hens. Five isolates showed decreased susceptibility to ampicillin (minimum inhibitory concentration 16 to >32 µg/ml), including two "B. pulli" and one B. alvinipulli from laying hens, and isolates of B. pilosicoli and "B. pulli" from mallards. Decreased susceptibility to ampicillin was associated with β-lactamase activity in four isolates. A new variant of a class D β-lactamase gene designated bla (oxa-192) was identified in a B. pilosicoli isolate of mallard origin. This is the first time the genetic basis for antimicrobial resistance is described in Brachyspira spp. from a free-living wild bird. Isolates displaying decreased susceptibility to ampicillin were accompanied by fully susceptible isolates of the same species or other genotypes within three laying hen flocks. This underlines the need for performing antimicrobial susceptibility tests on single clones/genotypes, and to analyse multiple isolates from the same flock.

  18. Intestinal spirochaetes (genus Brachyspira colonise wild birds in the southern Atlantic region and Antarctica

    Directory of Open Access Journals (Sweden)

    Désirée S. Jansson

    2015-11-01

    Full Text Available Introduction: The genus Brachyspira contains well-known enteric pathogens of veterinary significance, suggested agents of colonic disease in humans, and one potentially zoonotic agent. There are recent studies showing that Brachyspira are more widespread in the wildlife community than previously thought. There are no records of this genus in wildlife from the southern Atlantic region and Antarctica. Our aim was therefore, to determine whether intestinal spirochaetes of genus Brachyspira colonise marine and coastal birds in this region. Method: Faecal samples were collected from marine and coastal birds in the southern Atlantic region, including sub-Antarctic islands and Antarctica, in 2002, 2009, and 2012, with the aim to isolate and characterise zoonotic agents. In total, 205 samples from 11 bird species were selectively cultured for intestinal spirochaetes of genus Brachyspira. To identify isolates to species level, they were subjected to phenotyping, species-specific polymerase chain reactions, sequencing of partial 16S rRNA, NADH oxidase (nox, and tlyA genes, and phylogenetic analysis. Antimicrobial susceptibility tests were performed. Results: Fourteen unique strains were obtained from 10 birds of three species: four snowy sheathbills (Chionis albus, three kelp geese (Chloephaga hybrida subsp. malvinarum, and three brown skua (Stercorarius antarcticus subsp. lonnbergi sampled on the Falkland Islands, Tierra del Fuego in Argentina, South Georgia, South Shetland Islands, and the Antarctic Peninsula. Five Brachyspira strains were closely related to potentially enteropathogenic Brachyspira sp. of chickens: B. intermedia (n=2, from snowy sheathbills, and B. alvinipulli (n=3, from a kelp goose and two snowy sheathbills. Three strains from kelp geese were most similar to the presumed non-pathogenic species ‘B. pulli’ and B. murdochii, whereas the remaining six strains could not be attributed to currently known species. No isolates related to

  19. Intestinal spirochaetes (genus Brachyspira) colonise wild birds in the southern Atlantic region and Antarctica.

    Science.gov (United States)

    Jansson, Désirée S; Mushtaq, Memoona; Johansson, Karl-Erik; Bonnedahl, Jonas; Waldenström, Jonas; Andersson, Dan I; Broman, Tina; Berg, Charlotte; Olsen, Björn

    2015-01-01

    The genus Brachyspira contains well-known enteric pathogens of veterinary significance, suggested agents of colonic disease in humans, and one potentially zoonotic agent. There are recent studies showing that Brachyspira are more widespread in the wildlife community than previously thought. There are no records of this genus in wildlife from the southern Atlantic region and Antarctica. Our aim was therefore, to determine whether intestinal spirochaetes of genus Brachyspira colonise marine and coastal birds in this region. Faecal samples were collected from marine and coastal birds in the southern Atlantic region, including sub-Antarctic islands and Antarctica, in 2002, 2009, and 2012, with the aim to isolate and characterise zoonotic agents. In total, 205 samples from 11 bird species were selectively cultured for intestinal spirochaetes of genus Brachyspira. To identify isolates to species level, they were subjected to phenotyping, species-specific polymerase chain reactions, sequencing of partial 16S rRNA, NADH oxidase (nox), and tlyA genes, and phylogenetic analysis. Antimicrobial susceptibility tests were performed. Fourteen unique strains were obtained from 10 birds of three species: four snowy sheathbills (Chionis albus), three kelp geese (Chloephaga hybrida subsp. malvinarum), and three brown skua (Stercorarius antarcticus subsp. lonnbergi) sampled on the Falkland Islands, Tierra del Fuego in Argentina, South Georgia, South Shetland Islands, and the Antarctic Peninsula. Five Brachyspira strains were closely related to potentially enteropathogenic Brachyspira sp. of chickens: B. intermedia (n=2, from snowy sheathbills), and B. alvinipulli (n=3, from a kelp goose and two snowy sheathbills). Three strains from kelp geese were most similar to the presumed non-pathogenic species 'B. pulli' and B. murdochii, whereas the remaining six strains could not be attributed to currently known species. No isolates related to human strains were found. None of the tested

  20. Intestinal spirochaetes (Brachyspira spp.) colonizing flocks of layer and breeder chickens in Malaysia.

    Science.gov (United States)

    Amin, Maswati Mat; Phillips, Nyree D; La, Tom; Robertson, Ian D; Hampson, David J

    2014-01-01

    Avian intestinal spirochaetosis causes problems including delayed onset of lay and wet litter in adult chickens, and results from colonization of the caecae/rectum with pathogenic intestinal spirochaetes (genus Brachyspira). Because avian intestinal spirochaetosis has not previously been studied in South East Asia, this investigation was undertaken in Malaysia. Faecal samples were collected from 25 farms and a questionnaire was administered. Brachyspira species were detected by polymerase chain reaction in 198 of 500 (39%) faecal samples from 20 (80%) farms, including 16 (94%) layer and four (50%) breeder farms. Pathogenic Brachyspira pilosicoli was identified in five (29%) layer and two (25%) breeder farms whilst pathogenic Brachyspira intermedia was detected in nine (53%) layer and one (12.5%) of the breeder farms. Twelve (80%) layer farms had egg production problems and 11 (92%) were positive for Brachyspira: three (25%) for B. pilosicoli and six (50%) for B. intermedia. Of three breeder farms with egg production problems, one was colonized with B. pilosicoli. Three of ten layer farms with wet litter were positive for B. pilosicoli and six for B. intermedia. Of four breeder farms with wet litter, one was colonized with B. pilosicoli and one with B. intermedia. No significant associations were found between colonization and reduced egg production or wet litter, perhaps because so many flocks were colonized. A significant association (P = 0.041) occurred between a high prevalence of colonization and faecal staining of eggs. There were significant positive associations between open-sided housing (P = 0.006), and flocks aged >40 weeks (P colonization by pathogenic species.

  1. Neither Hippurate-negative Brachyspira pilosicoli nor Brachyspira pilosicoli Type Strain Caused Diarrhoea in Early-weaned Pigs by Experimental Infection

    Directory of Open Access Journals (Sweden)

    Pelkola K

    2005-12-01

    Full Text Available A hippurate-negative biovariant of Brachyspira pilosicoli (B. pilosicolihipp- is occasionally isolated in diarrhoeic pigs in Finland, often concomitantly with hippurate-positive B. pilosicoli or Lawsonia intracellularis. We studied pathogenicity of B. pilosicolihipp- with special attention paid to avoiding co-infection with other enteric pathogens. Pigs were weaned and moved to barrier facilities at the age of 11 days. At 46 days, 8 pigs were inoculated with B. pilosicolihipp- strain Br1622, 8 pigs were inoculated with B. pilosicoli type strain P43/6/78 and 7 pigs were sham-inoculated. No signs of spirochaetal diarrhoea were detected; only one pig, inoculated with P43/6/78, had soft faeces from day 9 to 10 post inoculation. The pigs were necropsied between days 7 and 23 after inoculation. Live pigs were culture-negative for Brachyspira spp., but B. pilosicolihipp- was reisolated from necropsy samples of two pigs. The lesions on large colons were minor and did not significantly differ between the three trial groups. In silver-stained sections, invasive spirochaetes were detected in colonic mucosae of several pigs in all groups. Fluorescent in situ hybridisation for genus Brachyspira, B. pilosicoli and strain Br1622 was negative. However, in situ detection for members of the genus Leptospira was positive for spirochaete-like bacteria in the colonic epithelium of several pigs in both infected groups as well as in the control group. L. intracellularis, Salmonella spp., Yersinia spp. and intestinal parasites were not detected. The failure of B. pilosicoli strains to cause diarrhoea is discussed with respect to infectivity of the challenge strains, absence of certain intestinal pathogens and feed and management factors.

  2. Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards

    OpenAIRE

    Jansson, Desiree Seger; Pringle, Märit

    2011-01-01

    Abstract In vitro antimicrobial susceptibility to tylosin, valnemulin, tiamulin, doxycycline, lincomycin and ampicillin was investigated by broth dilution in 48 Brachyspira spp. isolates from commercial laying hens (n=30) and free-living wild mallards (Anas platyrhynchos) (n=18). Presumed pathogens (B. alvinipulli, B. intermedia, B. pilosicoli), commensals (B. murdochii, B. innocens, ?B. pulli?), and isolates of undetermined species affiliation were included. The laying hens had no...

  3. Lactobacilli antagonize the growth, motility, and adherence of Brachyspira pilosicoli: a potential intervention against avian intestinal spirochetosis.

    Science.gov (United States)

    Mappley, Luke J; Tchórzewska, Monika A; Cooley, William A; Woodward, Martin J; La Ragione, Roberto M

    2011-08-01

    Avian intestinal spirochetosis (AIS) results from the colonization of the ceca and colorectum of poultry by pathogenic Brachyspira species. The number of cases of AIS has increased since the 2006 European Union ban on the use of antibiotic growth promoters, which, together with emerging antimicrobial resistance in Brachyspira, has driven renewed interest in alternative intervention strategies. Probiotics have been reported as protecting livestock against infection with common enteric pathogens, and here we investigate which aspects of the biology of Brachyspira they antagonize in order to identify possible interventions against AIS. The cell-free supernatants (CFS) of two Lactobacillus strains, Lactobacillus reuteri LM1 and Lactobacillus salivarius LM2, suppressed the growth of Brachyspira pilosicoli B2904 in a pH-dependent manner. In in vitro adherence and invasion assays with HT29-16E three-dimensional (3D) cells and in a novel avian cecal in vitro organ culture (IVOC) model, the adherence and invasion of B. pilosicoli in epithelial cells were reduced significantly by the presence of lactobacilli (P < 0.001). In addition, live and heat-inactivated lactobacilli inhibited the motility of B. pilosicoli, and electron microscopic observations indicated that contact between the lactobacilli and Brachyspira was crucial in inhibiting both adherence and motility. These data suggest that motility is essential for B. pilosicoli to adhere to and invade the gut epithelium and that any interference of motility may be a useful tool for the development of control strategies.

  4. Lactobacilli Antagonize the Growth, Motility, and Adherence of Brachyspira pilosicoli: a Potential Intervention against Avian Intestinal Spirochetosis ▿

    Science.gov (United States)

    Mappley, Luke J.; Tchórzewska, Monika A.; Cooley, William A.; Woodward, Martin J.; La Ragione, Roberto M.

    2011-01-01

    Avian intestinal spirochetosis (AIS) results from the colonization of the ceca and colorectum of poultry by pathogenic Brachyspira species. The number of cases of AIS has increased since the 2006 European Union ban on the use of antibiotic growth promoters, which, together with emerging antimicrobial resistance in Brachyspira, has driven renewed interest in alternative intervention strategies. Probiotics have been reported as protecting livestock against infection with common enteric pathogens, and here we investigate which aspects of the biology of Brachyspira they antagonize in order to identify possible interventions against AIS. The cell-free supernatants (CFS) of two Lactobacillus strains, Lactobacillus reuteri LM1 and Lactobacillus salivarius LM2, suppressed the growth of Brachyspira pilosicoli B2904 in a pH-dependent manner. In in vitro adherence and invasion assays with HT29-16E three-dimensional (3D) cells and in a novel avian cecal in vitro organ culture (IVOC) model, the adherence and invasion of B. pilosicoli in epithelial cells were reduced significantly by the presence of lactobacilli (P < 0.001). In addition, live and heat-inactivated lactobacilli inhibited the motility of B. pilosicoli, and electron microscopic observations indicated that contact between the lactobacilli and Brachyspira was crucial in inhibiting both adherence and motility. These data suggest that motility is essential for B. pilosicoli to adhere to and invade the gut epithelium and that any interference of motility may be a useful tool for the development of control strategies. PMID:21666022

  5. Antimicrobial susceptibility test in Brachyspira pilosicoli strains isolated from commercial layers farms in Colombia PRUEBAS DE SENSIBILIDAD FRENTE A AGENTES ANTIMICROBIANOS EN CEPAS DE Brachyspira pilosicoli AISLADAS A PARTIR DE PONEDORAS COMERCIALES EN COLOMBIA

    Directory of Open Access Journals (Sweden)

    Figueroa Ramìrez Judith

    2009-04-01

    Full Text Available Intestinal Spirochaetes of the genus Brachyspira cause important diseases in swine and poultry. An increasing problem in the presentation of resistant strains to the antimicrobial drugs usually used to treat the intestinal spirochaetosis in swine has been evidenced and this could be applicable to the isolations from poultry. There are very few reports of in vitro antimicrobial susceptibility of Brachyspira spp. isolated from birds. In this study the antimicrobial susceptibility of twelve Brachyspira pilosicoli isolates obtain from commercial layers was evaluated against tiamulin, tylosin and lincomycin establishing the Minimum Inhibitory Concentration (MIC by agar dilution technique. All bacteria analyzed were sensitive to tiamulin (MIC ≤0,1μg/ml, and lincomycin (MIC 1μg/ml and resistant to tylosin (MIC 5μg/ml.Las espiroquetas intestinales del género Brachyspira ocasionan enfermedades importantes en porcinos y aves. Se ha evidenciado un problema de incremento en la presentación de cepas resistentes a los antimicrobianos utilizados normalmente para tratar las espiroquetosis intestinales en porcinos, y esto podría ser aplicable a los aislamientos de aves. Hay muy pocos reportes de sensibilidad antimicrobiana in vitro de cepas de Brachyspira spp. Aisladas en aves. En este estudio se evaluó la sensibilidad de doce aislamientos de Brachyspira pilosicoli obtenidos de granjas de ponedoras comerciales a los agentes antimicrobianos tiamulina, tilosina y lincomicina, y se estableció la concentración mínima inhibitoria (CMI mediante la técnica de dilución en agar. Todas las bacterias analizadas fueron sensibles a tiamulina (CMI ≤0,1 μg/ml y lincomicina (CMI 1 μg/ml y resistentes a tilosina (CMI 5 μg/ml.

  6. Characterization of the fecal microbiota of pigs before and after inoculation with "Brachyspira hampsonii".

    Directory of Open Access Journals (Sweden)

    Matheus O Costa

    Full Text Available "Brachyspira hampsonii" causes disease indistinguishable from swine dysentery, and the structure of the intestinal microbiome likely plays a role in determining susceptibility of individual pigs to infection and development of clinical disease. The objectives of the current study were to determine if the pre-inoculation fecal microbiota differed between inoculated pigs that did (INOC MH or did not (INOC non-MH develop mucohaemorrhagic diarrhea following challenge with "B. hampsonii", and to quantify changes in the structure of the microbiome following development of clinical disease. Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at -8, -5, -3 and 0 days post-inoculation, and at termination. No significant differences in richness, diversity or taxonomic composition distinguished the pre-inoculation microbiomes of INOC MH and INOC non-MH pigs. However, the development of bloody diarrhea in inoculated pigs was associated with perturbation of the microbiota relative to INOC non-MH or sham-inoculated control pigs. Specifically, the fecal microbiota of INOC MH pigs was less dense (fewer total 16S rRNA copies per gram of feces, and had a lower Bacteroidetes:Firmicutes ratio. Further investigation of the potential long-term effects of Brachyspira disease on intestinal health and performance is warranted.

  7. Extensive intestinal spirochaetosis in pigs challenged with Brachyspira pilosicoli

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Boye, Mette; Møller, Kristian

    2004-01-01

    of the study). Mild mucosal reddening and flecks of pus characterized the gross lesions, while diffuse, catarrhal colitis was revealed microscopically in all animals. Intestinal spirochaetosis with moderate to densely packed end-attached B. pilosicoli organisms was revealed extensively on the mucosal surface...

  8. Specific detection of Serpulina hyodysenteriae and potentially pathogenic weakly beta-haemolytic porcine intestinal spirochetes by polymerase chain reaction targeting 23S rDNA

    DEFF Research Database (Denmark)

    Leser, Thomas; Møller, Kristian; Jensen, Tim Kåre

    1997-01-01

    of the clinically important S. hyodysenteriae and biochemical group II and IV. PCR amplification was accomplished with DNA extracted from bacterial colonies by a simple boiling procedure, and with DNA extracted directly from porcine stool samples using a bead beating extraction procedure. The level of detection...... for the direct extraction and amplification method was 5 x 10(5) cells added g(-1) normal faeces.......A 2470-bp section of the 23S ribosomal DNA from Serpulina hyodysenteriae and five biochemical ly different groups of weakly beta-haemolytic porcine intestinal Serpulina strains was sequenced. The similarity between the sequenced strains was high (96.85% to 99.84%). A phylogenetic tree was estimated...

  9. Detection of Lawsonia intracellularis, Serpulina hyodysenteriae, weakly beta-haemolytic intestinal spirochaetes, Salmonella enterica, and haemolytic Escherichia coli from swine herds with and without diarrhoea among growing pigs

    DEFF Research Database (Denmark)

    Møller, Kristian; Jensen, Tim Kåre; Jorsal, Sven Erik Lind

    1998-01-01

    was used together with conventional culture techniques to detect Serpulina hyodysenteriae, weakly beta-haemolytic intestinal spirochaetes (WBHIS), Salmonella enterica, and haemolytic Escherichia coli, in a case control study to examine selected risk factors for the development of diarrhoea in growing pigs......A polymerase chain reaction (PCR) was optimized to detect Lawsonia intracellularis in faeces from naturally infected pigs. By combining a boiling procedure to extract DNA and a nested PCR procedure, a detection limit at 2x10(2) bacterial cells per gram of faeces was achieved. The optimized PCR....... Herds with diarrhoea were selected as cases and randomly chosen herds without diarrhoea were chosen as controls. Infection with L. intracellularis significantly enhanced the chance of diarrhoea. S. hyodysenteriae, WBHIS group IV (Serpulina pilosicoli), and S. enterica were isolated only from case herds...

  10. PRUEBAS DE SENSIBILIDAD FRENTE A AGENTES ANTIMICROBIANOS EN CEPAS DE Brachyspira pilosicoli AISLADAS A PARTIR DE PONEDORAS COMERCIALES EN COLOMBIA

    Directory of Open Access Journals (Sweden)

    DM Álvarez

    2009-01-01

    Full Text Available Las espiroquetas intestinales del género Brachyspira ocasionan enfermedades importantes en porcinos y aves. Se ha evidenciado un problema de incremento en la presentación de cepas resistentes a los antimicrobianos utilizados normalmente para tratar las espiroquetosis intestinales en porcinos, y esto podría ser aplicable a los aislamientos de aves. Hay muy pocos reportes de sensibilidad antimicrobiana in vitro de cepas de Brachyspira spp. aisladas en aves. En este estudio se evaluó la sensibilidad de doce aislamientos de Brachyspira pilosicoli obtenidos de granjas de ponedoras comerciales a los agentes antimicrobianos tiamulina, tilosina y lincomicina, y se estableció la concentración mínima inhibitoria (CMImediante la técnica de dilución en agar. Todas las bacterias analizadas fueron sensibles a tiamulina (CMI ≤0,1 μg/ml y lincomicina (CMI 1 μg/ml y resistentes a tilosina (CMI 5 μg/ml.

  11. Rapid detection and identification of Brachyspira aalborgi from rectal biopsies and faeces of a patient.

    Science.gov (United States)

    Calderaro, Adriana; Villanacci, Vincenzo; Conter, Mauro; Ragni, Patrizia; Piccolo, Giovanna; Zuelli, Claudia; Bommezzadri, Simona; Guégan, Rozenn; Zambelli, Claudia; Perandin, Francesca; Arcangeletti, Maria Cristina; Medici, Maria Cristina; Manca, Nino; Dettori, Giuseppe; Chezzi, Carlo

    2003-03-01

    This study reports for the first time the detection of Brachyspira aalborgi in faeces and rectal biopsies of a female suffering for 3-4 months of abdominal pain with long-standing mucosal diarrhoea, rectal bleeding and suspected carcinoma of the rectum. After pre-treatment of samples (faeces and biopsies) with a liquid medium (trypticase soy broth-TSB) containing foetal calf serum (FCS, 10%) and spectinomycin and rifampicin (TSB-SR) the first detection of B. aalborgi isolate HBS1 was observed after 48 h in the primary plates of selective blood agar modified medium (BAM) containing spectinomycin and rifampicin (BAM-SR), where growth zones were signalled by a small weakly beta-haemolytic halo. Attempts to subculture spirochaetes in agar media failed. The new HBS1 isolate was only propagated in TSB broth and at electron microscopy it showed 4 endoflagella inserted at each tapered end. The phenotypic characterization of HBS1 demonstrated absence of hippurate hydrolysis, indole production, alpha-galactosidase, alpha- and beta-glucosidase activities in accordance with the B. aalborgi type strain. Rapid identification of B. aalborgi isolate HBS1 was performed directly from faeces and rectal biopsies and subsequently from pure cultures by a genetic method based on 16S DNA restriction fragment length polymorphism (RFLP)-polymerase chain reaction (PCR). The sequence of 16S DNA amplicon of the isolate HBS1 was found 99.2% corresponding to that of the B. aalborgi type strain. Our results encourage further investigations for the development of a suitable selective agar medium for the isolating and cultivating B. aalborgi from human specimens.

  12. Isolation of Brachyspira Pilocicoli from Gastrointestinal Tract of Commercial Chickens in Khuzestan, South West Iran

    Directory of Open Access Journals (Sweden)

    Leila Alavi

    2013-11-01

    Full Text Available Background: Brachyspira pilosicoli is an intestinal spirochete which colonizes in cecum, colon and rectum of the birds. This infection in broiler and laying chicken may cause disorders such as: diarrhea, reduced egg production, pasty vents, fecal staining of egg shells, poor shell quality, pale egg yolks, increased feed consumption, slower growth and poor feed digestion. Objectives: The aim of this study was to isolate and identify B. pilosicoli from broiler and laying chicken. Materials and Methods: This study was conducted by using bacteriological examination and PCR in Khuzestan located in the South West of Iran. Totally 150 samples of broiler chicken feces and 100 samples of laying chicken feces were collected. The samples were cultured on blood agar containing three antibiotics (vancomycin 12.5μg/mL, spiramaycin 25μg/mL and spectinomycin 400 μg/mL.The colonies of intestinal spirochetes were studied by PCR. Results: Intestinal spirochetes were isolated in 21 out of 150 fecal samples of broiler chicken and in 9 out of 100 fecal samples of laying chicken. Species identification of isolates was done by PCR using 16SrRNA gene specific for B. pilosicoli. B. pilosicoli was isolated in 13 out of 21 positive broilers and in 4 out of 9 positive laying chickens. Conclusions: This study showed that B. pilosicoli exists in the broiler and laying chicken in the region. This intestinal pathogen may be considered as a major cause of production threats and economic losses in chicken farms in the region of study.

  13. Demonstration of Brachyspira aalborgi lineages 2 and 3 in human colonic biopsies with intestinal spirochaetosis by specific fluorescent in situ hybridization

    DEFF Research Database (Denmark)

    Jensen, Tim Kåre; Teglbjærg, Peter S.; Lindboe, Christian F.

    2004-01-01

    Sequences of known 16S rRNA genes, derived from sequence analysis of cloned 16S rDNA, were used to design a specific oligonucleotide probe targeting spirochaetes of Brachyspira aalborgi lineages 2 and 3. The probe was used with fluorescent in situ hybridization to study the involvement of these o......Sequences of known 16S rRNA genes, derived from sequence analysis of cloned 16S rDNA, were used to design a specific oligonucleotide probe targeting spirochaetes of Brachyspira aalborgi lineages 2 and 3. The probe was used with fluorescent in situ hybridization to study the involvement...... of these organisms in human intestinal spirochaetosis. Seventeen human colonic biopsies from Norway and Denmark with intestinal spirochaetosis caused by Brachyspira-like organisms different from the type strain of B. aalborgi (lineage 1) were examined. Application of the probe gave a positive signal in two Norwegian...... biopsies, whereas the 15 other biopsies were hybridization-negative. The positive reaction visualized the spirochaetes as a fluorescent, 3-5 mum-high fringe on the surface epithelium, extending into the crypts. The study verified the presence of B. aalborgi lineages 2 and 3 and identified the bacteria...

  14. Brachyspira (Serpulina) pilosicoli of human origin interfere with the growth of Clostridium perfringens alpha-toxin producer.

    Science.gov (United States)

    Calderaro, A; Dettori, G; Ragni, P; Guégan, R; Arcangeletti, M C; Medici, M C; Chezzi, C

    2002-04-01

    Brachyspira (Serpulina) pilosicoli of human origin interfere with the growth of Clostridium perfringens alpha-toxin producer reducing the clostridial growth area and colonies number when bacteria were cultivated together in sheep blood agar plates. The growth inhibition of C. perfringens was only observed when B. (S.) pilosicoli grew 72-96 hours sooner than C. perfringens and after the inoculum of this latter the plates were anaerobically incubated for additional 48 hours. The phenomenon was observed at concentrations of B. (S.) pilosicoli ranging from 10(7) to 10(4) CFU/ml and at concentrations of C. perfringens ranging from 10(7) to 10(1) CFU/ml when the bacteria were 0-10 mm away from each other. When B. (S.) pilosicoli and C. perfringens were inoculated at the same time and when B. (S.) pilosicoli grew 24-48 hours sooner than C. perfringens, the clostridial growth inhibition was not appreciated and only a cooperative haemolysis was observed between the bacteria.

  15. The use of quantitative PCR for identification and quantification of Brachyspira pilosicoli, Lawsonia intracellularis and Escherichia coli fimbrial types F4 and F18 in pig feces

    DEFF Research Database (Denmark)

    Ståhl, Marie; Kokotovic, Branko; Hjulsager, Charlotte Kristiane

    2011-01-01

    Four quantitative PCR (qPCR) assays were evaluated for quantitative detection of Brachyspira pilosicoli, Lawsonia intracellularis, and E. coli fimbrial types F4 and F18 in pig feces. Standard curves were based on feces spiked with the respective reference strains. The detection limits from...... DNA from reference strains and feces spiked with the respective strains. The linear ranges found for spiked fecal samples differed both from the linear ranges from pure culture of the reference strains and between the qPCR tests. The linear ranges were five log units for F4- qPCR, and Laws-qPCR, six...

  16. Intestinal Spirochaetes of the Genus Share a Partially Conserved 26 Kilobase Genomic Region with and

    Directory of Open Access Journals (Sweden)

    Yair Motro

    2008-01-01

    Full Text Available Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species. Analysis of near-complete genome sequences of these two species identified a highly conserved 26 kilobase (kb region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplification was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli , and B. aalborgi , and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained five genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5’ end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer.

  17. Brachyspira (Serpulina) pilosicoli of human origin interfere with the haemolytic activity and the growth of Staphylococcus aureus beta-toxin producer.

    Science.gov (United States)

    Calderaro, A; Dettori, G; Ragni, P; Guegan, R; Arcangeletti, M C; Medici, M C; Chezzi, C

    2002-04-01

    Brachyspira (Serpulina) pilosicoli related to intestinal spirochaetosis were found to interfere in vitro with the haemolytic activity and the growth of Staphylococcus aureus beta-toxin producer. This interference was clearly appreciated because a reduction of the zone of the staphylococcal beta-toxin activity, the reduction and/or absence of cooperative haemolysis between bacteria, and the growth reduction of S. aureus were observed when B. (S.) pilosicoli were grown 72-96 hours sooner than S. aureus and after the inoculum of the latter the plates were anaerobically incubated for additional 48-72 hours. The phenomenon was more clearly observed when B. (S.) pilosicoli had a concentration of 8x10(6)-8x10(7) CFU/ml and S. aureus at a concentration ranging from 10(7) to 10(1) CFU/ml was inoculated at a distance from the streaks of B. (S.) pilosicoli ranging from 0-10 mm. When B. (S.) pilosicoli and S. aureus were inoculated at the same time and when B. (S.) pilosicoli grew 24-48 hours sooner than S. aureus only a cooperative haemolysis was observed.

  18. Effect of zinc chelate and valnemulin for the treatment of swine dysentery in an experimental challenge study.

    Science.gov (United States)

    Šperling, Daniel; Čížek, Alois; Smola, Jiří

    2014-02-01

    The aim of study was to determine the influence of zinc chelate, valnemulin and it's combination on Brachyspira hyodysenteriae shedding and morphological changes of colonic mucosa in an experimental model of swine dysentery (SD). The study was performed on pigs coming from a dysentery-free herd. Animals were inoculated by B. hyodysenteriae strain B204. When the clinical signs of SD and B. hyodysenteriae shedding developed, the pigs were divided into four treatment groups. The first group was treated with zinc chelate (250 ml/1000 L in water), second group was given valnemulin in feed at 75 ppm; the third group was given a combination of both and the fourth group was control. The results demonstrated therapeutic effect of valnemulin in pigs with serious SD and did not show therapeutic effect of chelated zinc. Copyright © 2013. Published by Elsevier Ltd.

  19. Agentes bacterianos enteropatogênicos em suínos de diferentes faixas etárias e perfil de resistência a antimicrobianos de cepas de Escherichia coli e Salmonella spp Enteropathogenic bacterial agents in pigs of different age groups and profile of resistance in strains of Escherichia coli and Salmonella spp. to antimicrobial agents

    Directory of Open Access Journals (Sweden)

    Álvaro Menin

    2008-09-01

    Full Text Available As enterites infecciosas bacterianas provocam severas perdas para a indústria suína em todo o mundo. Os objetivos deste trabalho foram determinar os agentes bacterianos, associados com a ocorrência de diarréia em suínos, em diferentes faixas etárias, no Estado de Santa Catarina, Brasil, e verificar o perfil de resistência das cepas de Escherichia coli e Salmonella spp, frente aos principais antimicrobianos utilizados em granjas de suínos. Os principais gêneros/espécies bacterianos diagnosticados foram Escherichia coli, Clostridium spp, Salmonella spp Brachyspira hyodysenteriae, Brachyspira pilosicoli e Lawsonia intracellularis. Os fatores de virulência de E. coli mais prevalentes na fase de maternidade foram F5 / (K99 20%, F6 / (987P 16,3%, F42 6,8% e F41 5,7%, já nas fases de creche e terminação, predominaram cepas com fimbrias F4 (K88 11,2% e 5,4%, respectivamente. Para E. coli os maiores índices de resistência foram encontrados para oxitetraciclina (94% e tetraciclina (89,5% e os menores índices de resistência para neomicina (55%, ceftiofur (57,4%. Quanto às amostras de Salmonella spp, estas apresentaram maior resistência à oxitetraciclina (77%, e à tetraciclina (42,1% e menor à gentamicina (3,5% e amoxicilina (4,8%.Infectious bacterial enteritis causes severe losses to the swine industry worldwide. The objective of this study was to determine the epidemiology of bacterial agents that are associated with the occurrence of diarrhea in pigs at different age groups, and to verify the profile of resistance of strains of Escherichia coli and Salmonella spp to the main antimicrobial agents. The main bacterial species diagnosed were Escherichia coli, Clostridium spp, Salmonella spp, Brachyspira hyodysenteriae, Brachyspira pilosicoli and Lawsonia intracellularis. The E. coli virulence factors of higher prevalence in preweaning piglets were F5 / (K99 20%, F6 / (987P 16.3%, F42 6.8% and F41 5.7%, whereas at the nursery and with

  20. Android Emotions Revealed

    DEFF Research Database (Denmark)

    Vlachos, Evgenios; Schärfe, Henrik

    2012-01-01

    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...

  1. 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...

  2. 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

  3. Mysterious Blob Galaxies Revealed

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2Figure 3 This image composite shows a giant galactic blob (red, figure 2) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow, figure 3). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images like the one shown in figure 2, reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together (figure 3). Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile.

  4. [Eradication of swine dysentery as modified partial depopulation in a nucleus sow breeding farm].

    Science.gov (United States)

    Figi; Goldinger; Fuschini; Hartnack; Sidler

    2014-08-01

    On a Swiss nucleus sow breeding farm with 170 sows and 600 gilts/fatteners, an eradication of swine dysentery as modified partial depopulation was conducted in stages over a period of 12 weeks in 2011 after Brachyspira (B.) hyodysenteriae was detected in the herd. In addition to administering oral medication (8.1 mg tiamulin per kg body weight) for 4 weeks to the pigs remaining on the farm, all stables were cleaned thoroughly and the residual slurry was disinfected with Alzogur(®) (3 l/m(3)) while the surfaces were disinfected with Venno Vet 1 Super(®) (1.5 %). At the same time rodent and fly control was intensified. Upon completion of the eradication programme, the farm was monitored for 6 months by carrying out fecal swab analyses of pigs with diarrhea. All fecal samples were negative for B. hyodysenteriae. The costs of the eradication amounted to approximately CHF 104'500. The eradication yielded significantly higher live daily weight gain (+ 23.8 g, ± 10.1 g, P per year.

  5. [Vulvar oedema revealing systemic mastocytosis].

    Science.gov (United States)

    Deveza, E; Locatelli, F; Girardin, M; Valmary-Degano, S; Daguindau, E; Aubin, F; Humbert, P; Pelletier, F

    2015-11-01

    Systemic mastocytosis is characterised by abnormal proliferation of mast cells in various organs. We report an original case of systemic mastocytosis revealed by vulvar oedema. A 24-year-old patient was examined in the dermatology department for vulvar oedema appearing during sexual intercourse. She presented vasomotor dysfunction of the lower limbs, urticaria on the trunk on exertion, diarrhoea and bone pains. Laboratory tests showed serum tryptase of 29.7μg and plasma histamine at twice the normal value. Myelogram results showed infiltration by dysmorphic mast cells. Screening for c-kit D816V mutation was positive. Duodenal biopsies revealed mast-cell clusters with aggregation involving over 15 mast cells. CD2 staining was inconclusive and CD25 staining could not be done. Trabecular osteopenia was found, and we thus made a diagnosis of indolent systemic mastocytosis (ISM variant Ia) as per the WHO 2008 criteria. Symptomatic treatment was initiated (antiH1, H2, antileukotrienes) and clinical and laboratory follow-up was instituted. The cutaneous signs leading to diagnosis in this patient of systemic mastocytosis involving several organs were seemingly minimal signs associated with mastocyte degranulation. This is the third recorded case of mastocytosis revealed by vulvar oedema and the first case revealing systemic involvement. The two previously reported cases of vulvar oedema revealed cutaneous mastocytosis alone. Mastocytosis, whether systemic or cutaneous, must be included among the differential diagnoses considered in the presence of vulvar oedema. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  6. 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...

  7. [Cervicofacial cellulitis revealing cutaneous lymphomas].

    Science.gov (United States)

    Benbouzid, M A; Bencheikh, R; Benhammou, A; El Edghiri, H; Boulaich, M; Essakali, L; Kzadri, M

    2007-06-01

    The cervicofacial localization of cutaneous lymphomas is rare. These lymphomas usually present as a long-lasting and treatment-refractory papule or nodule. Lymphomas can also be revealed by cervicofacial cellulitis. We report 2 cases of cervicofacial cellulitis revealing a cutaneous lymphoma. The diagnosis was proved by multiple biopsies, performed because there was no clinical improvement in spite of an aggressive and adequate antibiotherapy. Our 2 patients were treated by radio and chemotherapy. Cutaneous lymphomas are lymphocytic proliferations stemming from cutaneous lymphoid tissue, without nodal, medullary, or visceral localization. Their clinical presentation is quite polymorphic, and cellulitis is one of the modes of revelation, especially forehead and neck localization. They have no portal of entry and are resistant to treatment. The diagnosis relies on histology, and biopsies must be performed if there is a suspicion of lymphoma. The treatment is radio and chemotherapy, and the evolution depends on the tumoral stage.

  8. 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...

  9. 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.

  10. Neither hippurate-negative Brachyspira pilosicoli nor Brachyspira pilosicoli type strain caused diarrhoea in early-weaned pigs by experimental infection

    DEFF Research Database (Denmark)

    Fossi, M.; Ahlsten, K.; Pohjanvirta, T.

    2005-01-01

    and strain Br1622 was negative. However, in situ detection for members of the genus Leptospira was positive for spirochaete-like bacteria in the colonic epithelium of several pigs in both infected groups as well as in the control group. L. intracellularis, Salmonella spp., Yersinia spp. and intestinal...

  11. 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

  12. To Reveal Thy Heart Perchance to Reveal the World

    Directory of Open Access Journals (Sweden)

    Robert B. Faux

    2005-05-01

    Full Text Available Ronald PELIAS, a professor of speech communications, employs a variety of writing methods as examples of alternative ways to do research and to share with the reader a seldom seen and seldom considered aspect of academic life: Heart. In the early chapters of the book, PELIAS sets out to establish a way to place his Heart in the foreground; baring his emotional vulnerability, his humanness, his being in the world. Later chapters of the book encompass an autoethnographic study of academic life in which the previously revealed Heart is placed in context. In this review essay I discuss PELIAS' book in relation to the larger literature on autoethnography and subjectivist research; I follow this by discussing the need for and usefulness of such alternative methods using PELIAS' autoethnography of academic life as a context. URN: urn:nbn:de:0114-fqs050279

  13. Communication Games Reveal Preparation Contextuality

    Science.gov (United States)

    Hameedi, Alley; Tavakoli, Armin; Marques, Breno; Bourennane, Mohamed

    2017-12-01

    A communication game consists of distributed parties attempting to jointly complete a task with restricted communication. Such games are useful tools for studying limitations of physical theories. A theory exhibits preparation contextuality whenever its predictions cannot be explained by a preparation noncontextual model. Here, we show that communication games performed in operational theories reveal the preparation contextuality of that theory. For statistics obtained in a particular family of communication games, we show a direct correspondence with correlations in spacelike separated events obeying the no-signaling principle. Using this, we prove that all mixed quantum states of any finite dimension are preparation contextual. We report on an experimental realization of a communication game involving three-level quantum systems from which we observe a strong violation of the constraints of preparation noncontextuality.

  14. 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.

  15. Revealing Non-Covalent Interactions

    Science.gov (United States)

    Johnson, Erin R.; Keinan, Shahar; Mori-Sánchez, Paula; Contreras-García, Julia; Cohen, Aron J.; Yang, Weitao

    2010-01-01

    Molecular structure does not easily identify the intricate non-covalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. Our approach reveals underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of non-bonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands. PMID:20394428

  16. Hubble Images Reveal Jupiter's Auroras

    Science.gov (United States)

    1996-01-01

    These images, taken by the Hubble Space Telescope, reveal changes in Jupiter's auroral emissions and how small auroral spots just outside the emission rings are linked to the planet's volcanic moon, Io. The images represent the most sensitive and sharply-detailed views ever taken of Jovian auroras.The top panel pinpoints the effects of emissions from Io, which is about the size of Earth's moon. The black-and-white image on the left, taken in visible light, shows how Io and Jupiter are linked by an invisible electrical current of charged particles called a 'flux tube.' The particles - ejected from Io (the bright spot on Jupiter's right) by volcanic eruptions - flow along Jupiter's magnetic field lines, which thread through Io, to the planet's north and south magnetic poles. This image also shows the belts of clouds surrounding Jupiter as well as the Great Red Spot.The black-and-white image on the right, taken in ultraviolet light about 15 minutes later, shows Jupiter's auroral emissions at the north and south poles. Just outside these emissions are the auroral spots. Called 'footprints,' the spots are created when the particles in Io's 'flux tube' reach Jupiter's upper atmosphere and interact with hydrogen gas, making it fluoresce. In this image, Io is not observable because it is faint in the ultraviolet.The two ultraviolet images at the bottom of the picture show how the auroral emissions change in brightness and structure as Jupiter rotates. These false-color images also reveal how the magnetic field is offset from Jupiter's spin axis by 10 to 15 degrees. In the right image, the north auroral emission is rising over the left limb; the south auroral oval is beginning to set. The image on the left, obtained on a different date, shows a full view of the north aurora, with a strong emission inside the main auroral oval.The images were taken by the telescope's Wide Field and Planetary Camera 2 between May 1994 and September 1995.This image and other images and data

  17. Ocorrência e identificação de espiroquetas intestinais em suínos em granjas de porte industrial de duas regiões criatórias do Estado do Rio Grande do Sul, em relação à medicação da ração Ocurrence and identification of swine intestinal spirochetes in industrial pig herds from two raising areas in the State of Rio Grande do Ssul, Brazil, in relation to feed medication

    Directory of Open Access Journals (Sweden)

    David Emilio Barcellos

    2003-08-01

    Full Text Available As infecções intestinais por espiroquetas em suínos, na fase que se segue ao alojamento nos prédios de recria, são predispostas por fatores como o estresse da movimentação, mistura entre animais imunes e excretores com leitões não imunes, deficiências nas condições ambientais e troca no tipo da ração usada. Para contrabalançar esses efeitos, é uma prática rotineira a inclusão de antimicrobianos à ração, em doses de promoção de crescimento ou de controle. O presente trabalho avaliou a ocorrência da infecção por Brachyspira spp. em rebanhos suínos do Estado do Rio Grande do Sul, tentando relacionar com o tipo de programa de uso de antimicrobianos adotado. Foram examinados 393 suabes retais colhidos de 38 granjas do RS (22 usando rações medicadas e 16 com ração sem medicação. A B. hyodysenteriae e B. pilosicoli foram detectadas respectivamente em 0% e 6,25% das granjas medicadas e de 31,8% e 45,5% das granjas não medicadas. Entre os suabes examinados, a B. hyodysenteriae e B. pilosicoli estavam presentes respectivamente em 0 e 0,6% dos materiais colhidos de granjas medicadas e de 3,9% e 7,3% em granjas não medicadas. O presente trabalho suporta a opinião de diversos autores que sugeriram a influência direta da inclusão de antimicrobianos à ração em doses de promoção de crescimento ou em dose de controle e a ocorrência de diarréias espiroquetais em leitões. Entretanto, pelas características multifatoriais desse tipo de patologia, seriam necessários estudos adicionais abrangendo um número maior de variáveis entre aquelas possivelmente envolvidas no desencadeamento das diarréias, antes que fosse obtida uma conclusão definitiva.Intestinal spirochaetal infections in pigs following transportation to growing facilities is predisposed by stressful factors such as contact between carriers and non-immune piglets, defficient environment and diet changes. To neutralize such effects, it is a common practice to

  18. Tadpole begging reveals high quality.

    Science.gov (United States)

    Dugas, M B; Strickler, S A; Stynoski, J L

    2017-05-01

    Parents can benefit from allocating limited resources nonrandomly among offspring, and offspring solicitation (i.e. begging) is often hypothesized to evolve because it contains information valuable to choosy parents. We tested the predictions of three 'honest begging' hypotheses - Signal of Need, Signal of Quality and Signal of Hunger - in the tadpoles of a terrestrial frog (Oophaga pumilio). In this frog, mothers provision tadpoles with trophic eggs, and when mothers visit, tadpoles perform a putative begging signal by stiffening their bodies and vibrating rapidly. We assessed the information content of intense tadpole begging with an experimental manipulation of tadpole condition (need/quality) and food deprivation (hunger). This experiment revealed patterns consistent with the Signal of Quality hypothesis and directly counter to predictions of Signal of Need and Signal of Hunger. Begging effort and performance were higher in more developed and higher condition tadpoles and declined with food deprivation. Free-living mothers were unlikely to feed tadpoles of a nonbegging species experimentally cross-fostered with their own, and allocated larger meals to more developed tadpoles and those that vibrated at higher speed. Mother O. pumilio favour their high-quality young, and because their concurrent offspring are reared in separate nurseries, must do so by making active allocation decisions. Our results suggest that these maternal choices are based at least in part on offspring signals, indicating that offspring solicitation can evolve to signal high quality. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  19. 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

  20. Revealing conceptual understanding of international business

    NARCIS (Netherlands)

    Ashley, S.; Schaap, H.; Bruijn, E. de

    2017-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students’ conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual

  1. Revealing conceptual understanding of international business

    NARCIS (Netherlands)

    Ashley, S.M.; Schaap, H.; de Bruijn, E.

    2016-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students’ conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual

  2. Puerto Rico Revealed Preference Survey Data 2004

    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...

  3. Disease: H01454 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available Brachyspira genus, Brachyspira aalborgi and Brachyspira pilosicoli. B. pilosicoli induces disease in both humans and animals... A04.9 A69.9 PMID:16013401 (description) ... AUTHORS ... Smith JL ... TITLE ... Colonic spirochetosis in animals

  4. Revealing Conceptual Understanding of International Business

    Science.gov (United States)

    Ashley, Sue; Schaap, Harmen; de Bruijn, Elly

    2017-01-01

    This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students' conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual understanding in higher education. Essays and concept…

  5. [Cholangitis revealing an intrahepatic Osler's disease].

    Science.gov (United States)

    Asma, Kochlef; Dalila, Gargouri; Olfa, Bousnina; Malika, Romani; Afef, Kilani; Najet, BelHadg; Jamel, Kharrat; Abdeljabbar, Gorbel; Sarra, Shili; Chiraz, Jemli; Mohamed, Habib Daghfous; Slim, Khlifi; Anis, Ben Maamer; Abdelmajid, Letaïef

    2005-08-01

    Osler Weber Rendu Disease is an hereditary haemorrhagic télangectasia habitually revealed by reccurent bleeding (epistaxis). Hepatic involvement in Osler disease is found in 8 to 31%, manifested by cholestasis. We report an original observation of a cholangitis revealing Osler disease.

  6. Pleuromutilins: use in food-producing animals in the European Union, development of resistance and impact on human and animal health.

    Science.gov (United States)

    van Duijkeren, Engeline; Greko, Christina; Pringle, Märit; Baptiste, Keith Edward; Catry, Boudewijn; Jukes, Helen; Moreno, Miguel A; Pomba, M Constança Matias Ferreira; Pyörälä, Satu; Rantala, Merja; Ružauskas, Modestas; Sanders, Pascal; Teale, Christopher; Threlfall, E John; Torren-Edo, Jordi; Törneke, Karolina

    2014-08-01

    Pleuromutilins (tiamulin and valnemulin) are antimicrobial agents that are used mainly in veterinary medicine, especially for swine and to a lesser extent for poultry and rabbits. In pigs, tiamulin and valnemulin are used to treat swine dysentery, spirochaete-associated diarrhoea, porcine proliferative enteropathy, enzootic pneumonia and other infections where Mycoplasma is involved. There are concerns about the reported increases in the MICs of tiamulin and valnemulin for porcine Brachyspira hyodysenteriae isolates from different European countries, as only a limited number of antimicrobials are available for the treatment of swine dysentery where resistance to these antimicrobials is already common and widespread. The loss of pleuromutilins as effective tools to treat swine dysentery because of further increases in resistance or as a consequence of restrictions would present a considerable threat to pig health, welfare and productivity. In humans, only one product containing pleuromutilins (retapamulin) is authorized currently for topical use; however, products for oral and intravenous administration to humans with serious multidrug-resistant skin infections and respiratory infections, including those caused by methicillin-resistant Staphylococcus aureus (MRSA), are being developed. The objective of this review is to summarize the current knowledge on the usage of pleuromutilins, resistance development and the potential impact of this resistance on animal and human health. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  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. [Cervical Pott's disease revealed by retropharyngeal abscesses].

    Science.gov (United States)

    Benhammou, A; Bencheikh, R; Benbouzid, M-A; Boulaich, M; Essakali, L; Kzadri, M

    2007-12-01

    Retropharyngeal abscesses are exceptional in adults. The etiologies are numerous, cervical spine tuberculosis is one of them. We report two cases of cervical Pott's disease revealed by a retropharyngeal abscess. The clinical presentation was non-specific, dominated by oropharyngeal obstruction. Radiological findings suggested the diagnosis, showing a retropharyngeal collection with vertebral osteolysis. The bacteriological and histological assessment confirmed the diagnosis. The evolution was favorable after treatment by antituberculosis drugs. Vertebral tuberculosis is rare. Cervical involvement is exceptional, and retropharyngeal abscesses can be the revealing feature of this condition. Symptoms are not specific. The diagnosis is based on radiological and bacteriological assessment. Treatment with antituberculosis drugs leads to a good outcome.

  9. Revealed preference analysis of noncooperative household consumption

    NARCIS (Netherlands)

    Cherchye, L.J.H.; Demuynck, T.; de Rock, B.

    2011-01-01

    We develop a revealed preference approach to analyse non-unitary household consumption behaviour that is not cooperative (or Pareto efficient). We derive global necessary and sufficient conditions for data consistency with the model. We show that the conditions can be verified by means of relatively

  10. Revealed preference tests for collective household behavior

    NARCIS (Netherlands)

    Cherchye, L.J.H.; de Rock, B.; Vermeulen, F.M.P.; Verriest, E.; Molina, J.A.

    2011-01-01

    This chapter contains a state of the art of revealed preference tests for consistency of observed household behavior with Pareto efficiency. These tests are entirely nonparametric, since they do not require any assumptions regarding the parametric form of individual preferences or the intrahousehold

  11. Hypoglycemia revealing arachnoidocele in infant | Jellouli | Pan ...

    African Journals Online (AJOL)

    Arachnoidocele is characterized by the herniation of the subarachnoid space within the sella turcica, associated with some degree of flattening of the pituitary ... An exploration of the pituitary was requested, finding an achievement of the cortical axis revealed by the occurrence of multiple episodes of hypoglycemia with ...

  12. Genetic variation and geographical differentiation revealed using ...

    Indian Academy of Sciences (India)

    [Zhang L., Lu S., Sun D., and Peng J. 2015 Genetic variation and geographical differentiation revealed using ISSR markers in tung tree,. Vernicia fordii. J. Genet. 94, e5–e9. Online only: http://www.ias.ac.in/jgenet/OnlineResources/94/e5.pdf]. Introduction. Tung tree, Vernicia fordii is an oil-bearing woody plant species of ...

  13. Commentary: Revealing the workings of universal grammar

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 28; Issue 5. Commentary: Revealing the workings of universal grammar. Mohinish Shukla. Volume 28 Issue 5 September 2003 pp 535-537. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/jbsc/028/05/0535-0537. Author Affiliations.

  14. Systemic lupus erythematous revealed by cytomegalovirus infection ...

    African Journals Online (AJOL)

    Cytomegalovirus (CMV) infection have been described as exacerbing systemic lupus erythematous (SLE). The role of CMV in starting off SLE remains object of debate. We report a severe presentation of SLE revealed by CMV infection with hemophogocytic syndrome. A 22 old women without a history of systemic disease ...

  15. [Mastitis revealing Churg-Strauss syndrome].

    Science.gov (United States)

    Dannepond, C; Le Fourn, E; de Muret, A; Ouldamer, L; Carmier, D; Machet, L

    2014-01-01

    Churg-Strauss syndrome often involves the skin, and this may sometimes reveal the disease. A 25-year-old woman was referred to a gynaecologist for inflammation of the right breast with breast discharge. Cytological analysis of the liquid showed numerous inflammatory cells, particularly polymorphonuclear eosinophils and neutrophils. Ultrasound examination of the breast was consistent with galactophoritis. CRP was normal, and hypereosinophilia was seen. The patient was subsequently referred to a dermatology unit. Skin examination revealed inflammation of the entire breast, which was painful, warm and erythematous; the border was oedematous with blisters. Necrotic lesions were also present on the thumbs and knees. Skin biopsy of the breast showed a dermal infiltrate with abundant infiltrate of polymorphonuclear eosinophils, including patchy necrosis and intraepidermal vesicles. Histological examination of a biopsy sample from a thumb revealed eosinophilic granuloma and leukocytoclastic vasculitis. The patient was also presenting asthma, pulmonary infiltrates and mononeuropathy at L3, consistent with Churg-Strauss syndrome. Breast involvement in Churg-Strauss syndrome is very rare (only one other case has been reported). This is the first case in which the breast condition revealed the disease. Cutaneous involvement of the breast is, however, also compatible with Wells' cellulitis. The lesions quickly disappeared with 1mg/kg/d oral prednisolone. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  16. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    Genetic relationship among Musa genotypes revealed by microsatellite markers. NAP Abdullah, GB Saleh, ETS Putra, ZB Wahab. Abstract. A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among ...

  17. Revealed Preference Theory, Rationality, and Neoclassical ...

    African Journals Online (AJOL)

    Revealed Preference Theory (Samuelson 1938) is an attempt to establish economic theory as a genuine empirical science by ridding it of nonempirical psychological concepts. Samuelson's goal was to rid economic theory of the last vestiges of utility analysis. Samuelson structured his theory on a set of preference axioms ...

  18. Bilateral stellate neuroretinitis revealing a pheochromocytoma ...

    African Journals Online (AJOL)

    Fundus examination showed bilateral stellate neuroretinitis. Physical examination revealed a malignant hypertension of 210/150mmHg. Magnetic resonance imaging identified a left suprarenal mass, whereas urinary catecholamine level was abnormally high which supported a diagnosis of pheochromocytoma.The patient ...

  19. 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…

  20. Open chromatin reveals the functional maize genome

    Science.gov (United States)

    Every cellular process mediated through nuclear DNA must contend with chromatin. As results from ENCODE show, open chromatin assays can efficiently integrate across diverse regulatory elements, revealing functional non-coding genome. In this study, we use a MNase hypersensitivity assay to discover o...

  1. Septic sacroiliitis revealing an infectious endocarditis

    Science.gov (United States)

    Mahfoudhi, Madiha; Hariz, Anis; Turki, Sami; Kheder, Adel

    2014-01-01

    We report the case of a 43-year-old man admitted for right hip ache and fever. Physical examination revealed a fever, an ache at the manipulation of the sacroiliac joint and a limitation of abduction and external rotation of the right hip. There was no murmur in cardiac auscultation. No anomaly was found at the conventional radiographs of the sacroiliac joint, while the pelvic MRI confirmed a right sacroiliitis. A sacroiliac puncture with a study of synovial fluid demonstrated the presence of Streptococcus viridans. The blood culture revealed the same germ. Transthoracic and transoesophageal echocardiography confirmed infectious endocarditis with vegetation in the mitral valve. He received penicillin G and gentamicin relayed by pristinamycin because of an allergy to penicillin G with a total duration of treatment of 40 days. His symptoms and the laboratory and radiological tests abnormalities resolved totally with no recurrence. PMID:25123569

  2. Septic sacroiliitis revealing an infectious endocarditis.

    Science.gov (United States)

    Mahfoudhi, Madiha; Hariz, Anis; Turki, Sami; Kheder, Adel

    2014-08-14

    We report the case of a 43-year-old man admitted for right hip ache and fever. Physical examination revealed a fever, an ache at the manipulation of the sacroiliac joint and a limitation of abduction and external rotation of the right hip. There was no murmur in cardiac auscultation. No anomaly was found at the conventional radiographs of the sacroiliac joint, while the pelvic MRI confirmed a right sacroiliitis. A sacroiliac puncture with a study of synovial fluid demonstrated the presence of Streptococcus viridans. The blood culture revealed the same germ. Transthoracic and transoesophageal echocardiography confirmed infectious endocarditis with vegetation in the mitral valve. He received penicillin G and gentamicin relayed by pristinamycin because of an allergy to penicillin G with a total duration of treatment of 40 days. His symptoms and the laboratory and radiological tests abnormalities resolved totally with no recurrence. 2014 BMJ Publishing Group Ltd.

  3. Revealing the Anatomy of Vote Trading

    CERN Document Server

    Guerrero, Omar A

    2016-01-01

    Cooperation in the form of vote trading, also known as logrolling, is central for law-making processes, shaping the development of democratic societies. Empirical evidence of logrolling is scarce and limited to highly specific situations because existing methods are not easily applicable to broader contexts. We have developed a general and scalable methodology for revealing a network of vote traders, allowing us to measure logrolling on a large scale. Analysis on more than 9 million votes spanning 40 years in the U.S. Congress reveals a higher logrolling prevalence in the Senate and an overall decreasing trend over recent congresses, coincidental with high levels of political polarization. Our method is applicable in multiple contexts, shedding light on many aspects of logrolling and opening new doors in the study of hidden cooperation.

  4. Revealed Comparative Advantage in the Internal Market

    OpenAIRE

    Widgrén, Mika

    2005-01-01

    This paper investigates comparative advantage and its development across selected Asian, American and European countries between 1996 and 2002. In doing so, we calculate the Balassa index of revealed comparative advantage using industry data at the HS 4-digit level. The major part of the analysis concentrates on the factor intensities of the sample countries’ comparative advantage and the overlap between them in the Internal Market. The paper shows that there is clearly some convergence in te...

  5. Comparative genomics reveals novel biochemical pathways.

    Science.gov (United States)

    Piskur, Jure; Schnackerz, Klaus D; Andersen, Gorm; Björnberg, Olof

    2007-08-01

    How well do we understand which enzymes are involved in the primary metabolism of the cell? A recent study using comparative genomics and postgenomics approaches revealed a novel pathway in the most studied organism, Escherichia coli. The analysis of a new operon consisting of seven previously uncharacterized genes thought to be involved in the degradation of nucleic acid precursors shows the impact of comparative genomics on the discovery of novel pathways and enzymes.

  6. Hyposplenism revealed by Plasmodium malariae infection

    OpenAIRE

    Hommel, Benjamin; Galloula, Alexandre; Simon, Anne; Buffet, Pierre

    2013-01-01

    International audience; BACKGROUND: Hyposplenism, due to splenectomy, inherited red blood cell disorders or acquired conditions such as celiac disease, has an important impact on the severity of malaria, especially in non-immune patients. Conversely, that malaria may reveal functional hyposplenism has not been described previously. METHODS: A 31-year old gardener was diagnosed with an uncomplicated attack of Plasmodium malariae 11 years after leaving the endemic area. In addition to trophozoi...

  7. 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.

  8. Hyposplenism revealed by Plasmodium malariae infection.

    Science.gov (United States)

    Hommel, Benjamin; Galloula, Alexandre; Simon, Anne; Buffet, Pierre

    2013-08-02

    Hyposplenism, due to splenectomy, inherited red blood cell disorders or acquired conditions such as celiac disease, has an important impact on the severity of malaria, especially in non-immune patients. Conversely, that malaria may reveal functional hyposplenism has not been described previously. A 31-year old gardener was diagnosed with an uncomplicated attack of Plasmodium malariae 11 years after leaving the endemic area. In addition to trophozoites and schizonts, thick and thin smears also showed Howell-Jolly bodies, pointing to functional hyposplenism. This was later confirmed by the presence of a calcified spleen in the context of S/β + sickle-cell syndrome in a patient previously unaware of this condition. Malaria may reveal hyposplenism. Although Howell-Jolly bodies are morphologically similar to nuclei of young Plasmodium trophozoite, distinction on smears is based on the absence of cytoplasm and irregular size of Howell-Jolly bodies. In the patient reported here, hyposplenism was revealed by the occurrence of P. malariae infection relatively late in life. Timely diagnosis of hyposplenism resulted in the implementation of appropriate measures to prevent overwhelming infection with capsulated bacteria. This observation highlights the importance of diagnosing hyposplenism in patients with malaria despite the morphological similarities between ring nuclei and Howell-Jolly bodies on thick smears.

  9. [Dermohypodermitis on the face revealing TIBOLA].

    Science.gov (United States)

    Gaston, J; Durox, H; Sparsa, A; Bonnetblanc, J-M; Doffoel-Hantz, V

    2011-05-01

    Tick-borne lymphadenopathy (TIBOLA) is an emerging rickettsiosis in Europe, transmitted by the Dermacentor tick. This syndrome is defined as the association of an inoculation eschar on the scalp that may be surrounded by an erythema scalp, fever, and painful cervical lymphadenopathy in colder months. Children and women are at higher risk for TIBOLA. We report the case of a 9 year-old French child with an acute hemifacial edema and erythema revealing TIBOLA. Early empirical antibiotic therapy should be prescribed in any suspected TIBOLA, before confirmation of the diagnosis. The recommended treatment is doxycycline or macrolide. Copyright © 2011. Published by Elsevier SAS.

  10. Changes in Pluto's Atmosphere Revealed by Occultations

    Science.gov (United States)

    Sicardy, Bruno; Widemann, Thomas; Lellouch, Emmanuel; Veillet, Christian; Colas, Francois; Roques, Francoise; Beisker, Wolfgang; Kretlow, Mike; Cuillandre, Jean-Charles; Hainaut, Olivier

    After the discovery and study of Pluto's tenuous atmosphere in 1985 and 1988 with stellar occultations 14 years were necessary before two other occultations by the planet could be observed on 20 July 2002 and 21 August 2002 from Northern Chile with a portable telescope and from CFHT in Hawaii respectively. These occultations reveal drastric changes in Pluto's nitrogen atmosphere whose pressure increased by a factor two or more since 1988. In spite of an increasing distance to the Sun (and a correlated decrease of solar energy input at Pluto) this increase can be explained by the fact that Pluto's south pole went from permanent darkness to permanent illumination between 1988 and 2002. This might cause the sublimation of the south polar cap and the increase of pressure which could go on till 2015 according to current nitrogen cycle models. Furthermore we detect temperature contrasts between the polar and the equatorial regions probed on Pluto possibly caused by different diurnally averaged insolations at those locations. Finally spikes observed in the light curves reveal a dynamical activity in Pluto's atmosphere.

  11. [Severe pulmonary embolism revealed by status epilepticus].

    Science.gov (United States)

    Allou, N; Coolen-Allou, N; Delmas, B; Cordier, C; Allyn, J

    2016-12-01

    High-risk pulmonary embolism (PE) is associated with high mortality rate (>50%). In some cases, diagnosis of PE remains a challenge with atypical presentations like in this case report with a PE revealed by status epilepticus. We report the case of a 40-year-old man without prior disease, hospitalized in ICU for status epilepticus. All paraclinical examinations at admission did not show any significant abnormalities (laboratory tests, cardiologic and neurological investigations). On day 1, he presented a sudden circulatory collapse and echocardiography showed right intra-auricular thrombus. He was treated by thrombolysis and arteriovenous extracorporeal membrane oxygenation. After stabilization, computed tomography showed severe bilateral PE. He developed multi-organ failure and died 4days after admission. Pulmonary embolism revealed by status epilepticus has rarely been reported and is associated with poor prognosis. Physicians should be aware and think of the possibility of PE in patients with status epilepticus without any history or risk factors of seizure and normal neurological investigations. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  12. Wegener Granulomatosis Revealed by Pleural Effusion

    Science.gov (United States)

    Toffart, Anne-Claire; Arbib, François; Lantuejoul, Sylvie; Roux, Jean-François; Bland, Vincent; Ferretti, Gilbert; Diab, Samia

    2009-01-01

    Pulmonary signs are common in Wegener's granulomatosis (WG). However, an initial presentation including pleural effusion has not been described. We describe a case of WG in which pleural effusion was the first clinical manifestation. A 45-year-old man with dorsal pain presented with pleural thickening and effusion, and a visible nodule on a thoracic scan. A dense chronic inflammatory infiltrate was obtained by pleural biopsy and an open lung biopsy revealed necrotizing granulomatous vasculitis. Serologies were positive for antineutrophil cytoplasmic antibodies and antiproteinase 3 antibodies. A diagnosis of WG was conducted and the patient was started on cyclophosphamide and methylprednisolone as an initial treatment, with a favorable evolution. Although pleural effusion is rarely described in WG, this pathology must be considered in the presence of this clinical manifestation. PMID:20168982

  13. Wegener Granulomatosis Revealed by Pleural Effusion

    Directory of Open Access Journals (Sweden)

    Anne-Claire Toffart

    2009-01-01

    Full Text Available Pulmonary signs are common in Wegener's granulomatosis (WG. However, an initial presentation including pleural effusion has not been described. We describe a case of WG in which pleural effusion was the first clinical manifestation. A 45-year-old man with dorsal pain presented with pleural thickening and effusion, and a visible nodule on a thoracic scan. A dense chronic inflammatory infiltrate was obtained by pleural biopsy and an open lung biopsy revealed necrotizing granulomatous vasculitis. Serologies were positive for antineutrophil cytoplasmic antibodies and antiproteinase 3 antibodies. A diagnosis of WG was conducted and the patient was started on cyclophosphamide and methylprednisolone as an initial treatment, with a favorable evolution. Although pleural effusion is rarely described in WG, this pathology must be considered in the presence of this clinical manifestation.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Hidden acoustic information revealed by intentional nonlinearity

    Science.gov (United States)

    Dowling, David R.

    2017-11-01

    Acoustic waves are omnipresent in modern life and are well described by the linearized equations of fluid dynamics. Once generated, acoustic waves carry and collect information about their source and the environment through which they propagate, respectively, and this information may be retrieved by analyzing recordings of these waves. Because of this, acoustics is the primary means for observation, surveillance, reconnaissance, and remote sensing in otherwise opaque environments, such as the Earth's oceans and crust, and the interior of the human body. For such information-retrieval tasks, acoustic fields are nearly always interrogated within their recorded frequency range or bandwidth. However, this frequency-range restriction is not general; acoustic fields may also carry (hidden) information at frequencies outside their bandwidth. Although such a claim may seem counter intuitive, hidden acoustic-field information can be revealed by re-introducing a marquee trait of fluid dynamics: nonlinearity. In particular, an intentional quadratic nonlinearity - a form of intra-signal heterodyning - can be used to obtain acoustic field information at frequencies outside a recorded acoustic field's bandwidth. This quadratic nonlinearity enables a variety of acoustic remote sensing applications that were long thought to be impossible. In particular, it allows the detrimental effects of sparse recordings and random scattering to be suppressed when the original acoustic field has sufficient bandwidth. In this presentation, the topic is developed heuristically, with a just brief exposition of the relevant mathematics. Hidden acoustic field information is then revealed from simulated and measured acoustic fields in simple and complicated acoustic environments involving frequencies from a few Hertz to more than 100 kHz, and propagation distances from tens of centimeters to hundreds of kilometers. Sponsored by ONR, NAVSEA, and NSF.

  19. [Neuropsychiatric symptoms revealing pseudohypoparathyroidism with Fahr's syndrome].

    Science.gov (United States)

    Otheman, Y; Khalloufi, H; Benhima, I; Ouanass, A

    2011-02-01

    Fahr's syndrome is characterized by the presence of intracerebral, bilateral and symmetrical non-arteriosclerotic calcifications, located in the central grey nuclei. One of its main etiologies is pseudohypoparathyroidism (PHP), due to a resistance to the action of parathormone (PTH) with essentially hypocalcaemia and a normal or a high rate of PTH. Mr B.A. is a 36-year-old man, admitted to hospital because of refractory psychotic symptoms associated with alcohol abuse and fits of convulsion, for diagnostic and therapeutic update. Mr B.A. had presented convulsions since the age of 10, without regular medical treatment. He showed a decrease in his school performances and started using alcohol. Since the age of 17, he began expressing delusions of persecution and of enchantment fed by the persistence of the convulsions. He was administered phenobarbital, and classic antipsychotics (haloperidol and levomepromazine) and developed serious extrapyramidal side effects, treated with an anticholinergic (trihexyphenidyl). Evolution was rather disadvantageous: more epileptic fits, exaggeration of tremors; abuse of alcohol and persistence of psychotic symptoms. On admission, psychiatric examination objectified paranoid delusions of being possessed and persecuted by others. Neurological examination revealed the presence of limb tremors, with a positive Froment's sign on the right, and dysarthria. Other than this, the patient was shorter in comparison with his siblings and exhibited bad dentition. A CT brain scan found bilateral, symmetric basal ganglia calcifications, confirmed by MRI, in favour of Fahr's syndrome. Phosphocalcic investigations revealed a low concentration of serum calcium (65 mg/l) and a hyperphosphataemia (60.1mg/l). The blood level of parathyroid hormone was in the upper limit of normal (66 ng/l), and levels of thyroid hormones and thyroid-stimulating hormone were normal. The diagnosis of Fahr's syndrome, revealing a pseudohypoparathyroidism was posed, and the

  20. Speeding Clouds May Reveal Invisible Black Holes

    Science.gov (United States)

    Kohler, Susanna

    2017-07-01

    Several small, speeding clouds have been discovered at the center of our galaxy. A new study suggests that these unusual objects may reveal the lurking presence of inactive black holes.Peculiar Cloudsa) Velocity-integrated intensity map showing the location of the two high-velocity compact clouds, HCN0.0090.044 and HCN0.0850.094, in the context of larger molecular clouds. b) and c) Latitude-velocity and longitude-velocity maps for HCN0.0090.044 and HCN0.0850.094, respectively. d) and e) spectra for the two compacts clouds, respectively. Click for a closer look. [Takekawa et al. 2017]Sgr A*, the supermassive black hole marking the center of our galaxy, is surrounded by a region roughly 650 light-years across known as the Central Molecular Zone. This area at the heart of our galaxy is filled with large amounts of warm, dense molecular gas that has a complex distribution and turbulent kinematics.Several peculiar gas clouds have been discovered within the Central Molecular Zone within the past two decades. These clouds, dubbed high-velocity compact clouds, are characterized by their compact sizes and extremely broad velocity widths.What created this mysterious population of energetic clouds? The recent discovery of two new high-velocity compact clouds, reported on in a paper led by Shunya Takekawa (Keio University, Japan), may help us to answer this question.Two More to the CountUsing the James Clerk Maxwell Telescope in Hawaii, Takekawa and collaborators detected the small clouds near the circumnuclear disk at the centermost part of our galaxy. These two clouds have velocity spreads of -80 to -20 km/s and -80 to 0 km/s and compact sizes of just over 1 light-year. The clouds similar appearances and physical properties suggest that they may both have been formed by the same process.Takekawa and collaborators explore and discard several possible origins for these clouds, such as outflows from massive protostars (no massive, luminous stars have been detected affiliated

  1. Anticipatory looks reveal expectations about discourse relations.

    Science.gov (United States)

    Rohde, Hannah; Horton, William S

    2014-12-01

    Previous research provides evidence for expectation-driven processing within sentences at phonological, lexical, and syntactic levels of linguistic structure. Less well-established is whether comprehenders also anticipate pragmatic relationships between sentences. To address this, we evaluate a unit of discourse structure that comprehenders must infer to hold between sentences in order for a discourse to make sense-the intersentential coherence relation. In a novel eyetracking paradigm, we trained participants to associate particular spatial locations with particular coherence relations. Experiment 1 shows that the subset of listeners who successfully acquired the location∼relation mappings during training subsequently looked to these locations during testing in response to a coherence-signaling intersentential connective. Experiment 2 finds that listeners' looks during sentences containing coherence-biasing verbs reveal expectations about upcoming sentence types. This work extends existing research on prediction beyond sentence-internal structure and provides a new methodology for examining the cues that comprehenders use to establish relationships at the discourse level. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. 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

  3. [Polymyalgia rheumatica revealing a lung cancer].

    Science.gov (United States)

    Cocquempot, K; Defuentes, G; Duron-Martineau, S; Berets, O; Vaylet, F; Margery, J

    2013-01-01

    Polymyalgia rheumatica is an inflammatory condition belonging to the connective tissue diseases, which occurs quite frequently in the elderly. Previously, cases have been reported in association with malignant tumours, in a synchronous fashion or prior to the appearance of the cancer. In these cases, the polymyalgia rheumatica is considered to be a paraneoplastic syndrome. We report the cases of a 63-year-old woman and a 58-year-old man with severe proximal girdle pain associated to a high-level of systemic inflammatory markers and a diagnosis of polymyalgia rheumatica was made. In the face of a lack of ineffectiveness of analgesic and anti-inflammatory treatments, an intensive investigation was undertaken which in both cases revealed an adenocarcinoma of the lung. The rheumatic manifestations responded well to chemotherapy targeting the lung tumour. We present here a review of the literature to give prominence to the diagnostic pitfalls that can occur around paraneoplastic polymyalgia rheumatica. The presence of therapeutic resistance at the onset of treatment and other atypical features may suggest the presence of an occult malignancy. Copyright © 2012 SPLF. Published by Elsevier Masson SAS. All rights reserved.

  4. Photoacoustic imaging reveals hidden underdrawings in paintings.

    Science.gov (United States)

    Tserevelakis, George J; Vrouvaki, Ilianna; Siozos, Panagiotis; Melessanaki, Krystallia; Hatzigiannakis, Kostas; Fotakis, Costas; Zacharakis, Giannis

    2017-04-07

    A novel, non-invasive, imaging methodology, based on the photoacoustic effect, is introduced in the context of artwork diagnostics with emphasis on the uncovering of hidden features such as underdrawings or original sketch lines in paintings. Photoacoustic microscopy, a rapidly growing imaging method widely employed in biomedical research, exploits the ultrasonic acoustic waves, generated by light from a pulsed or intensity modulated source interacting with a medium, to map the spatial distribution of absorbing components. Having over three orders of magnitude higher transmission through strongly scattering media, compared to light in the visible and near infrared, the photoacoustic signal offers substantially improved detection sensitivity and achieves excellent optical absorption contrast at high spatial resolution. Photoacoustic images, collected from miniature oil paintings on canvas, illuminated with a nanosecond pulsed Nd:YAG laser at 1064 nm on their reverse side, reveal clearly the presence of pencil sketch lines coated over by several paint layers, exceeding 0.5 mm in thickness. By adjusting the detection bandwidth of the optically induced ultrasonic waves, photoacoustic imaging can be used for looking into a broad variety of artefacts having diverse optical properties and geometrical profiles, such as manuscripts, glass objects, plastic modern art or even stone sculpture.

  5. Featured Image: Revealing Hidden Objects with Color

    Science.gov (United States)

    Kohler, Susanna

    2018-02-01

    Stunning color astronomical images can often be the motivation for astronomers to continue slogging through countless data files, calculations, and simulations as we seek to understand the mysteries of the universe. But sometimes the stunning images can, themselves, be the source of scientific discovery. This is the case with the below image of Lynds Dark Nebula 673, located in the Aquila constellation, that was captured with the Mayall 4-meter telescope at Kitt Peak National Observatory by a team of scientists led by Travis Rector (University of Alaska Anchorage). After creating the image with a novel color-composite imaging method that reveals faint H emission (visible in red in both images here), Rector and collaborators identified the presence of a dozen new Herbig-Haro objects small cloud patches that are caused when material is energetically flung out from newly born stars. The image adapted above shows three of the new objects, HH 118789, aligned with two previously known objects, HH 32 and 332 suggesting they are driven by the same source. For more beautiful images and insight into the authors discoveries, check out the article linked below!Full view of Lynds Dark Nebula 673. Click for the larger view this beautiful composite image deserves! [T.A. Rector (University of Alaska Anchorage) and H. Schweiker (WIYN and NOAO/AURA/NSF)]CitationT. A. Rector et al 2018 ApJ 852 13. doi:10.3847/1538-4357/aa9ce1

  6. Facial appearance reveals immunity in African men.

    Science.gov (United States)

    Phalane, Khutso G; Tribe, Catherine; Steel, Helen C; Cholo, Moloko C; Coetzee, Vinet

    2017-08-07

    Facial appearance is thought to indicate immunity in humans, but very few studies have tested this relationship directly. The aim of this study was to test the relationship between direct measures of immunity, perceived facial health and attractiveness, and facial cues in African men. We show that men with a stronger cytokine response are considered significantly more attractive and healthy. Men with more masculine, heavier facial features (i.e. muscular appearance) have a significantly higher cytokine response and appear significantly healthier and more attractive, while men with a yellower, lighter, "carotenoid" skin colour, have a marginally higher immune response and are also considered significantly more healthy and attractive. In contrast, more symmetrical, skinnier looking men appeared more attractive and healthier, but did not have a stronger cytokine response. These findings also shed new light on the "androgen-mediated" traits proposed by the immunocompetence handicap hypothesis (ICHH) and we propose that facial muscularity serves as a better estimate of an "androgen-mediated" trait than facial masculinity. Finally, we build on previous evidence to show that men's facial features do indeed reveal aspects of immunity, even better than more traditional measures of health, such as body mass index (BMI).

  7. Revealing the interface in polymer nanocomposites.

    Science.gov (United States)

    Zammarano, Mauro; Maupin, Paul H; Sung, Li-Piin; Gilman, Jeffrey W; McCarthy, Edward D; Kim, Yeon S; Fox, Douglas M

    2011-04-26

    The morphological characterization of polymer nanocomposites over multiple length scales is a fundamental challenge. Here, we report a technique for high-throughput monitoring of interface and dispersion in polymer nanocomposites based on Förster resonance energy transfer (FRET). Nanofibrillated cellulose (NFC), fluorescently labeled with 5-(4,6-dichlorotriazinyl)-aminofluorescein (FL) and dispersed into polyethylene (PE) doped with Coumarin 30 (C30), is used as a model system to assess the ability of FRET to evaluate the effect of processing on NFC dispersion in PE. The level of energy transfer and its standard deviation, measured by fluorescence spectroscopy and laser scanning confocal microscopy (LSCM), are exploited to monitor the extent of interface formation and composite homogeneity, respectively. FRET algorithms are used to generate color-coded images for a real-space observation of energy transfer efficiency. These images reveal interface formation at a nanoscale while probing a macroscale area that is large enough to be representative of the entire sample. The unique ability of this technique to simultaneously provide orientation/spatial information at a macroscale and nanoscale features, encoded in the FRET signal, provides a new powerful tool for structure-property-processing investigation in polymer nanocomposites.

  8. Myasthenia Revealed Following Laparotomy - A Case Report

    Directory of Open Access Journals (Sweden)

    Abdelilah GHANNAM

    2015-06-01

    Full Text Available Myasthenia (muscle weakness is a rare neuromuscular disease of which respiratory failure is the main complication. The accidental discovery of such disease in the perioperative period is rare and potentially serious.We report a case of a woman who underwent emergency operation for appendiceal peritonitis, and failed repeatedly at weaning from postoperative mechanical ventilation. The usual etiologies such as postoperative respiratory complications, ventilator-associated pneumonia, acute respiratory distress syndrome complicating the septic shock or having no impact on it, and neuromyopathy’s resuscitation were considered, researched, examined or eliminated.Faced with the diagnostic impasse and the obvious weaning failure, another interview revealed signs of muscle fatigue which led to the diagnosis of myasthenia gravis decompensated perioperatively. Once the diagnosis was confirmed by means of a neostigmine test, the specific treatment began, particularly through plasma exchange sessions, and the process of weaning resumed. The result was complete weaning. A three-month follow-up showed a stable patient with no significant muscular disability.

  9. 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

  10. Biosignatures as revealed by spectropolarimetry of Earthshine.

    Science.gov (United States)

    Sterzik, Michael F; Bagnulo, Stefano; Palle, Enric

    2012-02-29

    Low-resolution intensity spectra of Earth's atmosphere obtained from space reveal strong signatures of life ('biosignatures'), such as molecular oxygen and methane with abundances far from chemical equilibrium, as well as the presence of a 'red edge' (a sharp increase of albedo for wavelengths longer than 700 nm) caused by surface vegetation. Light passing through the atmosphere is strongly linearly polarized by scattering (from air molecules, aerosols and cloud particles) and by reflection (from oceans and land). Spectropolarimetric observations of local patches of Earth's sky light from the ground contain signatures of oxygen, ozone and water, and are used to characterize the properties of clouds and aerosols. When applied to exoplanets, ground-based spectropolarimetry can better constrain properties of atmospheres and surfaces than can standard intensity spectroscopy. Here we report disk-integrated linear polarization spectra of Earthshine, which is sunlight that has been first reflected by Earth and then reflected back to Earth by the Moon. The observations allow us to determine the fractional contribution of clouds and ocean surface, and are sensitive to visible areas of vegetation as small as 10 per cent. They represent a benchmark for the diagnostics of the atmospheric composition, mean cloud height and surfaces of exoplanets.

  11. 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.

  12. 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

  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. Evaluating the risk of pathogen transmission from wild animals to domestic pigs in Australia.

    Science.gov (United States)

    Pearson, Hayley E; Toribio, Jenny-Ann L M L; Lapidge, Steven J; Hernández-Jover, Marta

    2016-01-01

    Wild animals contribute to endemic infection in livestock as well as the introduction, reintroduction and maintenance of pathogens. The source of introduction of endemic diseases to a piggery is often unknown and the extent of wildlife contribution to such local spread is largely unexplored. The aim of the current study was to quantitatively assess the probability of domestic pigs being exposed to different pathogens from wild animals commonly found around commercial piggeries in Australia. Specifically, this study aims to quantify the probability of exposure to the pathogens Escherichia coli, Salmonella spp. and Campylobacter spp. from European starlings (Sturnus vulgarus); Brachyspira hyodysenteriae, Lawsonia intracellularis and Salmonella spp. from rats (Rattus rattus and Rattus norvegicus); and Mycoplasma hyopneumoniae, Leptospira spp., Brucella suis and L. intracellularis from feral pigs (Sus scrofa). Exposure assessments, using scenario trees and Monte Carlo stochastic simulation modelling, were conducted to identify potential pathways of introduction and calculate the probabilities of these pathways occurring. Input parameters were estimated from a national postal survey of commercial pork producers and from disease detection studies conducted for European starlings, rats and feral pigs in close proximity to commercial piggeries in Australia. Based on the results of the exposure assessments, rats presented the highest probability of exposure of pathogens to domestic pigs at any point in time, and L. intracellularis (median 0.13, 5% and 95%, 0.05-0.23) and B. hyodysenteriae (median 0.10, 0.05-0.19) were the most likely pathogens to be transmitted. Regarding European starlings, the median probability of exposure of domestic pigs to pathogenic E. coli at any point in time was estimated to be 0.03 (0.02-0.04). The highest probability of domestic pig exposure to feral pig pathogens at any point in time was found to be for M. hyopneumoniae (median 0.013, 0

  15. What Facial Appearance Reveals Over Time: When Perceived Expressions in Neutral Faces Reveal Stable Emotion Dispositions.

    Science.gov (United States)

    Adams, Reginald B; Garrido, Carlos O; Albohn, Daniel N; Hess, Ursula; Kleck, Robert E

    2016-01-01

    It might seem a reasonable assumption that when we are not actively using our faces to express ourselves (i.e., when we display nonexpressive, or neutral faces), those around us will not be able to read our emotions. Herein, using a variety of expression-related ratings, we examined whether age-related changes in the face can accurately reveal one's innermost affective dispositions. In each study, we found that expressive ratings of neutral facial displays predicted self-reported positive/negative dispositional affect, but only for elderly women, and only for positive affect. These findings meaningfully replicate and extend earlier work examining age-related emotion cues in the face of elderly women (Malatesta et al., 1987a). We discuss these findings in light of evidence that women are expected to, and do, smile more than men, and that the quality of their smiles predicts their life satisfaction. Although ratings of old male faces did not significantly predict self-reported affective dispositions, the trend was similar to that found for old female faces. A plausible explanation for this gender difference is that in the process of attenuating emotional expressions over their lifetimes, old men reveal less evidence of their total emotional experiences in their faces than do old women.

  16. The Agricultural Antibiotic Carbadox Induces Phage-mediated Gene Transfer in Salmonella

    Directory of Open Access Journals (Sweden)

    Bradley L. Bearson

    2014-02-01

    Full Text Available Antibiotics are used for disease therapeutic or preventative effects in humans and animals, as well as for enhanced feed conversion efficiency in livestock. Antibiotics can also cause undesirable effects in microbial populations, including selection for antibiotic resistance, enhanced pathogen invasion, and stimulation of horizontal gene transfer. Carbadox is a veterinary antibiotic used in the U.S. during the starter phase of swine production for improved feed efficiency and control of swine dysentery and bacterial swine enteritis. Carbadox has been shown in vitro to induce phage-encoded Shiga toxin in Shiga toxin-producing Escherichia coli and a phage-like element transferring antibiotic resistance genes in Brachyspira hyodysenteriae, but the effect of carbadox on prophages in other bacteria is unknown. This study examined carbadox exposure on prophage induction and genetic transfer in Salmonella enterica serovar Typhimurium, a human foodborne pathogen that frequently colonizes swine without causing disease. S. Typhimurium LT2 exposed to carbadox induced prophage production, resulting in bacterial cell lysis and release of virions that were visible by electron microscopy. Carbadox induction of phage-mediated gene transfer was confirmed by monitoring the transduction of a sodCIII::neo cassette in the Fels-1 prophage from LT2 to a recipient Salmonella strain. Furthermore, carbadox frequently induced generalized transducing phages in multidrug-resistant phage type DT104 and DT120 isolates, resulting in the transfer of chromosomal and plasmid DNA that included antibiotic resistance genes. Our research indicates that exposure of Salmonella to carbadox induces prophages that can transfer virulence and antibiotic resistance genes to susceptible bacterial hosts. Carbadox-induced, phage-mediated gene transfer could serve as a contributing factor in bacterial evolution during animal production, with prophages being a reservoir for bacterial fitness

  17. Development and validation of an enzyme-linked immunosorbent assay for the diagnosis of porcine proliferative enteropathy.

    Science.gov (United States)

    Wattanaphansak, Suphot; Asawakarn, Tanong; Gebhart, Connie J; Deen, John

    2008-03-01

    The objective of this study was to develop an indirect enzyme-linked immunosorbent assay (ELISA) using a sonicated pure culture of Lawsonia intracellularis as the antigen (So-ELISA). A total of 332 serum samples, consisting of 232 experimentally infected animals and 100 animals naturally infected with L. intracellularis, were used to assess the diagnostic sensitivity. Three hundred and fifty-five sera from uninfected animals were used to determine the diagnostic specificity. The receiver operating characteristic and mean +3 standard deviation of optical density (OD) values from uninfected animals were used for selecting cut-off points. The diagnostic accuracy of So-ELISA was considered to be high as the area under the curve index was 0.991 with 0.0029 standard error. The optimal cut-off for So-ELISA was set at 0.45 OD with 89.8% sensitivity and 99.4% specificity based on a combination of good sensitivity and high specificity. No cross-reactivity was found in sera from pigs exposed to Brachyspira pilosicoli, B. hyodysenteriae, Campylobacter mucosalis, C. jejuni, or C. coli. Inter- and intracoefficient of variation of all control sera tested with So-ELISA was less than 10%. The observed agreements between So-ELISA and the immunoperoxidase monolayer assay tested with experimental challenge animals and field samples were 95.08% with 0.88 kappa and 90.65% with 0.74 kappa value, respectively. So-ELISA was able to detect the seroconversion of infected animals at 2 to 4 weeks after exposure to L. intracellularis. Based on the validation results, So-ELISA could be used as an alternative serology for proliferative enteropathy diagnosis.

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

    African Journals Online (AJOL)

    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 ...

  19. Mitochondrial DNA analysis reveals a low nucleotide diversity of ...

    African Journals Online (AJOL)

    Mitochondrial DNA analysis reveals a low nucleotide diversity of Caligula japonica in China. ... Mitochondrial DNA analysis reveals a low nucleotide diversity of Caligula japonica in China. Y Li, B Yang, H Wang, R Xia, L Wang, Z Zhang, L Qin, Y Liu ...

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

    Science.gov (United States)

    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 of facial cellulitis revealing choreo-acanthocytosis (ChAc) were found in a review of the literature.

  1. Revealing Slip Bands In A Metal-Matrix/Fiber Composite

    Science.gov (United States)

    Lerch, Bradley A.

    1995-01-01

    Experimental procedure includes heat treatments and metallographic techniques developed to facilitate studies of deformation of metal-matrix/fiber composite under stress. Reveals slip bands, indicative of plastic flow occurring in matrix during mechanical tests of specimens of composite.

  2. Gene Sequencing May Reveal Risks for Rare Diseases

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_166875.html Gene Sequencing May Reveal Risks for Rare Diseases But ... this study, the researchers analyzed nearly 5,000 genes associated with rare genetic conditions in 50 healthy ...

  3. Interaction proteomics reveals brain region-specific AMPA receptor complexes

    NARCIS (Netherlands)

    Chen, N.; Pandya, N.J.; Koopmans, F.T.W.; Castelo-Szekelv, V.; van der Schors, R.C.; Smit, A.B.; Li, K.W.

    2014-01-01

    Fast excitatory synaptic transmission in the brain is mediated by glutamate acting on postsynaptic AMPA receptors. Recent studies have revealed a substantial number of AMPA receptor auxiliary proteins, which potentially contribute to the regulation of AMPA receptor trafficking, subcellular receptor

  4. Genetic and biochemical evidences reveal novel insights into the ...

    Indian Academy of Sciences (India)

    Genetic and biochemical evidences reveal novel insights into the mechanism underlying Saccharomyces cerevisiae Sae2-mediated abrogation of DNA replication stress. Indrajeet Ghodke and K Muniyappa. Supplementary Material. Supplementary table 1. Plasmids used in this study ...

  5. 21 CFR 1.21 - Failure to reveal material facts.

    Science.gov (United States)

    2010-04-01

    ... possible product hazards) required in labeling for food, drugs, devices, or cosmetics under the act. (2...) Labeling of a food, drug, device, or cosmetic shall be deemed to be misleading if it fails to reveal facts...

  6. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

    Science.gov (United States)

    Popovic, Ana; Hai, Tran; Tchigvintsev, Anatoly; Hajighasemi, Mahbod; Nocek, Boguslaw; Khusnutdinova, Anna N.; Brown, Greg; Glinos, Julia; Flick, Robert; Skarina, Tatiana; Chernikova, Tatyana N.; Yim, Veronica; Brüls, Thomas; Paslier, Denis Le; Yakimov, Michail M.; Joachimiak, Andrzej; Ferrer, Manuel; Golyshina, Olga V.; Savchenko, Alexei; Golyshin, Peter N.; Yakunin, Alexander F.

    2017-01-01

    Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools. PMID:28272521

  7. [Chronic vulvar lymphedema revealing Crohn disease in a teenage girl].

    Science.gov (United States)

    Aounallah, A; Ghariani Fetoui, N; Ksiaa, M; Boussofara, L; Saidi, W; Mokni, S; Sriha, B; Belajouza, C; Denguezli, M; Ghariani, N; Nouira, R

    2017-04-01

    Cutaneous Crohn disease is a rare cutaneous manifestation of Crohn disease in children. Herein is reported a case of persistent vulvar lymphedema revealing Crohn disease in a teenage girl. A 14-year-old girl presented with an 8-month history of persistent vulvar swelling associated with chronic macrocheilia. Dermatologic examination showed an inflammatory vulvar lymphedema, associated with perianal fissures and hypertrophic gingivitis. Vulvar skin biopsy revealed non-necrotizing granulomatous inflammation. Gastrointestinal endoscopy yielded no significant findings. The diagnosis of Crohn disease presenting as vulvar lymphedema was established. Oral metronidazole therapy resulted in partial improvement of cutaneous lesions beginning the 1st week. The originality of this case lies in the presentation of chronic macrocheilia with persistent vulvar lymphedema in a child, revealing Crohn disease without gastrointestinal involvement. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  8. Burned-out seminoma revealed by solitary rib bone metastasis

    Energy Technology Data Exchange (ETDEWEB)

    Nishisho, Toshihiko; Miyagi, Ryo; Sairyo, Koichi [Tokushima University Graduate School, Department of Orthopedics, Institute of Biomedical Sciences, Tokushima-city, Tokushima (Japan); Sakaki, Mika [Saitama Medical University International Medical Center, Department of Pathology, Hidaka-city, Saitama (Japan); Takao, Shoichiro [Tokushima University Graduate School, Department of Radiology, Institute of Biomedical Sciences, Tokushima-city, Tokushima (Japan)

    2017-10-15

    Burned-out tumor is a rare phenomenon in which a testicular tumor regresses in the primary lesion and progresses in a metastatic lesion. We report the case of a 30-year-old male with burned-out seminoma revealed by open biopsy of solitary 10th rib bone metastasis. He underwent inguinal orchiectomy, which revealed hyalinization, indicating a spontaneously regressed testicular tumor. Chemotherapy for seminoma was administered in three cycles of bleomycin + etoposide + cisplatin therapy. The chemotherapy was effective, and wide resection of the rib was subsequently performed. No postoperative chemotherapy was performed, and there has been no evidence of recurrence for 3 years postoperatively. (orig.)

  9. Molecular variation in Cucumis melo as revealed by isoenzyme and ...

    African Journals Online (AJOL)

    Molecular variation in Cucumis melo as revealed by isoenzyme and RAPD markers. Tarek M Mohamed. Abstract. No Abstract. The Egyptian Journal of Biochemistry and Molecular Biology Vol. 23(2) 2005: 141-153. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT ...

  10. Sinai and Norfa chicken diversity revealed by microsatellite markers ...

    African Journals Online (AJOL)

    Sinai and Norfa chicken diversity revealed by microsatellite markers. M Soltan, S Farrag, A Enab, E Abou-Elewa, S El-Safty, A Abushady. Abstract. The present study aimed to outline the population differentiation of Sinai and Norfa chicken, native to Egypt, with microsatellite markers. Twenty microsatellite loci recommended ...

  11. 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

  12. In Reporting Lobbying Expenses, Some Institutions Do Not Reveal All.

    Science.gov (United States)

    Lederman, Douglas

    1998-01-01

    On a federal tax form, only 75 of 475 colleges and universities surveyed reported that they had spent money on lobbying, defined as direct contacts with legislators or executive-branch officials about specific bills. Guidelines concerning reporting are unclear and confusing, and some institutions reveal as little as possible. Data on 78…

  13. ID-check: Online concealed information test reveals true identity

    NARCIS (Netherlands)

    Verschuere, B.; Kleinberg, B.

    2016-01-01

    The Internet has already changed people's lives considerably and is likely to drastically change forensic research. We developed a web-based test to reveal concealed autobiographical information. Initial studies identified a number of conditions that affect diagnostic efficiency. By combining these

  14. UTV Expansion Pack: Special-Purpose Rank-Revealing Algorithms

    DEFF Research Database (Denmark)

    Fierro, Ricardo D.; Hansen, Per Christian

    2005-01-01

    -revealing VSV decompositions, we expand the algorithms for the ULLV decomposition of a matrix pair to handle interference-type problems with a rank-deficient covariance matrix, and we provide a robust and reliable Lanczos algorithm which - despite its simplicity - is able to capture all the dominant singular...

  15. SSR markers reveal genetic variation between improved cassava ...

    African Journals Online (AJOL)

    Five SSR primers that have PIC values between 0.50 and 0.67 were selected and further assessed using simple arithmetic progression combination method. The results obtained revealed a combination of these 5 primers from SSR primers collection at IITA that could readily distinguish the 36 cassava genotypes at 0.93 ...

  16. Genetic diversity of taraxacum germplasm revealed by sequence ...

    African Journals Online (AJOL)

    Genetic diversity of taraxacum germplasm revealed by sequence-related amplified polymorphism (SRAP) analysis. ... African Journal of Biotechnology ... The genetic relationships analyzed with un-weighed pairgroup method with arithmetic mean (UPMGA) showed that 11 population of taraxacum were grouped into three ...

  17. Cotranslational protein folding reveals the selective use of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 3. Cotranslational protein folding reveals the selective use of synonymous codons along the coding sequence of a low expression gene. Suvendra Kumar Ray Vishwa Jyoti Baruah Siddhartha Sankar Satapathy Rajat Banerjee. Research Commentary Volume 93 Issue ...

  18. Heat islands over Mumbai as revealed by autorecorded ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 125; Issue 1. Heat islands over Mumbai as revealed by autorecorded thermograph data. A K Srivastava James Voogt ... 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 ...

  19. Genetic relationships revealed by simple sequence repeat (SSR ...

    African Journals Online (AJOL)

    Genetic relationships revealed by simple sequence repeat (SSR) markers among Ghanaian cassava cultivars released by different research groups. ... Genetic diversity was observed within populations (HS = 0.552) and, therefore, suggesting a low rate of inter-population gene flow among the individuals constituting the ...

  20. 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.)

  1. Genetic and biochemical evidences reveal novel insights into the ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 41; Issue 4. Genetic and biochemical evidences reveal novel insights into the mechanism underlying Saccharomyces cerevisiae Sae2-mediated abrogation of DNA replication stress. INDRAJEET GHODKE K MUNIYAPPA. ARTICLE Volume 41 Issue 4 December 2016 pp ...

  2. Whole exome sequencing reveals a MLL de novo mutation ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 4. Whole exome sequencing reveals a de novo mutation associated with mild developmental delay ... Keywords. Wiedemann–Steiner syndrome; whole exome sequencing; hairy elbows; hypertrichosis cubiti; gene; KMT2A; developmental delay; children.

  3. Natural Disasters that Reveal Cracks in Our Social Foundation

    Science.gov (United States)

    Langer, Nieli

    2004-01-01

    The recent deaths of more than 13,000 French elderly in the European heat wave of 2003 revealed cracks in the social foundation of urban communities, here and abroad. The breakdown occurred in community services, neighborhood networks, and governmental agencies that were responsible for warning of impending dangers to at-risk elderly. This paper…

  4. An acute adrenal insufficiency revealing pituitary metastases of lung ...

    African Journals Online (AJOL)

    The chest X Rays revealed pulmonary opacity. Computed tomography scan of the chest showed a multiples tumors with mediastinal lymphadenopathy. Bronchoscopy and biopsy demonstrated a pulmonary adenocarcinoma. Hence we concluded to a lung cancer with multiple pituitary and adrenal gland metastases.

  5. Mitochondrial and nuclear DNA reveals a complete lineage sorti ng ...

    African Journals Online (AJOL)

    Glossogobius callidus exhibits broad salinity tolerance and is distributed in both estuarine and freshwater environments in southern Africa. Previous studies revealed substantial morphological and molecular variation among populations, suggesting they constitute a species complex. The present study utilised phylogenetic ...

  6. Puzzles in modern biology. I. Male sterility, failure reveals design

    OpenAIRE

    Frank, Steven A.

    2016-01-01

    Many human males produce dysfunctional sperm. Various plants frequently abort pollen. Hybrid matings often produce sterile males. Widespread male sterility is puzzling. Natural selection prunes reproductive failure. Puzzling failure implies something that we do not understand about how organisms are designed. Solving the puzzle reveals the hidden processes of design.

  7. Proteomic and transcriptomic analysis reveals evidence for the basis ...

    African Journals Online (AJOL)

    Proteomic and transcriptomic analysis reveals evidence for the basis of salt sensitivity in Thai jasmine rice ( Oryza sativa L. cv. ... African Journal of Biotechnology ... the posttranscriptional mechanisms controlling protein expression levels were not as efficient as in Pokkali, indicating targets for future genetic improvement.

  8. Microbiota analysis to reveal temperature abuse of fresh pork

    DEFF Research Database (Denmark)

    Buschhardt, Tasja; Bahl, Martin Iain; Hansen, Tina Beck

    Violations of temperature regulations in the meat chain may affect meat safety. Methods are lacking to estimate whether meat has been subjected to temperature abuse. Exposure to too high temperatures may lead to systematic changes in the diverse bacterial communities of fresh meat. We investigated...... whether temperature induced changes in the community composition on fresh meat surfaces can reflect the temperature-history (combination of time and temperature). Sterile pieces of pork were inoculated with a carcass swab homogenate, to which Salmonella was added. Changes in the meat microbiota were...... was dominated by Pseudomonas only. We also showed that the initial community affects subsequent changes during storage. The results suggest that principal coordinate analysis of beta diversity could be a useful tool to reveal temperature abused meat. Sequence data and culturing data revealed a strong positive...

  9. Ascites and other incidental findings revealing undiagnosed systemic rheumatoid arthritis.

    Science.gov (United States)

    Szeto, Matthew Chak Hin; Disney, Benjamin; Perkins, Philip; Wood, Gordon

    2015-06-08

    We describe a case of a 43-year-old man presenting to the gastroenterology outpatient department with exudative ascites. Mediastinal lymphadenopathy, pericardial effusion and pleural effusion were detected on further imaging. Further clinical examination revealed subcutaneous nodules on the left arm, which were confirmed to be rheumatoid nodules on histology. Inflammatory markers were elevated with positive serology for rheumatoid factor and anticyclic citrullinated protein antibody. Our investigations excluded tuberculosis, pancreatitis and malignancy in the patient. Following review by a rheumatologist, a diagnosis of systemic rheumatoid arthritis (RA) was made. Pleuritis and pericarditis are well recognised as extra-articular manifestation of RA. Ascites, however, is rarely recognised as a manifestation of RA. Our literature search revealed two other cases of ascites due to RA disease activity, and both patients had long-standing known RA. This case adds to the discussion on whether ascites and peritonitis should be classified as extra-articular manifestations of RA. 2015 BMJ Publishing Group Ltd.

  10. Intracranial Hemorrhage Revealing Pseudohypoparathyroidism as a Cause of Fahr Syndrome

    Directory of Open Access Journals (Sweden)

    Abhijit Swami

    2011-01-01

    Full Text Available Pseudohypoparathyroidism is an infrequently encountered disease. It is one of the causes of Fahr syndrome which also is a rare clinical entity caused by multiple diseases. A 4-year-old man hospitalized for sudden onset left hemiparesis and hypertension was diagnosed to have right thalamic and midbrain hemorrhage on plain CT scan of the head which also revealed co-existent extensive intracranial calcifications involving the basal ganglia and cerebellum bilaterally. General physical examination revealed features of Albright hereditary osteodystrophy, goitre, hypertension, left hemiparesis, and signs of cerebellar dysfunction. Laboratory findings suggested hypocalcemia, hyperphosphatemia along with high TSH, low FT4, low FT3, and high anti-TPO antibody. Though bilateral intracranial calcifications are usually encountered as an incidental radiological finding in the CT scan of brain, in this case, the patient admitted for thalamic and midbrain hemorrhage was on investigation for associated intracranial calcification, and goitre was also found to have coexisting pseudohypoparathyroidism and autoimmune hypothyroidism.

  11. Maps of random walks on complex networks reveal community structure.

    Science.gov (United States)

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  12. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...... misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan-and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity...

  13. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.

    Directory of Open Access Journals (Sweden)

    Erin A Lynch

    Full Text Available We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications. Seven genomes were sequenced to ∼20×coverage and assembled to an average of 50 contigs (range 5 scaffolds-168 contigs. Comparisons of protein-coding gene compliments revealed large-scale differences in COG functional group enrichment between these genera. Analysis of genes encoding machinery for DNA metabolism reveals genera-specific expansions of the general transcription factor TATA binding protein as well as a history of extensive duplication and horizontal transfer of the proliferating cell nuclear antigen. Insights gained from this study emphasize the importance of haloarchaea for investigation of archaeal biology.

  14. Expansion by regions: revealing potential and Glauber regions automatically

    Energy Technology Data Exchange (ETDEWEB)

    Jantzen, Bernd [RWTH Aachen University, Institut fuer Theoretische Teilchenphysik und Kosmologie, Aachen (Germany); Smirnov, Alexander V. [Moscow State University, Scientific Research Computing Center, Moscow (Russian Federation); KIT, Institut fuer Theoretische Teilchenphysik, Karlsruhe (Germany); Smirnov, Vladimir A. [Moscow State University, Skobeltsyn Institute of Nuclear Physics, Moscow (Russian Federation); KIT, Institut fuer Theoretische Teilchenphysik, Karlsruhe (Germany)

    2012-09-15

    When performing asymptotic expansions using the strategy of expansion by regions, it is a non-trivial task to find the relevant regions. The recently published Mathematica code asy.m automates this task, but it has not been able to detect potential regions in threshold expansions or Glauber regions. In this work we present an algorithm and its implementation in the update asy2.m which also reveals potential and Glauber regions automatically. (orig.)

  15. Digital tissue and what it may reveal about the brain.

    Science.gov (United States)

    Morgan, Josh L; Lichtman, Jeff W

    2017-10-30

    Imaging as a means of scientific data storage has evolved rapidly over the past century from hand drawings, to photography, to digital images. Only recently can sufficiently large datasets be acquired, stored, and processed such that tissue digitization can actually reveal more than direct observation of tissue. One field where this transformation is occurring is connectomics: the mapping of neural connections in large volumes of digitized brain tissue.

  16. Spontaneous chylothorax revealing a mediastinal and abdominal lymph node tuberculosis.

    Science.gov (United States)

    Amar, Jihen Ben; Zaibi, Haifa; Dahri, Besma; Aouina, Hichem

    2017-04-01

    Chylothorax is a rare manifestation of tuberculosis. We report a case of spontaneous chylothorax due to tuberculosis. A 62-year-old woman was admitted with fever, chest pain and dyspnea. Chest and abdominal computed tomography revealed a fluid collection with necrotic mediastinal and abdominal lymph nodes. Biopsy of lymph nodes by mediastinoscopy. The patient was treated with anti-tuberculosis medication. He is clinically improved and his pleural effusion also completely resolved. Copyright © 2016. Published by Elsevier B.V.

  17. King Lear Reveals the Tragic Pattern of Shakespeare

    OpenAIRE

    Salim Eflih Al-Ibia

    2017-01-01

    Rather than focusing on the obvious traditions of evaluating Shakespearean tragic heroes, this paper presents a groundbreaking approach to unfold the pattern William Shakespeare follows as he designed his unique characters. This pattern applies to most, if not all, Shakespearean tragic heroes. I argue that Shakespeare himself reveals a great portion of this pattern on the tongue of Lear as the latter disowns Goneril and Regan promising to have “such revenges on [them] both” in King Lear. Lear...

  18. Cavitary lung lesion suspicious for malignancy reveals Mycobacterium xenopi.

    Science.gov (United States)

    Fogla, Sumit; Pansare, Vaishali M; Camero, Luis G; Syeda, Uzma; Patil, Naveen; Chaudhury, Arun

    2018-01-01

    We report the case of a 68-year-old gentleman who presented with musculoskeletal chest pain which appeared suddenly when he bent over with his dog. The chest pain was localized to the left lower chest and increased with movement and deep breathing. The patient did not complain weight loss, night sweat, fever or chill. He complained of mild cough, with expectoration of whitish mucus. Imaging revealed cavitary chest lesion in the right upper lobe, which was initially suspected to be lung cancer. The patient had a 50-year-old history of smoking 2 packs per day. PET CT imaging did not reveal any specific activity. Needle biopsy and bronchoalveolar lavage, however, did not reveal any malignant cells. Rather, necrotic tissues were observed. A wedge resection of the lung mass was performed. No common organisms or fungi could be grown. However, acid fast bacilli were observed in clumps. The morphology hinted towards non-tuberculous mycobacterial organism(s). Molecular studies revealed infection with Mycobacterium xenopi. The patient was started on an anti-tuberculous regimen of INH, rifampicin, ethambutol and PZA, with pyridoxine. The patient is a Vietnam veteran and complained of exposure to dust from a bird's nest and asbestos exposure in childhood, but no specific exposure to tuberculosis. The patient had an uneventful recovery post-surgery. He complained of some nausea after initiation of the antituberculous medications, but his pain subsided with time. The patient had diabetes, though specific reasons of compromise of immune status could not be pinpointed as causative of his nontuberculous mycobacterial lung infection.

  19. Blue whale earplug reveals lifetime contaminant exposure and hormone profiles

    OpenAIRE

    Trumble, Stephen J.; Robinson, Eleanor M.; Berman-Kowalewski, Michelle; Potter, Charles W.; Usenko, Sascha

    2013-01-01

    Currently, obtaining lifetime chemical profiles (i.e., from birth to death) is extremely rare and difficult for most of Earth’s animals. We have developed a unique approach to quantify hormone and contaminant lifetime profiles for an individual blue whale with a 6-mo resolution using the wax earplug as a natural matrix capable of archiving and preserving these temporal profiles. Using a male blue whale earplug, chemical analysis reveals lifetime patterns of mercury and organic pollutant expos...

  20. Inheritance patterns in citation networks reveal scientific memes

    OpenAIRE

    Tobias Kuhn; Matjaž Perc; Dirk Helbing

    2014-01-01

    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 we validate i...

  1. Revealing the invisible: the paradox of picturing a phantom limb.

    Science.gov (United States)

    Schott, G D

    2014-03-01

    Illustrations of phantom limbs are intriguing as they depict an invisible perception. But such illustrations are also important: they provide a form of objectivity to phenomena, which particularly in the past, have often stretched credulity. Acknowledging the paradox of using images to reveal an absent though sensate body part, depictions of phantom limbs are discussed from the neurological perspective, starting with medieval pictures that showed the miraculous restoration of limbs, and which possibly represented pictorial metaphors for a phantom limb. Centuries later, phantom limbs-whether resulting from amputation or deafferentation-became illustrated, and some reasons for their illustration are considered. Although often depicted by others, the most precise and perhaps revealing illustrations of these phantoms have been those made when patients guide the artist, or draw the phantom themselves. In the case of phantom pains, the painful component too is sometimes illustrated, again, as with the miraculous, in metaphorical terms. More recently, depictions of phantoms have also been revealing in studies of some underlying mechanisms of phantom phenomena, notably in demonstrating novel patterns of referred sensations after amputation and attributable to cortical plasticity. Mention is made of photographs of phantom hands visualized using a mirror box, such visualization recalling full circle the miraculous restoration of limbs pictured in the past. The nature of the outline of the phantom is included in a discussion of demarcation of an invisible body part, before concluding that images of phantom limbs provide an invaluable background to understanding and studying these remarkable sensory phenomena.

  2. 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.

  3. Active medulloblastoma enhancers reveal subgroup-specific cellular origins

    Science.gov (United States)

    Lin, Charles Y.; Erkek, Serap; Tong, Yiai; Yin, Linlin; Federation, Alexander J.; Zapatka, Marc; Haldipur, Parthiv; Kawauchi, Daisuke; Risch, Thomas; Warnatz, Hans-Jörg; Worst, Barbara C.; Ju, Bensheng; Orr, Brent A.; Zeid, Rhamy; Polaski, Donald R.; Segura-Wang, Maia; Waszak, Sebastian M.; Jones, David T.W.; Kool, Marcel; Hovestadt, Volker; Buchhalter, Ivo; Sieber, Laura; Johann, Pascal; Chavez, Lukas; Gröschel, Stefan; Ryzhova, Marina; Korshunov, Andrey; Chen, Wenbiao; Chizhikov, Victor V.; Millen, Kathleen J.; Amstislavskiy, Vyacheslav; Lehrach, Hans; Yaspo, Marie-Laure; Eils, Roland; Lichter, Peter; Korbel, Jan O.; Pfister, Stefan M.; Bradner, James E.; Northcott, Paul A.

    2016-01-01

    Summary Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Using H3K27ac and BRD4 ChIP-Seq, coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-Seq, that are responsible for subgroup divergence and implicate candidate cells-of-origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins. PMID:26814967

  4. 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

  5. Revealed Comparative Advantage of Services in Cariforum Countries

    Directory of Open Access Journals (Sweden)

    Marie Freckleton

    2014-09-01

    Full Text Available A pesar de la importancia de las exportaciones de servicios a los países del CARIFORUM no hay muchos estudios sobre de la competitividad de las exportaciones. Este artículo examina la ventaja comparativa revelada de las exportaciones de servicios de los países del CARIFORUM. El análisis muestra que la mayoría de los países del CARIFORUM han puesto de manifiesto las ventajas comparativas en el turismo, pero también hay casos de ventaja comparativa revelada en otros servicios como transporte, seguros y servicios empresariales, servicios personales, culturales y recreativos. Los resultados sugieren que existe un potencial de CARIFORUM para diversificar las exportaciones de servicios con el fin de pro-mover el crecimiento económico y reducir la vulnerabilidad. Sin embargo, en la medida en que los países del CARIFORUM pueden tomar ventaja de las oportunidades existentes de acceso al Mercado de los servicios depende de su capacidad de mejorar la capacidad de oferta de servicios y promover la competitividad de los servicios. English: Despite the importance of services ex-ports to CARIFORUM countries there is limited research on the competitiveness of such exports. This article examines the revealed comparative advantage of services exports in CARIFORUM countries. The analysis shows that most CARIFORUM countries have revealed comparative advantage in tourism but there are also cases of revealed comparative advantage in other services including transport, insurance, business services and personal, cultural and recreational services. The results suggest that there is potential for CARIFORUM to diversify exports of services in order to promote economic growth and reduce vulnerability. However, the extent to which CARIFORUM countries can take advantage of existing market access opportunities for services depends on their ability to improve the capacity to supply services and to promote the competitiveness of services.

  6. The features of Drosophila core promoters revealed by statistical analysis

    Directory of Open Access Journals (Sweden)

    Trifonov Edward N

    2006-06-01

    Full Text Available Abstract Background Experimental investigation of transcription is still a very labor- and time-consuming process. Only a few transcription initiation scenarios have been studied in detail. The mechanism of interaction between basal machinery and promoter, in particular core promoter elements, is not known for the majority of identified promoters. In this study, we reveal various transcription initiation mechanisms by statistical analysis of 3393 nonredundant Drosophila promoters. Results Using Drosophila-specific position-weight matrices, we identified promoters containing TATA box, Initiator, Downstream Promoter Element (DPE, and Motif Ten Element (MTE, as well as core elements discovered in Human (TFIIB Recognition Element (BRE and Downstream Core Element (DCE. Promoters utilizing known synergetic combinations of two core elements (TATA_Inr, Inr_MTE, Inr_DPE, and DPE_MTE were identified. We also establish the existence of promoters with potentially novel synergetic combinations: TATA_DPE and TATA_MTE. Our analysis revealed several motifs with the features of promoter elements, including possible novel core promoter element(s. Comparison of Human and Drosophila showed consistent percentages of promoters with TATA, Inr, DPE, and synergetic combinations thereof, as well as most of the same functional and mutual positions of the core elements. No statistical evidence of MTE utilization in Human was found. Distinct nucleosome positioning in particular promoter classes was revealed. Conclusion We present lists of promoters that potentially utilize the aforementioned elements/combinations. The number of these promoters is two orders of magnitude larger than the number of promoters in which transcription initiation was experimentally studied. The sequences are ready to be experimentally tested or used for further statistical analysis. The developed approach may be utilized for other species.

  7. Genetics of aplasia cutis reveal novel regulators of skin morphogenesis.

    Science.gov (United States)

    Marneros, Alexander G

    2015-03-01

    The molecular mechanisms that control skin morphogenesis are complex and only incompletely understood. Aplasia cutis manifests with localized skin defects at birth and is a feature in various syndromes. Identifying the genes that cause these genetic skin conditions provides the opportunity to define novel regulators of skin morphogenesis. Recently, human genetic approaches have led to the identification of aplasia cutis-causing mutations in genes that have previously not been implicated to have an important role in skin biology. These findings reveal novel molecular mechanisms that are involved in skin formation during development.

  8. Dr. Oscar Costa Mandry: a life in the tropics revealed.

    Science.gov (United States)

    Christenson, Bernard

    2007-01-01

    Dr. Oscar Costa-Mandry, "The Father of Medical Technology in Puerto Rico"; his lifetime achievements in the tropics are revealed in the context of his influential role in the School of Tropical Medicine and his clear visionary perspective for the creation of the University of Puerto Rico School of Medicine. With his unique and diverse contributions for more than 40 years in the fields of clinical laboratory medicine, public health and medical education, and as an insightful historian, he dramatically influenced and reshaped the Puerto Rican medical and social landscape for future generations to come.

  9. 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.

  10. Contrast-enhanced ultrasonography revealed active thoracic bleeding.

    Science.gov (United States)

    Sugihara, Takaaki; Koda, Masahiko; Tokunaga, Shiho; Matono, Tomomitsu; Nagahara, Takakazu; Ueki, Masaru; Murawaki, Yoshikazu; Kaminou, Toshio

    2010-07-01

    A 61-year-old woman with a hepatocellular carcinoma located in the subphrenic region was treated by radiofrequency ablation (RFA) under artificial pleural effusion. During RFA, B-mode ultrasonography showed a swirling high echoic lesion in the artificial pleural effusion. A real-time scan performed using contrast-enhanced ultrasonography (CEUS) revealed a jet-like extravasation of contrast medium and pooling of microbubbles in the pleural cavity, which were confirmed by angiography. CEUS successfully identified the site of bleeding and can be regarded an effective tool for detecting active bleeding in an emergency.

  11. Hepatobiliary Cystadenoma Revealed by a Jaundice: A Case Report

    Directory of Open Access Journals (Sweden)

    Taoufiq Harmouch

    2011-01-01

    Full Text Available Introduction. Hepatobiliary cystadenomas are rare benign cystic tumors and have a potential for recurrence and malignant transformation. The diagnosis may be very difficult because of absence of typical imaging feature in some cases. Case Presentation. In this paper, the authors discuss a 57-year-old woman who presented a jaundice related to hepatobiliary cystadenoma. Biological and radiological examinations have led to surgery, and the diagnosis is made after a histological examination of surgical specimens. Conclusion. This observation illustrates a hepatobiliary cystadenoma revealed by jaundice. Histology examination contributed to diagnosis. The authors discussed the mechanisms of biliary obstruction and differential diagnoses through a review of the literature.

  12. 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.

  13. 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

  14. Seasonal succession in zooplankton feeding traits reveals trophic trait coupling

    DEFF Research Database (Denmark)

    Kenitz, Kasia; Visser, Andre; Mariani, Patrizio

    2017-01-01

    acquisition and photosynthesis, it also depends on grazing which couples feeding and motility traits across trophic guilds. Despite interannual variations in the species dominating the protist plankton community, the seasonal trait distribution reveals robust and repeatable seasonal patterns, changing between...... succession and shows how the physical environment controls the vertical structure of plankton communities, where ambush feeders exhibit a preference for greater depths during summer. We characterize the seasonal succession as trophic trait coupling and conjecture that this coupling leads to a trophic trait...... cascade where successive trophic levels alternate in their expression of activity traits further up in the food chain...

  15. The revealed competitiveness of U.S. exports

    OpenAIRE

    J. Gruber; B. Mandel; M. Del Gatto; di Mauro, F.

    2011-01-01

    We investigate the factors behind the recent decline in the U.S. share of world merchandise exports in an attempt to determine how big a role the changing productivity of U.S. firms has played. We do so against the backdrop of a measure of cost competitiveness which, insofar it is inferred from actual trade ows, we refer to as 'revealed marginal costs' (RMC). Although, in line with our purpose, we derive such measure as an implication of a trade model with (intra-industry) firm heterogeneity,...

  16. 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.

  17. 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.

  18. Using patients' narratives to reveal gender stereotypes among medical students.

    Science.gov (United States)

    Andersson, Jenny; Salander, Pär; Hamberg, Katarina

    2013-07-01

    Gender bias exists in patient treatment, and, like most people, health care providers harbor gender stereotypes. In this study, the authors examined the gender stereotypes that medical students hold about patients. In 2005, in Umeå, Sweden, the authors collected 81 narratives written by patients who had undergone cancer treatment; all information that might reveal the patients' gender was removed from the texts. Eighty-seven medical students read 40 or 41 narratives each, guessed the patient's gender, and explained their guess. The authors analyzed the students' explanations qualitatively and quantitatively to reveal the students' gender stereotypes and to determine whether those stereotypes had any predictive value for correctly guessing a patient's gender. The students' explanations contained 21 categories of justifications, 12 of which were significantly associated with the students guessing one gender or the other. Only three categories successfully predicted a correct identification of gender; two categories were more often associated with incorrect guesses. Medical students enter their training program with culturally shared stereotypes about male and female patients that could cause bias during their future careers as physicians. To prevent this, medical curricula must address gender stereotypes and their possible consequences. The impact of implicit stereotypes must be included in discussions about gender bias in health care.

  19. Ananke: temporal clustering reveals ecological dynamics of microbial communities

    Directory of Open Access Journals (Sweden)

    Michael W. Hall

    2017-09-01

    Full Text Available Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.

  20. [Apparent worsening of psoriasis lesions revealing methotrexate overdosage].

    Science.gov (United States)

    Haber, R; Baroudjian, B; Battistella, M; Bagot, M; Petit, A

    2017-09-13

    Methotrexate (MTX) is an antimetabolite drug used in the treatment of cancers and autoimmune diseases and frequently in dermatology for cutaneous and/or arthritic psoriasis. Toxicities due to MTX overdosage are mainly cutaneous, hepatic and hematologic. Herein, we report a case of MTX overdosage presenting as an erosive and an inflammatory flare of preexisting psoriatic plaques and with new palmar lesions. A 51-year-old male with a 6-year history of plaque psoriasis resistant to topical corticosteroids was started for the first time on MTX 20mg weekly. One week later, he presented with fever, general weakness and mucocutaneous ulcerations. Physical examination revealed inflammatory, erythematous and partially erosive annular plaques strictly confined to preexisting psoriatic lesions, along with keratotic psoriatic palmar plaques. Further questioning indicated that the patient was taking MTX 20mg daily. Investigations revealed neutropenia (1040/mm3) and skin histology showed prominent dystrophic keratinocytes and confirmed the diagnosis of methotrexate toxicity. Clinical and biological improvements were observed after cessation of MTX and treatment with folinic acid, IV hydration and urine alkalization. Skin lesions due to acute MTX toxicity are rare, but they herald later-onset pancytopenia. Identification of these cutaneous lesions might enable earlier treatment initiation. The predilection of MTX toxicity for preexisting lesions or the de novo appearance of palmoplantar pustules should not lead to the erroneous diagnosis of psoriasis flare. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  1. Elastic network normal mode dynamics reveal the GPCR activation mechanism.

    Science.gov (United States)

    Kolan, Dikla; Fonar, Gennadiy; Samson, Abraham O

    2014-04-01

    G-protein-coupled receptors (GPCR) are a family of membrane-embedded metabotropic receptors which translate extracellular ligand binding into an intracellular response. Here, we calculate the motion of several GPCR family members such as the M2 and M3 muscarinic acetylcholine receptors, the A2A adenosine receptor, the β2 -adrenergic receptor, and the CXCR4 chemokine receptor using elastic network normal modes. The normal modes reveal a dilation and a contraction of the GPCR vestibule associated with ligand passage, and activation, respectively. Contraction of the vestibule on the extracellular side is correlated with cavity formation of the G-protein binding pocket on the intracellular side, which initiates intracellular signaling. Interestingly, the normal modes of rhodopsin do not correlate well with the motion of other GPCR family members. Electrostatic potential calculation of the GPCRs reveal a negatively charged field around the ligand binding site acting as a siphon to draw-in positively charged ligands on the membrane surface. Altogether, these results expose the GPCR activation mechanism and show how conformational changes on the cell surface side of the receptor are allosterically translated into structural changes on the inside. Copyright © 2013 Wiley Periodicals, Inc.

  2. 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.

  3. Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment.

    Science.gov (United States)

    Shaffer, John R; Li, Jinxi; Lee, Myoung Keun; Roosenboom, Jasmien; Orlova, Ekaterina; Adhikari, Kaustabh; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; González-José, Rolando; Pfeffer, Paige E; Wollenschlaeger, Christopher A; Hecht, Jacqueline T; Wehby, George L; Moreno, Lina M; Ding, Anan; Jin, Li; Yang, Yajun; Carlson, Jenna C; Leslie, Elizabeth J; Feingold, Eleanor; Marazita, Mary L; Hinds, David A; Cox, Timothy C; Wang, Sijia; Ruiz-Linares, Andrés; Weinberg, Seth M

    2017-12-07

    The genetic basis of earlobe attachment has been a matter of debate since the early 20th century, such that geneticists argue both for and against polygenic inheritance. Recent genetic studies have identified a few loci associated with the trait, but large-scale analyses are still lacking. Here, we performed a genome-wide association study of lobe attachment in a multiethnic sample of 74,660 individuals from four cohorts (three with the trait scored by an expert rater and one with the trait self-reported). Meta-analysis of the three expert-rater-scored cohorts revealed six associated loci harboring numerous candidate genes, including EDAR, SP5, MRPS22, ADGRG6 (GPR126), KIAA1217, and PAX9. The large self-reported 23andMe cohort recapitulated each of these six loci. Moreover, meta-analysis across all four cohorts revealed a total of 49 significant (p < 5 × 10-8) loci. Annotation and enrichment analyses of these 49 loci showed strong evidence of genes involved in ear development and syndromes with auricular phenotypes. RNA sequencing data from both human fetal ear and mouse second branchial arch tissue confirmed that genes located among associated loci showed evidence of expression. These results provide strong evidence for the polygenic nature of earlobe attachment and offer insights into the biological basis of normal and abnormal ear development. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  4. King Lear Reveals the Tragic Pattern of Shakespeare

    Directory of Open Access Journals (Sweden)

    Salim Eflih Al-Ibia

    2017-04-01

    Full Text Available Rather than focusing on the obvious traditions of evaluating Shakespearean tragic heroes, this paper presents a groundbreaking approach to unfold the pattern William Shakespeare follows as he designed his unique characters. This pattern applies to most, if not all, Shakespearean tragic heroes. I argue that Shakespeare himself reveals a great portion of this pattern on the tongue of Lear as the latter disowns Goneril and Regan promising to have “such revenges on [them] both” in King Lear. Lear’s threats bestow four unique aspects that apply not only to his character but they also apply to Shakespearean tragic heroes. Lear’s speech tells us that he is determined to have an awful type of revenge on his daughters. However, the very same speech tells us that he seems uncertain about the method through which he should carry out this revenge. Lear does not express any type of remorse as he pursues his vengeful plans nor should he aim at amnesty. He also admits his own madness as he closes his revealing speech. This research develops these facts about Lear to unfold the unique pattern Shakespeare follows as he portrayed his major tragic figures. This pattern is examined, described and analyzed in King Lear, Othello, and Hamlet. We will find out that the pattern suggested in this study helps us better understand Shakespeare’s tragedies and enables us to provide better explanations for some controversial scenes in the tragedies discussed.

  5. Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.

    Science.gov (United States)

    Marcoline, Frank V; Bethel, Neville; Guerriero, Christopher J; Brodsky, Jeffrey L; Grabe, Michael

    2015-08-04

    The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Economic choices reveal probability distortion in macaque monkeys.

    Science.gov (United States)

    Stauffer, William R; Lak, Armin; Bossaerts, Peter; Schultz, Wolfram

    2015-02-18

    Economic choices are largely determined by two principal elements, reward value (utility) and probability. Although nonlinear utility functions have been acknowledged for centuries, nonlinear probability weighting (probability distortion) was only recently recognized as a ubiquitous aspect of real-world choice behavior. Even when outcome probabilities are known and acknowledged, human decision makers often overweight low probability outcomes and underweight high probability outcomes. Whereas recent studies measured utility functions and their corresponding neural correlates in monkeys, it is not known whether monkeys distort probability in a manner similar to humans. Therefore, we investigated economic choices in macaque monkeys for evidence of probability distortion. We trained two monkeys to predict reward from probabilistic gambles with constant outcome values (0.5 ml or nothing). The probability of winning was conveyed using explicit visual cues (sector stimuli). Choices between the gambles revealed that the monkeys used the explicit probability information to make meaningful decisions. Using these cues, we measured probability distortion from choices between the gambles and safe rewards. Parametric modeling of the choices revealed classic probability weighting functions with inverted-S shape. Therefore, the animals overweighted low probability rewards and underweighted high probability rewards. Empirical investigation of the behavior verified that the choices were best explained by a combination of nonlinear value and nonlinear probability distortion. Together, these results suggest that probability distortion may reflect evolutionarily preserved neuronal processing. Copyright © 2015 Stauffer et al.

  7. The new galaxy evolution paradigm revealed by the Herschel surveys

    Science.gov (United States)

    Eales, Stephen; Smith, Dan; Bourne, Nathan; Loveday, Jon; Rowlands, Kate; van der Werf, Paul; Driver, Simon; Dunne, Loretta; Dye, Simon; Furlanetto, Cristina; Ivison, R. J.; Maddox, Steve; Robotham, Aaron; Smith, Matthew W. L.; Taylor, Edward N.; Valiante, Elisabetta; Wright, Angus; Cigan, Philip; De Zotti, Gianfranco; Jarvis, Matt J.; Marchetti, Lucia; Michałowski, Michał J.; Phillipps, Steven; Viaene, Sebastien; Vlahakis, Catherine

    2018-01-01

    The Herschel Space Observatory has revealed a very different galaxyscape from that shown by optical surveys which presents a challenge for galaxy-evolution models. The Herschel surveys reveal (1) that there was rapid galaxy evolution in the very recent past and (2) that galaxies lie on a single Galaxy Sequence (GS) rather than a star-forming 'main sequence' and a separate region of 'passive' or 'red-and-dead' galaxies. The form of the GS is now clearer because far-infrared surveys such as the Herschel ATLAS pick up a population of optically red star-forming galaxies that would have been classified as passive using most optical criteria. The space-density of this population is at least as high as the traditional star-forming population. By stacking spectra of H-ATLAS galaxies over the redshift range 0.001 < z < 0.4, we show that the galaxies responsible for the rapid low-redshift evolution have high stellar masses, high star-formation rates but, even several billion years in the past, old stellar populations - they are thus likely to be relatively recent ancestors of early-type galaxies in the Universe today. The form of the GS is inconsistent with rapid quenching models and neither the analytic bathtub model nor the hydrodynamical EAGLE simulation can reproduce the rapid cosmic evolution. We propose a new gentler model of galaxy evolution that can explain the new Herschel results and other key properties of the galaxy population.

  8. Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

    Science.gov (United States)

    Mueller, Nikola S.; Krumsiek, Jan; Theis, Fabian J.; Böhm, Christian; Meyer-Bäse, Anke

    2011-06-01

    Advances in high-throughput measurements of biological specimens necessitate the development of biologically driven computational techniques. To understand the molecular level of many human diseases, such as cancer, lipid quantifications have been shown to offer an excellent opportunity to reveal disease-specific regulations. The data analysis of the cell lipidome, however, remains a challenging task and cannot be accomplished solely based on intuitive reasoning. We have developed a method to identify a lipid correlation network which is entirely disease-specific. A powerful method to correlate experimentally measured lipid levels across the various samples is a Gaussian Graphical Model (GGM), which is based on partial correlation coefficients. In contrast to regular Pearson correlations, partial correlations aim to identify only direct correlations while eliminating indirect associations. Conventional GGM calculations on the entire dataset can, however, not provide information on whether a correlation is truly disease-specific with respect to the disease samples and not a correlation of control samples. Thus, we implemented a novel differential GGM approach unraveling only the disease-specific correlations, and applied it to the lipidome of immortal Glioblastoma tumor cells. A large set of lipid species were measured by mass spectrometry in order to evaluate lipid remodeling as a result to a combination of perturbation of cells inducing programmed cell death, while the other perturbations served solely as biological controls. With the differential GGM, we were able to reveal Glioblastoma-specific lipid correlations to advance biomedical research on novel gene therapies.

  9. Drastic changes in Pluto atmosphere revealed by stellar occultations

    Science.gov (United States)

    Sicardy, B.; Widemann, T.; Lellouch, T.; Colas, F.; Roques, F.; Veillet, C.; Cuillandre, J.-C.

    Pluto's tenuous nitrogen atmosphere was first detected by stellar occultations from Israel in 1985, and more extensively studied during a second event from Australia in June 1988. This atmosphere is poorly known, however, due to the rarity of these events. We report here the first Pluto occultation observations in 2002 (July 20 and august 21), after a lapse of fourteen years. The July data were gathered from northern Chile with a portable telescope, in the frame of a large campaign in South America, while the August event was observed from Hawaii (CFHT). Results of our analysis reveal drastic changes undergone by the atmosphere since 1988, namely a two-fold pressure increase, revealing the effect of seasonal changes on Pluto over this fourteen year interval. This provides insights into surface-atmosphere interactions and temporal variability on distant icy bodies of the solar system. Spikes observed in the CFHT lightcurve betrays the presence of a dynamical activity, either associated with shear instabilities caused by strong winds, or with a hypothetical troposphere near the surface of the planet.

  10. 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

    2013-01-01

    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

  11. 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.

  12. Molecular conformation changes along the malignancy revealed by optical nanosensors

    Science.gov (United States)

    Cinta Pinzaru, Simona; Falamas, Alexandra; Dehelean, Cristina Adriana

    2013-01-01

    An interdisciplinary approach employing functionalized nanoparticles and ultrasensitive spectroscopic techniques is reported here to track the molecular changes in early stage of malignancy. Melanoma tissue tracking at molecular level using both labelled and unlabelled silver and gold nanoparticles has been achieved using surface enhanced Raman scattering (SERS) technique. We used skin tissue from ex vivo mice with induced melanoma. Raman and SERS molecular characterization of melanoma tissue is proposed here for the first time. Optical nanosensors based on Ag and Au nanoparticles with chemisorbed cresyl violet molecular species as labels revealed sensitive capability to tissues tagging and local molecular characterization. Sensitive information originating from surrounding native biological molecules is provided by the tissue SERS spectra obtained either with visible or NIR laser line. Labelled nanoparticles introduced systematic differences in tissue response compared with unlabelled ones, suggesting that the label functional groups tag specific tissue components revealed by proteins or nucleic acids bands. Vibrational data collected from tissue are presented in conjunction with the immunohistochemical analysis. The results obtained here open perspectives in applied plasmonic nanoparticles and SERS for the early cancer diagnostic based on the appropriate spectral databank. PMID:23301881

  13. 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

  14. A Survey of Electronic Serials Managers Reveals Diversity in Practice

    Directory of Open Access Journals (Sweden)

    Laura Costello

    2014-09-01

    Full Text Available A Review of: Branscome, B. A. (2013. Management of electronic serials in academic libraries: The results of an online survey. Serials Review, 39(4, 216-226. http://dx.doi.org/10.1016/j.serrev.2013.10.004 Abstract Objective – To examine industry standards for the management of electronic serials and measure the adoption of electronic serials over print. Design – Survey questionnaire. Setting – Email lists aimed at academic librarians working in serials management. Subjects – 195 self-selected subscribers to serials email lists. Methods – The author created a 20 question survey that consisted primarily of closed-ended questions pertaining to the collection demographics, staff, budget, and tools of serials management groups in academic libraries. The survey was conducted via Survey Monkey and examined using the analytical features of the tool. Participants remained anonymous and the survey questions did not ask them to reveal identifiable information about their libraries. Main Results – Collection demographics questions revealed that 78% of surveyed librarians estimated that print-only collections represented 40% or fewer of their serials holdings. The author observed diversity in the factors that influence print to digital transitions in academic libraries. However 71.5% of participants indicated that publisher technology support like IP authentication was required before adopting digital subscriptions. A lack of standardization also marked serials workflows, department responsibilities, and department titles. The author did not find a correlation between serials budget and the enrollment size of the institution. Participants reported that they used tools from popular serials management vendors like Serials Solutions, Innovative Interfaces, EBSCO, and Ex Libris, but most indicated that they used more than one tool for serials management. Participants specified 52 unique serials management products used in their libraries. Conclusion

  15. An Addison disease revealed with a serious hyponatremia.

    Science.gov (United States)

    Maguet, Hadrien; Carreau, Agnès; Hautefeuille, Serge; Bonnin, Pierre; Beaune, Gaspard

    2017-02-01

    We present the case of an Addison's disease revealed by a serious hyponatremia. The serum concentration of ACTH and 21-hydroxylase antibodies were increased and lead to the diagnosis. The cortisol blood level was lowered but required to take into account the stress induced by the hospitalisation of the patient. Addison's disease is characterized by the destruction of the adrenal cortex. Autoimmune adrenalitis is the main cause of adrenal insufficiency. Treatment involves normalisation of sodium concentration and corticosteroids replacement. With a good patient compliance, the survival rate of Addisonian patient is similar to that of the normal population. Management of patient requires vigilance because of the occurrence of others autoimmunes diseases during patient life.

  16. 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.

  17. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-01-01

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics).

  18. Sequencing of 50 human exomes reveals adaptation to high altitude

    DEFF Research Database (Denmark)

    Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

    2010-01-01

    represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency......Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus...

  19. 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.

  20. Spring-block model reveals region-like structures.

    Directory of Open Access Journals (Sweden)

    Gabriell Máté

    Full Text Available A mechanical spring-block model is used for realizing an objective space partition of settlements from a geographic territory in region-like structures. The method is based on the relaxation-dynamics of the spring-block system and reveals in a hierarchical manner region-like entities at different spatial scales. It takes into account in an elegant manner both the spatiality of the elements and the connectivity relations among them. Spatiality is taken into account by using the geographic coordinates of the settlements, and by detecting the neighbors with the help of a Delaunay triangulation. Connectivity between neighboring settlements are quantified using a Pearson-like correlation for the relative variation of a relevant socio-economic parameter (population size, GDP, tax payed per inhabitant, etc.. The method is implemented in an interactive JAVA application and it is applied with success for an artificially generated society and for the case of USA, Hungary and Transylvania.

  1. Airborne observations reveal elevational gradient in tropical forest isoprene emissions

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Dasa; Guenther, Alex B.; Shilling, John E.; Yu, Haofei; Huang, Maoyi; Zhao, Chun; Yang, Qing; Martin, Scot T.; Artaxo, Paulo; Kim, Saewung; Seco, Roger; Stavrakou, Trissevgeni; Longo, Karla M.; Tóta, Julio; de Souza, Rodrigo Augusto Ferreira; Vega, Oscar; Liu, Ying; Shrivastava, Manish; Alves, Eliane G.; Santos, Fernando C.; Leng, Guoyong; Hu, Zhiyuan

    2017-05-23

    Isoprene dominates global non-methane volatile organic compound emissions, and impacts tropospheric chemistry by influencing oxidants and aerosols. Isoprene emission rates vary over several orders of magnitude for different plants, and characterizing this immense biological chemodiversity is a challenge for estimating isoprene emission from tropical forests. Here we present the isoprene emission estimates from aircraft eddy covariance measurements over the Amazonian forest. We report isoprene emission rates that are three times higher than satellite top-down estimates and 35% higher than model predictions. The results reveal strong correlations between observed isoprene emission rates and terrain elevations, which are confirmed by similar correlations between satellite-derived isoprene emissions and terrain elevations. We propose that the elevational gradient in the Amazonian forest isoprene emission capacity is determined by plant species distributions and can substantially explain isoprene emission variability in tropical forests, and use a model to demonstrate the resulting impacts on regional air quality.

  2. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

    Science.gov (United States)

    Ma, Li-Jun; van der Does, H. Charlotte; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Josée; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Woloshuk, Charles; Xie, Xiaohui; Xu, Jin-Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A. E.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G. J.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald M.; Goff, Stephen; Hammond-Kosack, Kim E.; Hilburn, Karen; Hua-Van, Aurélie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong-Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook-Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. Carmen; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, B. Gillian; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

    2011-01-01

    Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective. PMID:20237561

  3. 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 energy...... 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 levels...

  4. 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.

  5. Comparative genomics reveals insights into avian genome evolution and adaptation

    Science.gov (United States)

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    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. PMID:25504712

  6. Revealing Tripartite Quantum Discord with Tripartite Information Diagram

    Science.gov (United States)

    Lee, Wei-Ting; Li, Che-Ming

    2017-11-01

    A new measure based on the tripartite information diagram is proposed for identifying quantum discord in tripartite systems. The proposed measure generalizes the mutual information underlying discord from bipartite to tripartite systems, and utilizes both one-particle and two-particle projective measurements to reveal the characteristics of the tripartite quantum discord. The feasibility of the proposed measure is demonstrated by evaluating the tripartite quantum discord for systems with states close to Greenberger-Horne-Zeilinger, W, and biseparable states. In addition, the connections between tripartite quantum discord and two other quantum correlations---namely genuine tripartite entanglement and genuine tripartite Einstein-Podolsky-Rosen steering---are briefly discussed. The present study considers the case of quantum discord in tripartite systems. However, the proposed framework can be readily extended to general N-partite systems.

  7. Airborne observations reveal elevational gradient in tropical forest isoprene emissions

    Science.gov (United States)

    Gu, Dasa; Guenther, Alex B.; Shilling, John E.; Yu, Haofei; Huang, Maoyi; Zhao, Chun; Yang, Qing; Martin, Scot T.; Artaxo, Paulo; Kim, Saewung; Seco, Roger; Stavrakou, Trissevgeni; Longo, Karla M.; Tóta, Julio; de Souza, Rodrigo Augusto Ferreira; Vega, Oscar; Liu, Ying; Shrivastava, Manish; Alves, Eliane G.; Santos, Fernando C.; Leng, Guoyong; Hu, Zhiyuan

    2017-05-01

    Isoprene dominates global non-methane volatile organic compound emissions, and impacts tropospheric chemistry by influencing oxidants and aerosols. Isoprene emission rates vary over several orders of magnitude for different plants, and characterizing this immense biological chemodiversity is a challenge for estimating isoprene emission from tropical forests. Here we present the isoprene emission estimates from aircraft eddy covariance measurements over the Amazonian forest. We report isoprene emission rates that are three times higher than satellite top-down estimates and 35% higher than model predictions. The results reveal strong correlations between observed isoprene emission rates and terrain elevations, which are confirmed by similar correlations between satellite-derived isoprene emissions and terrain elevations. We propose that the elevational gradient in the Amazonian forest isoprene emission capacity is determined by plant species distributions and can substantially explain isoprene emission variability in tropical forests, and use a model to demonstrate the resulting impacts on regional air quality.

  8. Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics.

    Science.gov (United States)

    Wang, Xiaoli; Cai, Xiaofeng; Xu, Chenxi; Wang, Quanhua; Dai, Shaojun

    2016-10-18

    Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.

  9. Diffusion Tensor Tractography Reveals Disrupted Structural Connectivity during Brain Aging

    Science.gov (United States)

    Lin, Lan; Tian, Miao; Wang, Qi; Wu, Shuicai

    2017-10-01

    Brain aging is one of the most crucial biological processes that entail many physical, biological, chemical, and psychological changes, and also a major risk factor for most common neurodegenerative diseases. To improve the quality of life for the elderly, it is important to understand how the brain is changed during the normal aging process. We compared diffusion tensor imaging (DTI)-based brain networks in a cohort of 75 healthy old subjects by using graph theory metrics to describe the anatomical networks and connectivity patterns, and network-based statistic (NBS) analysis was used to identify pairs of regions with altered structural connectivity. The NBS analysis revealed a significant network comprising nine distinct fiber bundles linking 10 different brain regions showed altered white matter structures in young-old group compare with middle-aged group (p < .05, family-wise error-corrected). Our results might guide future studies and help to gain a better understanding of brain aging.

  10. Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution.

    Science.gov (United States)

    Bell, Phil R; Campione, Nicolás E; Persons, W Scott; Currie, Philip J; Larson, Peter L; Tanke, Darren H; Bakker, Robert T

    2017-06-01

    Recent evidence for feathers in theropods has led to speculations that the largest tyrannosaurids, including Tyrannosaurus rex, were extensively feathered. We describe fossil integument from Tyrannosaurus and other tyrannosaurids (Albertosaurus, Daspletosaurus, Gorgosaurus and Tarbosaurus), confirming that these large-bodied forms possessed scaly, reptilian-like skin. Body size evolution in tyrannosauroids reveals two independent occurrences of gigantism; specifically, the large sizes in Yutyrannus and tyrannosaurids were independently derived. These new findings demonstrate that extensive feather coverings observed in some early tyrannosauroids were lost by the Albian, basal to Tyrannosauridae. This loss is unrelated to palaeoclimate but possibly tied to the evolution of gigantism, although other mechanisms exist. © 2017 The Author(s).

  11. Dramatic changes in electronic structure revealed by fractionally charged nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Aron J. [Department of Chemistry, Lensfield Rd., University of Cambridge, Cambridge CB2 1EW (United Kingdom); Mori-Sánchez, Paula, E-mail: paula.mori@uam.es [Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid (Spain)

    2014-01-28

    Discontinuous changes in the electronic structure upon infinitesimal changes to the Hamiltonian are demonstrated. These are revealed in one and two electron molecular systems by full configuration interaction (FCI) calculations when the realm of the nuclear charge is extended to be fractional. FCI electron densities in these systems show dramatic changes in real space and illustrate the transfer, hopping, and removal of electrons. This is due to the particle nature of electrons seen in stretched systems and is a manifestation of an energy derivative discontinuity at constant number of electrons. Dramatic errors of density functional theory densities are seen in real space as this physics is missing from currently used approximations. The movements of electrons in these simple systems encapsulate those in real physical processes, from chemical reactions to electron transport and pose a great challenge for the development of new electronic structure methods.

  12. Genomic Perturbations Reveal Distinct Regulatory Networks in Intrahepatic Cholangiocarcinoma

    DEFF Research Database (Denmark)

    Nepal, Chirag; O'Rourke, Colm J; Oliveira, Douglas Vnp

    2018-01-01

    -exome sequencing, targeted exome sequencing) and epigenomic data from 496 patients, and used the three most recurrently mutated genes to stratify patients (IDH, KRAS, TP53, 'undetermined'). Using this molecular dissection approach, each subgroup was determined to possess unique mutational signature preferences, co...... all 3 mutations ('undetermined') harbored the most extensive structural alterations while IDH mutant tumors displayed the most extensive DNA methylome dysregulation, consistent with previous findings. CONCLUSION: Stratification of iCCA patients based on occurrence of mutations in three classifier...... genes (IDH, KRAS, TP53) revealed unique oncogenic programs (mutational, structural, epi-mutational) that influence pharmacologic response in drug repositioning protocols. This genome dissection approach highlights the potential of individual mutations to induce extensive molecular heterogeneity...

  13. [Thoracic aortic dissection revealed by systemic cholesterol embolism].

    Science.gov (United States)

    Braem, L; Paule, P; Héno, P; Morand, J J; Mafart, B; La Folie, T; Varlet, P; Mioulet, D; Fourcade, L

    2006-10-01

    Systemic cholesterol embolism is a rare complication of atherosclerosis, and has various presentations. Arterial catheterisms are a common cause. However, the association with an aortic dissection has been exceptionally reported. We report the observation of a 70 year-old man, with coronary artery disease, hypertension, diabetes and dyslipidemia. Six months before hospitalization, a coronary angioplasty was performed due to recurrent angina. The association of purpuric lesions on the feet, with acute renal failure confirmed cholesterol embolism syndrome. Transoesophageal echocardiography showed a dissection of the descending thoracic aorta associated with complex atheroma. The evolution was marked by the pulpar necrosis of a toe and by a worsening of the renal failure, requiring definitive hemodialysis. Further echographic control highlighted the rupture of the intimal veil of the dissection. Cholesterol embolism syndrome may reveal an aortic dissection in patients without thoracic symptoms. In such cases, transoesophageal echocardiography is a useful and non-invasive examination.

  14. Structure of mega-hemocyanin reveals protein origami in snails.

    Science.gov (United States)

    Gatsogiannis, Christos; Hofnagel, Oliver; Markl, Jürgen; Raunser, Stefan

    2015-01-06

    Mega-hemocyanin is a 13.5 MDa oxygen transporter found in the hemolymph of some snails. Similar to typical gastropod hemocyanins, it is composed of 400 kDa building blocks but has additional 550 kDa subunits. Together, they form a large, completely filled cylinder. The structural basis for this highly complex protein packing is not known so far. Here, we report the electron cryomicroscopy (cryo-EM) structure of mega-hemocyanin complexes from two different snail species. The structures reveal that mega-hemocyanin is composed of flexible building blocks that differ in their conformation, but not in their primary structure. Like a protein origami, these flexible blocks are optimally packed, implementing different local symmetries and pseudosymmetries. A comparison between the two structures suggests a surprisingly simple evolutionary mechanism leading to these large oxygen transporters. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Adipsic diabetes insipidus revealing a bifocal intracranial germinoma.

    Science.gov (United States)

    Kreutz, Julie; Potorac, Iulia; Lutteri, Laurence; Gennigens, Christine; Martin, Didier; Daly, Adrian F; Bonneville, Jean-Francois; Tshibanda, Luaba; Beckers, Albert

    2017-07-01

    Adipsic diabetes insipidus is a rare complication of intracranial tumors in which impaired antidiuretic hormone secretion is associated with the loss of thirst sensation. Here, we present the case of a patient with bifocal intracranial germinoma, diagnosed due to symptoms mainly caused by adipsic diabetes insipidus. This is, to our knowledge, the first case of adipsic diabetes insipidus revealing an intracranial germinoma reported in the literature. We describe the diagnostic procedures and the three-year follow-up of this patient. Management of intracranial germ-cell tumors is made complex by the wide range of histological features. Although germinomas have a generally better prognosis than most nongerminomatous tumors, they can have severe or even life-threatening presentations. Adipsic diabetes insipidus is one such severe presentation and its rarity can make it difficult to recognize and manage. Awareness of this potential entity is therefore important for clinical practice. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  16. Mathematical Analysis of Biomolecular Network Reveals Connections Between Diseases

    Science.gov (United States)

    Wang, Guanyu

    2012-02-01

    Connections between cancer and metabolic diseases may consist in the complex network of interactions among a common set of biomolecules. By applying singularity and bifurcation analysis, the phenotypes constrained by the AKT signaling pathway are identified and mapped onto the parameter space, which include cancer and certain metabolic diseases. By considering physiologic properties (sensitivity, robustness and adaptivity) the AKT pathway must possess in order to efficiently sense growth factors and nutrients, the region of normal responses is located. The analysis illuminates the parameter space and reveals system-level mechanisms in regulating biological functions (cell growth, survival, proliferation and metabolism) and how their deregulation may lead to the development of diseases. The analytical expressions summarize the synergistic interactions among many molecules, which provides valuable insights into therapeutic interventions.

  17. High-frequency microrheology reveals cytoskeleton dynamics in living cells

    Science.gov (United States)

    Rigato, Annafrancesca; Miyagi, Atsushi; Scheuring, Simon; Rico, Felix

    2017-08-01

    Living cells are viscoelastic materials, dominated by an elastic response on timescales longer than a millisecond. On shorter timescales, the dynamics of individual cytoskeleton filaments are expected to emerge, but active microrheology measurements on cells accessing this regime are scarce. Here, we develop high-frequency microrheology experiments to probe the viscoelastic response of living cells from 1 Hz to 100 kHz. We report the viscoelasticity of different cell types under cytoskeletal drug treatments. On previously inaccessible short timescales, cells exhibit rich viscoelastic responses that depend on the state of the cytoskeleton. Benign and malignant cancer cells revealed remarkably different scaling laws at high frequencies, providing a unique mechanical fingerprint. Microrheology over a wide dynamic range--up to the frequency characterizing the molecular components--provides a mechanistic understanding of cell mechanics.

  18. Multicentric Castleman's Disease in a Child Revealed by Chronic Diarrhea.

    Science.gov (United States)

    Benmiloud, Sarra; Chaouki, Sana; Atmani, Samir; Hida, Moustapha

    2015-01-01

    Multicentric Castleman's disease is a rare benign and unexplained lymphoproliferative disorder that is extremely uncommon in children. It presents with fever, systemic symptoms, generalized lymphadenopathy, and laboratory markers of inflammation. Its treatment is not standardized and its prognosis is poor. We report a novel case of multicentric Castleman's disease in a 13-year-old girl who had presented with chronic diarrhea as the only initial presenting symptom. The diagnosis of celiac or inflammatory bowel diseases was suspected, but two and a half years later, the diagnosis of multicentric Castleman's disease was brought following the appearance of abdominal mass whose biopsy revealed Castleman's disease in the plasma cell form. The outcome was favorable after treatment by corticosteroid, chemotherapy, and surgery. The occurrence of diarrhea as the initial symptom of multicentric Castleman's disease without lymph node involvement is very rare. This case report underlines the diagnostic difficulties and the long interval between onset and diagnosis when diarrhea occurs first.

  19. Electron tomography reveals unbranched networks of actin filaments in lamellipodia.

    Science.gov (United States)

    Urban, Edit; Jacob, Sonja; Nemethova, Maria; Resch, Guenter P; Small, J Victor

    2010-05-01

    Eukaryotic cells can initiate movement using the forces exerted by polymerizing actin filaments to extend lamellipodial and filopodial protrusions. In the current model, actin filaments in lamellipodia are organized in a branched, dendritic network. We applied electron tomography to vitreously frozen 'live' cells, fixed cells and cytoskeletons, embedded in vitreous ice or in deep-negative stain. In lamellipodia from four cell types, including rapidly migrating fish keratocytes, we found that actin filaments are almost exclusively unbranched. The vast majority of apparent filament junctions proved to be overlapping filaments, rather than branched end-to-side junctions. Analysis of the tomograms revealed that actin filaments terminate at the membrane interface within a zone several hundred nanometres wide at the lamellipodium front, and yielded the first direct measurements of filament densities. Actin filament pairs were also identified as lamellipodium components and bundle precursors. These data provide a new structural basis for understanding actin-driven protrusion during cell migration.

  20. Offenders' crime narratives as revealed by the Narrative Roles Questionnaire.

    Science.gov (United States)

    Youngs, Donna; Canter, David V

    2013-03-01

    The study of narrative processes as part of the immediate factors that shape criminal action is limited by the lack of a methodology for differentiating the narrative themes that characterise specific crime events. The current study explores how the roles offenders see themselves as playing during an offence encapsulate their underlying crime narratives and thus provide the basis for a quantitative methodology. To test this possibility, a 33-item Narrative Roles Questionnaire (NRQ) was developed from intensive interviews with offenders about their experience of committing a recent offence. A multidimensional analysis of the NRQ completed by 71 convicted offenders revealed life narrative themes similar to those identified in fiction by Frye and with noncriminals by McAdams, labelled The Professional, Victim, Hero, and Revenger offence roles. The NRQ thus is a first step in opening up the possibility of empirical studies of the narrative aetiological perspective in criminology.

  1. Treated-skin temperature regularities revealed by IR thermography

    Science.gov (United States)

    Vainer, Boris G.

    2001-03-01

    Experimental results disclosing temperature change of human skin affected by various unnatural factors are presented in detail. Thermograms are obtained with the IR thermograph containing high performance InAs CID FPA-based photosensitive unit. Using logarithmic scale of time, evolution of skin temperature after moistening, spirit sponging, and olive oil lubrication is investigated. A comparative analysis of the resulting effects of treatments including alpha-hydroxy acid, cosmetic regenerating cream, spirit, and water, is made. Quantitative distinctions between skin regions characterized by ordinary, and depleted blood supply, including areas located directly above surface main vessels, are revealed. Strongly logarithmic time- dependence of a skin temperature is discovered when the skin is cooled down after its preliminary heating with a hot wax. Non-monotonic change of a local temperature during electrically active procedure is described. Low level light therapy equipment is also applied. A special role of the temperature of nose is discussed.

  2. [Metastatic cervical fasciitis revealing invasive lobular breast carcinoma].

    Science.gov (United States)

    Munoz, J; Garcia, C; Joujoux, J-M; Dandurand, M; Meunier, L; Stoebner, P-E

    2015-02-01

    We describe the case of a 71-year-old woman presenting cervical metastatic fasciitis with invasive lobular carcinoma (ILC) of the breast. The patient consulted for a deep and painless skin infiltration of the neck associated with dysphagia and restricted cervical mobility. Skin and muscle biopsies were normal. Muscle fascia biopsy showed a linear infiltration of metastatic cells in "single file", revealing ILC of the right breast. ILCs have a particular metastatic pattern. They can permeate through tissue planes, infiltrate solid organs and spread on serous membranes in an insidious fashion. Our case shows that ILC can metastasise into muscular fascia, causing "fasciitis-like" symptoms. Dermatologists should be aware of this particular pattern of dissemination. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  3. 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.

  4. Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues

    DEFF Research Database (Denmark)

    Wagner, Sebastian A; Beli, Petra; Weinert, Brian T

    2012-01-01

    including proteasomal degradation of proteins, DNA damage repair and innateimmune responses. Here we combine high-resolution mass spectrometry with single-stepimmunoenrichment of di-glycine modified peptides for mapping of endogenous putativeubiquitylation sites in murine tissues. We identify more than 20......Posttranslational modifications of proteins increase the complexity of the cellular proteome andenable rapid regulation of protein functions in response to environmental changes. Proteinubiquitylation is a central regulatory posttranslational modification that controls numerousbiological processes......,000 unique ubiquitylation sites onproteins involved in diverse biological processes. Our data reveals that ubiquitylation regulates coresignaling pathways common for each of the studied tissues. In addition, we discover thatubiquitylation regulates tissue-specific signaling networks. Many tissue...

  5. Inheritance Patterns in Citation Networks Reveal Scientific Memes

    Directory of Open Access Journals (Sweden)

    Tobias Kuhn

    2014-11-01

    Full Text Available 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.

  6. 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.

  7. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members.

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-01-05

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or 'hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). Graphical Abstract ᅟ.

  8. 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

  9. Probing protein flexibility reveals a mechanism for selective promiscuity.

    Science.gov (United States)

    Pabon, Nicolas A; Camacho, Carlos J

    2017-04-22

    Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anticancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity. Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes. Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly undruggable targets.

  10. The ecological origins of snakes as revealed by skull evolution.

    Science.gov (United States)

    Da Silva, Filipe O; Fabre, Anne-Claire; Savriama, Yoland; Ollonen, Joni; Mahlow, Kristin; Herrel, Anthony; Müller, Johannes; Di-Poï, Nicolas

    2018-01-25

    The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.

  11. Dynamical Processes within an Anticyclonic Eddy Revealed from Argo Floats

    Science.gov (United States)

    Zhang, W. Z.; Xue, H.; Chai, F.; Ni, Q.

    2016-02-01

    Mesoscale eddies play a significant role in supplying the nutrients required for phytoplankton blooms and redistributing biomass in the ocean. However, how anticyclonic eddies influence nutrient flux and biomass distribution remains unclear and controversial. Here we reveal two important dynamical processes (radial displacement and vertical fluctuations) within an anticyclonic eddy using observations from Argo floats. Particles in the eddy were displaced toward the eddy edge due to the imbalance of radial momentum. Vertical fluctuations below the mixed layer resulted in alternating upwelling and downwelling in the inner and outer parts of the eddy. High salinity deep water was uplifted tens of meters by the upwelling and further extended to the surface with the aid of wind effects and submesoscale effects. Vertical motions associated with the fluctuations penetrated into the layer of several hundred meters deep. These processes exhibit crucial dynamical mechanisms for the motion of particles in mature anticyclonic eddies.

  12. 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.

  13. 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

  14. 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.

  15. Vibrio cholerae classical biotype strains reveal distinct signatures in Mexico.

    Science.gov (United States)

    Alam, Munirul; Islam, M Tarequl; Rashed, Shah Manzur; Johura, Fatema-tuz; Bhuiyan, Nurul A; Delgado, Gabriela; Morales, Rosario; Mendez, Jose Luis; Navarro, Armando; Watanabe, Haruo; Hasan, Nur-A; Colwell, Rita R; Cravioto, Alejandro

    2012-07-01

    Vibrio cholerae O1 classical (CL) biotype caused the fifth and sixth pandemics, and probably the earlier cholera pandemics, before the El Tor (ET) biotype initiated the seventh pandemic in Asia in the 1970s by completely displacing the CL biotype. Although the CL biotype was thought to be extinct in Asia and although it had never been reported from Latin America, V. cholerae CL and ET biotypes, including a hybrid ET, were found associated with areas of cholera endemicity in Mexico between 1991 and 1997. In this study, CL biotype strains isolated from areas of cholera endemicity in Mexico between 1983 and 1997 were characterized in terms of major phenotypic and genetic traits and compared with CL biotype strains isolated in Bangladesh between 1962 and 1989. According to sero- and biotyping data, all V. cholerae strains tested had the major phenotypic and genotypic characteristics specific for the CL biotype. Antibiograms revealed the majority of the Bangladeshi strains to be resistant to trimethoprim-sulfamethoxazole, furazolidone, ampicillin, and gentamicin, while the Mexican strains were sensitive to all of these drugs, as well as to ciprofloxacin, erythromycin, and tetracycline. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA revealed characteristic banding patterns for all of the CL biotype strains although the Mexican strains differed from the Bangladeshi strains in 1 to 2 DNA bands. The difference was subtle but consistent, as confirmed by the subclustering patterns in the PFGE-based dendrogram, and can serve as a regional signature, suggesting the pre-1991 existence and evolution of the CL biotype strains in the Americas, independent from Asia.

  16. Architecture of cognitive flexibility revealed by lesion mapping

    Science.gov (United States)

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

    2013-01-01

    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 R2 = 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

  17. Impaired Phosphate Tolerance Revealed With an Acute Oral Challenge.

    Science.gov (United States)

    Turner, Mandy E; White, Christine A; Hopman, Wilma M; Ward, Emilie C; Jeronimo, Paul S; Adams, Michael A; Holden, Rachel M

    2018-01-01

    Elevated serum phosphate is consistently linked with cardiovascular disease (CVD) events and mortality in the setting of normal and impaired kidney function. However, serum phosphate does not often exceed the upper limit of normal until glomerular filtration rate (GFR) falls below 30 mL/min/m2 . It was hypothesized that the response to an oral, bioavailable phosphate load will unmask impaired phosphate tolerance, a maladaptation not revealed by baseline serum phosphate concentrations. In this study, rats with varying kidney function as well as normo-phosphatemic human subjects, with inulin-measured GFR (13.2 to 128.3mL/min), received an oral phosphate load. Hormonal and urinary responses were evaluated over 2 hours. Results revealed that the more rapid elevation of serum phosphate was associated with subjects and rats with higher levels of kidney function, greater responsiveness to acute changes in parathyroid hormone (PTH), and significantly more urinary phosphate at 2 hours. In humans, increases in urinary phosphate to creatinine ratio did not correlate with baseline serum phosphate concentrations but did correlate strongly to early increase of serum phosphate. The blunted rise in serum phosphate in rats with CKD was not the result of altered absorption. This result suggests acute tissue deposition may be altered in the setting of kidney function impairment. Early recognition of impaired phosphate tolerance could translate to important interventions, such as dietary phosphate restriction or phosphate binders, being initiated at much higher levels of kidney function than is current practice. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

  18. Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions.

    Science.gov (United States)

    de Mas, Igor Marin; Selivanov, Vitaly A; Marin, Silvia; Roca, Josep; Orešič, Matej; Agius, Loranne; Cascante, Marta

    2011-10-28

    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. 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. 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 phosphates in cytosol. In contrast, the observed distribution

  19. [Latent-disseminated tuberculosis revealed by atypical skin ulcerations].

    Science.gov (United States)

    Ferrati-Fidelin, G; Pham-Ledard, A; Fauconneau, A; Chauvel, A; Houard, C; Doutre, M-S; Beylot-Barry, M

    2016-10-01

    Cutaneous tuberculosis (CT) is rare in industrialized countries. Given the clinicopathological polymorphism and the difficulty of isolating the pathogen, diagnosis can be difficult. The condition may be associated with other known locations of the disease or in rare cases, it may be a tell-tale sign, as in our case, in which leg ulcers revealed paucisymptomatic disseminated tuberculosis. A 67-year-old man was referred for rapidly extensive ulcers of the right leg contiguous to debilitating arthritis of the knee of unknown aetiology for 18 months. Earlier investigations revealed thymoma and a pulmonary nodule considered to be sarcoidosis. A skin biopsy showed a granulomatous eosinophilic-rich infiltrate and vasculitis of the small vessels. Screening of the skin sample and gastric aspirate for Koch Bacillus (BK) was negative. A diagnosis of sarcoidosis was made. A positive QuantiFERON test eventually led to the correct diagnosis. On further testing of bronchoalveolar fluid and a synovial biopsy, culture for Mycobacterium tuberculosis (MT) was positive. The PET scan showed high metabolism in the prostate, bone, spleen, liver, nodes and heart. The quad- and then dual-antibiotic antitubercular therapies produced a rapid improvement but treatment was continued over 12 months, given the persistence of high metabolism on PET-CT scan and the low blood rifampicin concentration. A CT should be considered in the presence of giant-cell granulomas, even in the absence of caseous necrosis, and where both direct examination and culture for the skin are negative. Our case also underlines the importance of an extensive workup to rule out disseminated disease even if the patient is not symptomatic. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  20. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Astronomers Reveal Extinct Extra-Terrestrial Fusion Reactor

    Science.gov (United States)

    2004-06-01

    An international team of astronomers, studying the left-over remnants of stars like our own Sun, have found a remarkable object where the nuclear reactor that once powered it has only just shut down. This star, the hottest known white dwarf, H1504+65, seems to have been stripped of its entire outer regions during its death throes leaving behind the core that formed its power plant. Scientists from the United Kingdom, Germany and the USA focused two of NASA's space telescopes, the Chandra X-ray Observatory and the Far Ultraviolet Spectroscopic Explorer (FUSE), onto H1504+65 to probe its composition and measure its temperature. The data revealed that the stellar surface is extremely hot, 200,000 degrees, and is virtually free of hydrogen and helium, something never before observed in any star. Instead, the surface is composed mainly of carbon and oxygen, the 'ashes' of the fusion of helium in a nuclear reactor. An important question we must answer is why has this unique star lost the hydrogen and helium, which usually hide the stellar interior from our view? Professor Martin Barstow (University of Leicester) said. 'Studying the nature of the ashes of dead stars give us important clues as to how stars like the Sun live their lives and eventually die. The nuclear waste of carbon and oxygen produced in the process are essential elements for life and are eventually recycled into interstellar space to form new stars, planets and, possibly, living beings.' Professor Klaus Werner (University of Tübingen) said. 'We realized that this star has, on astronomical time scales, only very recently shut down nuclear fusion (about a hundred years ago). We clearly see the bare, now extinct reactor that once powered a bright giant star.' Dr Jeffrey Kruk (Johns Hopkins University) said: 'Astronomers have long predicted that many stars would have carbon-oxygen cores near the end of their lives, but I never expected we would actually be able to see one. This is a wonderful opportunity to

  2. Acoustic telemetry reveals cryptic residency of whale sharks.

    Science.gov (United States)

    Cagua, E Fernando; Cochran, Jesse E M; Rohner, Christoph A; Prebble, Clare E M; Sinclair-Taylor, Tane H; Pierce, Simon J; Berumen, Michael L

    2015-04-01

    Although whale sharks (Rhincodon typus) have been documented to move thousands of kilometres, they are most frequently observed at a few predictable seasonal aggregation sites. The absence of sharks at the surface during visual surveys has led to the assumption that sharks disperse to places unknown during the long 'off-seasons' at most of these locations. Here we compare 2 years of R. typus visual sighting records from Mafia Island in Tanzania to concurrent acoustic telemetry of tagged individuals. Sightings revealed a clear seasonal pattern with a peak between October and February and no sharks observed at other times. By contrast, acoustic telemetry demonstrated year-round residency of R. typus. The sharks use a different habitat in the off-season, swimming deeper and further away from shore, presumably in response to prey distributions. This behavioural change reduces the sharks' visibility, giving the false impression that they have left the area. We demonstrate, for the first time to our knowledge, year-round residency of unprovisioned, individual R. typus at an aggregation site, and highlight the importance of using multiple techniques to study the movement ecology of marine megafauna. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  3. Metabolomics reveals insect metabolic responses associated with fungal infection.

    Science.gov (United States)

    Xu, Yong-Jiang; Luo, Feifei; Gao, Qiang; Shang, Yanfang; Wang, Chengshu

    2015-06-01

    The interactions between insects and pathogenic fungi are complex. We employed metabolomic techniques to profile insect metabolic dynamics upon infection by the pathogenic fungus Beauveria bassiana. Silkworm larvae were infected with fungal spores and microscopic observations demonstrated that the exhaustion of insect hemocytes was coupled with fungal propagation in the insect body cavity. Metabolomic analyses revealed that fungal infection could significantly alter insect energy and nutrient metabolisms as well as the immune defense responses, including the upregulation of carbohydrates, amino acids, fatty acids, and lipids, but the downregulation of eicosanoids and amines. The insect antifeedant effect of the fungal infection was evident with the reduced level of maclurin (a component of mulberry leaves) in infected insects but elevated accumulations in control insects. Insecticidal and cytotoxic mycotoxins like oosporein and beauveriolides were also detected in insects at the later stages of infection. Taken together, the metabolomics data suggest that insect immune responses are energy-cost reactions and the strategies of nutrient deprivation, inhibition of host immune responses, and toxin production would be jointly employed by the fungus to kill insects. The data obtained in this study will facilitate future functional studies of genes and pathways associated with insect-fungus interactions.

  4. Effective connectivity reveals strategy differences in an expert calculator.

    Directory of Open Access Journals (Sweden)

    Ludovico Minati

    Full Text Available Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of "cortical hubs" supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material.

  5. Acoustic telemetry reveals cryptic residency of whale sharks

    KAUST Repository

    Cagua, Edgar F.

    2015-04-01

    Althoughwhale sharks (Rhincodon typus) have beendocumentedtomove thousands of kilometres, they are most frequently observed at a few predictable seasonal aggregation sites. The absence of sharks at the surface during visual surveys has led to the assumption that sharks disperse to places unknown during the long \\'off-seasons\\' at most of these locations. Here we compare 2 years of R. typus visual sighting records from Mafia Island in Tanzania to concurrent acoustic telemetry of tagged individuals. Sightings revealed a clear seasonal pattern with a peak between October and February and no sharks observed at other times. By contrast, acoustic telemetry demonstrated yearround residency of R. typus. The sharks use a different habitat in the offseason, swimming deeper and further away from shore, presumably in response to prey distributions. This behavioural change reduces the sharks\\' visibility, giving the false impression that they have left the area.We demonstrate, for the first timeto our knowledge, year-roundresidencyofunprovisioned, individual R. typus at an aggregation site, and highlight the importance of using multiple techniques to study the movement ecology of marine megafauna. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  6. Symbolic joint entropy reveals the coupling of various brain regions

    Science.gov (United States)

    Ma, Xiaofei; Huang, Xiaolin; Du, Sidan; Liu, Hongxing; Ning, Xinbao

    2018-01-01

    The convergence and divergence of oscillatory behavior of different brain regions are very important for the procedure of information processing. Measurements of coupling or correlation are very useful to study the difference of brain activities. In this study, EEG signals were collected from ten subjects under two conditions, i.e. eyes closed state and idle with eyes open. We propose a nonlinear algorithm, symbolic joint entropy, to compare the coupling strength among the frontal, temporal, parietal and occipital lobes and between two different states. Instead of decomposing the EEG into different frequency bands (theta, alpha, beta, gamma etc.), the novel algorithm is to investigate the coupling from the entire spectrum of brain wave activities above 4Hz. The coupling coefficients in two states with different time delay steps are compared and the group statistics are presented as well. We find that the coupling coefficient of eyes open state with delay consistently lower than that of eyes close state across the group except for one subject, whereas the results without delay are not consistent. The differences between two brain states with non-zero delay can reveal the intrinsic inter-region coupling better. We also use the well-known Hénon map data to validate the algorithm proposed in this paper. The result shows that the method is robust and has a great potential for other physiologic time series.

  7. Visual features underlying perceived brightness as revealed by classification images.

    Directory of Open Access Journals (Sweden)

    Ilmari Kurki

    Full Text Available Along with physical luminance, the perceived brightness is known to depend on the spatial structure of the stimulus. Often it is assumed that neural computation of the brightness is based on the analysis of luminance borders of the stimulus. However, this has not been tested directly. We introduce a new variant of the psychophysical reverse-correlation or classification image method to estimate and localize the physical features of the stimuli which correlate with the perceived brightness, using a brightness-matching task. We derive classification images for the illusory Craik-O'Brien-Cornsweet stimulus and a "real" uniform step stimulus. For both stimuli, classification images reveal a positive peak at the stimulus border, along with a negative peak at the background, but are flat at the center of the stimulus, suggesting that brightness is determined solely by the border information. Features in the perceptually completed area in the Craik-O'Brien-Cornsweet do not contribute to its brightness, nor could we see low-frequency boosting, which has been offered as an explanation for the illusion. Tuning of the classification image profiles changes remarkably little with stimulus size. This supports the idea that only certain spatial scales are used for computing the brightness of a surface.

  8. Spatial congruity effects reveal metaphorical thinking, not polarity correspondence

    Directory of Open Access Journals (Sweden)

    Sarah eDolscheid

    2015-11-01

    Full Text Available Spatial congruity effects have often been interpreted as evidence for metaphorical thinking, but an alternative account based on polarity correspondence (a.k.a. markedness has challenged this view. Here we compared metaphor- and polarity-correspondence-based explanations for spatial congruity effects, using musical pitch as a testbed. In one experiment, English speakers classified high- and low-frequency pitches as high and low, or as front and back, to determine whether space-pitch congruity effects could be elicited by any marked spatial continuum. Although both pairs of terms describe bipolar spatial continuums, we found congruity effects only for high/low judgments, indicating that markedness is not sufficient to produce space-pitch congruity effects. A second experiment confirmed that there were no space-pitch congruity effects for another pair of terms that have clear markedness (big/small, but which do not denote spatial height. By contrast, this experiment showed congruity effects for words that cued an appropriate vertical spatial schema (tall/short, even though these words are not used conventionally in English to describe pitches, ruling out explanations for the observed pattern of results based on verbal polysemy. Together, results suggest that space-pitch congruity effects reveal metaphorical uses of spatial schemas, not polarity correspondence effects.

  9. Spatial Congruity Effects Reveal Metaphorical Thinking, not Polarity Correspondence.

    Science.gov (United States)

    Dolscheid, Sarah; Casasanto, Daniel

    2015-01-01

    Spatial congruity effects have often been interpreted as evidence for metaphorical thinking, but an alternative account based on polarity correspondence (a.k.a. markedness) has challenged this view. Here we compared metaphor- and polarity-correspondence-based explanations for spatial congruity effects, using musical pitch as a testbed. In one experiment, English speakers classified high- and low-frequency pitches as "high" and "low," or as "front" and "back," to determine whether space-pitch congruity effects could be elicited by any marked spatial continuum. Although both pairs of terms describe bipolar spatial continuums, we found congruity effects only for high/low judgments, indicating that markedness is not sufficient to produce space-pitch congruity effects. A second experiment confirmed that there were no space-pitch congruity effects for another pair of terms that have clear markedness (big/small), but which do not denote spatial height. By contrast, this experiment showed congruity effects for words that cued an appropriate vertical spatial schema (tall/short), even though these words are not used conventionally in English to describe pitches, ruling out explanations for the observed pattern of results based on verbal polysemy. Together, results suggest that space-pitch congruity effects reveal metaphorical uses of spatial schemas, not polarity correspondence effects.

  10. Statistical universals reveal the structures and functions of human music.

    Science.gov (United States)

    Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

    2015-07-21

    Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.

  11. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

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

    Science.gov (United States)

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

    2014-03-01

    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-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease.

  13. Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube.

    Science.gov (United States)

    Liu, Peng; Wang, Xiao-Hui; Li, Jian-Gui; Qin, Wei; Xiao, Cheng-Ze; Zhao, Xu; Jiang, Hong-Xia; Sui, Jun-Kang; Sa, Rong-Bo; Wang, Wei-Yan; Liu, Xun-Li

    2015-01-01

    Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

  14. 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.

  15. Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer

    Directory of Open Access Journals (Sweden)

    Yongsheng Li

    2017-10-01

    Full Text Available It is increasingly appreciated that alternative splicing plays a key role in generating functional specificity and diversity in cancer. However, the mechanisms by which cancer mutations perturb splicing remain unknown. Here, we developed a network-based strategy, DrAS-Net, to investigate more than 2.5 million variants across cancer types and link somatic mutations with cancer-specific splicing events. We identified more than 40,000 driver variant candidates and their 80,000 putative splicing targets deregulated in 33 cancer types and inferred their functional impact. Strikingly, tumors with splicing perturbations show reduced expression of immune system-related genes and increased expression of cell proliferation markers. Tumors harboring different mutations in the same gene often exhibit distinct splicing perturbations. Further stratification of 10,000 patients based on their mutation-splicing relationships identifies subtypes with distinct clinical features, including survival rates. Our work reveals how single-nucleotide changes can alter the repertoires of splicing isoforms, providing insights into oncogenic mechanisms for precision medicine.

  16. Rapid Mobilization Reveals a Highly Engraftable Hematopoietic Stem Cell.

    Science.gov (United States)

    Hoggatt, Jonathan; Singh, Pratibha; Tate, Tiffany A; Chou, Bin-Kuan; Datari, Shruti R; Fukuda, Seiji; Liu, Liqiong; Kharchenko, Peter V; Schajnovitz, Amir; Baryawno, Ninib; Mercier, Francois E; Boyer, Joseph; Gardner, Jason; Morrow, Dwight M; Scadden, David T; Pelus, Louis M

    2018-01-11

    Hematopoietic stem cell transplantation is a potential curative therapy for malignant and nonmalignant diseases. Improving the efficiency of stem cell collection and the quality of the cells acquired can broaden the donor pool and improve patient outcomes. We developed a rapid stem cell mobilization regimen utilizing a unique CXCR2 agonist, GROβ, and the CXCR4 antagonist AMD3100. A single injection of both agents resulted in stem cell mobilization peaking within 15 min that was equivalent in magnitude to a standard multi-day regimen of granulocyte colony-stimulating factor (G-CSF). Mechanistic studies determined that rapid mobilization results from synergistic signaling on neutrophils, resulting in enhanced MMP-9 release, and unexpectedly revealed genetic polymorphisms in MMP-9 that alter activity. This mobilization regimen results in preferential trafficking of stem cells that demonstrate a higher engraftment efficiency than those mobilized by G-CSF. Our studies suggest a potential new strategy for the rapid collection of an improved hematopoietic graft. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Science.gov (United States)

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2015-01-01

    Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  18. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Li Jun; van der Does, H. C.; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Jose; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Wolochuk, Charles; Xie, Xiaohui; Xu, Jin Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald; Goff, Steven; Hammond-Kossack, Kim; Hilburn, Karen; Hua-Van, Aurelie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. C.; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, Barbara G.; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

    2010-03-18

    Fusarium species are among the most important phytopathogenic and toxigenic fungi, having significant impact on crop production and animal health. Distinctively, members of the F. oxysporum species complex exhibit wide host range but discontinuously distributed host specificity, reflecting remarkable genetic adaptability. To understand the molecular underpinnings of diverse phenotypic traits and their evolution in Fusarium, we compared the genomes of three economically important and phylogenetically related, yet phenotypically diverse plant-pathogenic species, F. graminearum, F. verticillioides and F. oxysporum f. sp. lycopersici. Our analysis revealed greatly expanded lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes, accounting for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity. Experimentally, we demonstrate for the first time the transfer of two LS chromosomes between strains of F. oxysporum, resulting in the conversion of a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in the F. oxysporum species complex, putting the evolution of fungal pathogenicity into a new perspective.

  19. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

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    Aamena Alshamsi

    Full Text Available Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  20. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

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    Wolfram Tempel

    2007-10-01

    Full Text Available The eukaryotic nicotinamide riboside kinase (Nrk pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+ by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.

  1. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

    Science.gov (United States)

    Tempel, Wolfram; Rabeh, Wael M; Bogan, Katrina L; Belenky, Peter; Wojcik, Marzena; Seidle, Heather F; Nedyalkova, Lyudmila; Yang, Tianle; Sauve, Anthony A; Park, Hee-Won; Brenner, Charles

    2007-10-02

    The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.

  2. Molecular Mechanisms Regulating Hepcidin Revealed by Hepcidin Disorders

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    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.

  3. Individual olfactory perception reveals meaningful nonolfactory genetic information.

    Science.gov (United States)

    Secundo, Lavi; Snitz, Kobi; Weissler, Kineret; Pinchover, Liron; Shoenfeld, Yehuda; Loewenthal, Ron; Agmon-Levin, Nancy; Frumin, Idan; Bar-Zvi, Dana; Shushan, Sagit; Sobel, Noam

    2015-07-14

    Each person expresses a potentially unique subset of ∼ 400 different olfactory receptor subtypes. Given that the receptors we express partially determine the odors we smell, it follows that each person may have a unique nose; to capture this, we devised a sensitive test of olfactory perception we termed the "olfactory fingerprint." Olfactory fingerprints relied on matrices of perceived odorant similarity derived from descriptors applied to the odorants. We initially fingerprinted 89 individuals using 28 odors and 54 descriptors. We found that each person had a unique olfactory fingerprint (P people on earth. Olfactory perception, however, fluctuates over time, calling into question our proposed perceptual readout of presumably stable genetic makeup. To test whether fingerprints remain informative despite this temporal fluctuation, building on the linkage between olfactory receptors and HLA, we hypothesized that olfactory perception may relate to HLA. We obtained olfactory fingerprints and HLA typing for 130 individuals, and found that olfactory fingerprint matching using only four odorants was significantly related to HLA matching (P < 10(-4)), such that olfactory fingerprints can save 32% of HLA tests in a population screen (P < 10(-6)). In conclusion, a precise measure of olfactory perception reveals meaningful nonolfactory genetic information.

  4. A novel assay reveals hygrotactic behavior in Drosophila.

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    Feiteng Ji

    Full Text Available Humidity is one of the most important factors that determines the geographical distribution and survival of terrestrial animals. The ability to detect variation in humidity is conserved across many species. Here, we established a novel behavioral assay that revealed the thirsty Drosophila exhibits strong hygrotactic behavior, and it can locate water by detecting humidity gradient. In addition, exposure to high levels of moisture was sufficient to elicit proboscis extension reflex behavior in thirsty flies. Furthermore, we found that the third antennal segment was necessary for hygrotactic behavior in thirsty flies, while arista was required for the avoidance of moist air in hydrated flies. These results indicated that two types of hygroreceptor cells exist in Drosophila: one located in the third antennal segment that mediates hygrotactic behavior in thirst status, and the other located in arista which is responsible for the aversive behavior toward moist air in hydration status. Using a neural silencing screen, we demonstrated that synaptic output from the mushroom body α/β surface and posterior neurons was required for both hygrotactic behavior and moisture-aversive behavior.

  5. Enzyme kinetics: the whole picture reveals hidden meanings.

    Science.gov (United States)

    Pinto, Maria F; Estevinho, Berta N; Crespo, Rosa; Rocha, Fernando A; Damas, Ana M; Martins, Pedro M

    2015-06-01

    The methodology adopted by Michaelis and Menten in 1913 is still routinely used to characterize the catalytic power and selectivity of enzymes. These kinetic measurements must be performed soon after the purified enzyme is mixed with a large excess of substrate. Other time scales and solution compositions are no less physiologically relevant, but fall outside the range of applicability of the classical formalism. Here we show that the complete picture of an enzyme's mode of function is critically obscured by the limited scope of conventional kinetic analysis, even in the simplest case of a single active site without inhibition. This picture is now unveiled in a mathematically closed form that remains valid over the reaction time for all combinations of enzyme/substrate concentrations and rate constants. Algebraic simplicity is maintained in the new formalism when stationary reaction phases are considered. By achieving this century-old objective, the otherwise hidden role of the reversible binding step is revealed and atypical kinetic profiles are explained. Most singular kinetic behaviors are identified in a critical region of conditions that coincide with typical cell conditions. Because it is not covered by the Michaelis-Menten model, the critical region has been missed until now by low- and high-throughput screenings of new drugs. New possibilities are therefore raised for novel and once-promising inhibitors to therapeutically target enzymes. © 2015 FEBS.

  6. Phylogenies reveal predictive power of traditional medicine in bioprospecting.

    Science.gov (United States)

    Saslis-Lagoudakis, C Haris; Savolainen, Vincent; Williamson, Elizabeth M; Forest, Félix; Wagstaff, Steven J; Baral, Sushim R; Watson, Mark F; Pendry, Colin A; Hawkins, Julie A

    2012-09-25

    There is controversy about whether traditional medicine can guide drug discovery, and investment in bioprospecting informed by ethnobotanical data has fluctuated. One view is that traditionally used medicinal plants are not necessarily efficacious and there are no robust methods for distinguishing those which are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogenetic tree representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand, and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This finding strongly indicates independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in random samples. We conclude that phylogenetic cross-cultural comparisons can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalize the use of traditional knowledge in bioprospecting.

  7. Polymyalgia Rheumatica Revealing a Lymphoma: A Two-Case Report

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    Frank Verhoeven

    2016-01-01

    Full Text Available Introduction. Polymyalgia rheumatica (PMR is one of the most common inflammatory rheumatism types in elderly population. The link between cancer and PMR is a matter of debate. Methods. We report two cases of PMR leading to the diagnosis of lymphoma and the growing interest of PET-TDM in this indication. Results. A 84-year-old man known for idiopathic neutropenia presented an inflammatory arthromyalgia of the limb girdle since one month. Blood exams highlighted the presence of a monoclonal B cell clone. Bone marrow concluded to a B cell lymphoma of the marginal zone. He was successfully treated with 0.3 mg/kg/d of prednisone, and response was sustained after 6 months. A 73-year-old man known for prostatic neoplasia in remission for 5 years presented arthromyalgia of the limb girdle since one month. PET-CT revealed bursitis of the hips and the shoulders, no prostatic cancer recurrence, and a metabolically active iliac lymphadenopathy whose pathologic exam concluded to a low grade follicular lymphoma. He was successfully treated with 0.3 mg/kg/d of prednisone. Conclusion. These observations may imply that lymphoma is sometimes already present when PMR is diagnosed and PET-CT is a useful tool in the initial assessment of PMR to avoid missing neoplasia.

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

    Science.gov (United States)

    Colom, Roberto; Grafman, Jordan

    2014-01-01

    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-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease. PMID:23171618

  9. When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.

    Science.gov (United States)

    Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Opler, Paul A; Otwinowski, Zbyszek; Grishin, Nick V

    2017-02-08

    Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value COI barcodes and mitochondrial DNA for species identification or discovery. © 2017 The Author(s).

  10. [Iliac venous leiomyosarcoma revealed by cruralgia: a case report].

    Science.gov (United States)

    Camiade, C; Deplas, A; Soyer, J; Menet, E; Ricco, J B

    2002-02-01

    The iliac venous leimyosarcoma is rare, usually malignant, and often occurs with oedema or phlebitis. We report one case of iliac venous leiomyosarcoma revealed by cruralgia. A 69 years old patient, presented with a left cruralgia which had been developing for three months and which happened after an insignificant trauma. The clinical examination objectified a stiff painful mass of the left iliac fossa together with left psoitis. The initial pelvic tomodensitometry showed a mass at the contact of the psoas muscle. At first, the diagnosis of a psoas haematoma complicated by a compressive cruralgia was evocated. Two months ago, the patient had a pulmonary embolism. At his hospitalisation, considering the persistent cruralgia, a tomodensitometry and a pelvic magnetic resonance imaging were carried out and had shown an heterogeneous mass that was including the iliac vessels. The result of the anatomopathologic examination was leiomysarcoma. Due to the disease's evolution (pulmonary metastasis), only a medical treatment by chemotherapy was undertaken and the patient died a few weeks later. The association of phlebitis and cruralgia should let us think of the diagnosis of vascular neoplasm. Indeed, only an early diagnosis enables a curative treatment.

  11. Covert waking brain activity reveals instantaneous sleep depth.

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    Scott M McKinney

    Full Text Available The neural correlates of the wake-sleep continuum remain incompletely understood, limiting the development of adaptive drug delivery systems for promoting sleep maintenance. The most useful measure for resolving early positions along this continuum is the alpha oscillation, an 8-13 Hz electroencephalographic rhythm prominent over posterior scalp locations. The brain activation signature of wakefulness, alpha expression discloses immediate levels of alertness and dissipates in concert with fading awareness as sleep begins. This brain activity pattern, however, is largely ignored once sleep begins. Here we show that the intensity of spectral power in the alpha band actually continues to disclose instantaneous responsiveness to noise--a measure of sleep depth--throughout a night of sleep. By systematically challenging sleep with realistic and varied acoustic disruption, we found that sleepers exhibited markedly greater sensitivity to sounds during moments of elevated alpha expression. This result demonstrates that alpha power is not a binary marker of the transition between sleep and wakefulness, but carries rich information about immediate sleep stability. Further, it shows that an empirical and ecologically relevant form of sleep depth is revealed in real-time by EEG spectral content in the alpha band, a measure that affords prediction on the order of minutes. This signal, which transcends the boundaries of classical sleep stages, could potentially be used for real-time feedback to novel, adaptive drug delivery systems for inducing sleep.

  12. Revealing large metagenomic regions through long DNA fragment hybridization capture.

    Science.gov (United States)

    Gasc, Cyrielle; Peyret, Pierre

    2017-03-14

    High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies. To overcome these limitations, we developed an innovative target enrichment method for the reconstruction of large unknown genomic regions. Based on a hybridization capture strategy, this approach enables the enrichment of large genomic regions allowing the reconstruction of tens of kilobase pairs flanking a short, targeted DNA sequence. Applied to a metagenomic soil sample targeting the linA gene, the biomarker of hexachlorocyclohexane (HCH) degradation, our method permitted the enrichment of the gene and its flanking regions leading to the reconstruction of several contigs and complete plasmids exceeding tens of kilobase pairs surrounding linA. Thus, through gene association and genome reconstruction, we identified microbial species involved in HCH degradation which constitute targets to improve biostimulation treatments. This new hybridization capture strategy makes surveying and deconvoluting complex genomic regions possible through large genomic regions enrichment and allows the efficient exploration of metagenomic diversity. Indeed, this approach enables to assign identity and function to microorganisms in natural environments, one of the ultimate goals of microbial ecology.

  13. Color-shape associations revealed with implicit association tests.

    Science.gov (United States)

    Chen, Na; Tanaka, Kanji; Watanabe, Katsumi

    2015-01-01

    Kandinsky proposed a correspondence theory that suggests associations between specific colors and shapes (i.e., circle-blue, square-red, triangle-yellow). Makin and Wuerger tested the theory using the Implicit Association Test (IAT) and did not find clear evidence for Kandinsky's color-shape associations among British participants. In the present study, we first replicated the previous study among Japanese participants and found similar results to those of Makin and Wuerger, showing little support for Kandinsky's theory. In the subsequent experiment, we tested another set of color-shape associations that had been revealed by using an explicit matching method (circle-red, square-blue, triangle-yellow) in Japanese participants. The IAT tests showed that response times were significantly faster when circle-red, square-blue, and triangle-yellow combinations were mapped onto the same response key, rather than different key combinations, indicating that these color-shape combinations were encoded. These results provide the first empirical evidence that color-shape associations can be measured by indirect behavioral methods, and in particular, Japanese people's color-shape associations (circle-red, square-blue, triangle-yellow) can be observed by both direct and indirect experimental methods.

  14. Color-shape associations revealed with implicit association tests.

    Directory of Open Access Journals (Sweden)

    Na Chen

    Full Text Available Kandinsky proposed a correspondence theory that suggests associations between specific colors and shapes (i.e., circle-blue, square-red, triangle-yellow. Makin and Wuerger tested the theory using the Implicit Association Test (IAT and did not find clear evidence for Kandinsky's color-shape associations among British participants. In the present study, we first replicated the previous study among Japanese participants and found similar results to those of Makin and Wuerger, showing little support for Kandinsky's theory. In the subsequent experiment, we tested another set of color-shape associations that had been revealed by using an explicit matching method (circle-red, square-blue, triangle-yellow in Japanese participants. The IAT tests showed that response times were significantly faster when circle-red, square-blue, and triangle-yellow combinations were mapped onto the same response key, rather than different key combinations, indicating that these color-shape combinations were encoded. These results provide the first empirical evidence that color-shape associations can be measured by indirect behavioral methods, and in particular, Japanese people's color-shape associations (circle-red, square-blue, triangle-yellow can be observed by both direct and indirect experimental methods.

  15. Historical Reconstruction Reveals Recovery in Hawaiian Coral Reefs

    Science.gov (United States)

    Kittinger, John N.; Pandolfi, John M.; Blodgett, Jonathan H.; Hunt, Terry L.; Jiang, Hong; Maly, Kepā; McClenachan, Loren E.; Schultz, Jennifer K.; Wilcox, Bruce A.

    2011-01-01

    Coral reef ecosystems are declining worldwide, yet regional differences in the trajectories, timing and extent of degradation highlight the need for in-depth regional case studies to understand the factors that contribute to either ecosystem sustainability or decline. We reconstructed social-ecological interactions in Hawaiian coral reef environments over 700 years using detailed datasets on ecological conditions, proximate anthropogenic stressor regimes and social change. Here we report previously undetected recovery periods in Hawaiian coral reefs, including a historical recovery in the MHI (∼AD 1400–1820) and an ongoing recovery in the NWHI (∼AD 1950–2009+). These recovery periods appear to be attributed to a complex set of changes in underlying social systems, which served to release reefs from direct anthropogenic stressor regimes. Recovery at the ecosystem level is associated with reductions in stressors over long time periods (decades+) and large spatial scales (>103 km2). Our results challenge conventional assumptions and reported findings that human impacts to ecosystems are cumulative and lead only to long-term trajectories of environmental decline. In contrast, recovery periods reveal that human societies have interacted sustainably with coral reef environments over long time periods, and that degraded ecosystems may still retain the adaptive capacity and resilience to recover from human impacts. PMID:21991311

  16. Dynamics of podosome stiffness revealed by atomic force microscopy

    Science.gov (United States)

    Labernadie, Anna; Thibault, Christophe; Vieu, Christophe; Maridonneau-Parini, Isabelle; Charrière, Guillaume M.

    2010-01-01

    Podosomes are unique cellular entities specifically found in macrophages and involved in cell–matrix interactions, matrix degradation, and 3D migration. They correspond to a core of F-actin surrounded at its base by matrix receptors. To investigate the structure/function relationships of podosomes, soft lithography, atomic force microscopy (AFM), and correlative fluorescence microscopy were used to characterize podosome physical properties in macrophages differentiated from human blood monocytes. Podosome formation was restricted to delineated areas with micropatterned fibrinogen to facilitate AFM analyses. Podosome height and stiffness were measured with great accuracy in living macrophages (578 ± 209 nm and 43.8 ± 9.3 kPa) and these physical properties were independent of the nature of the underlying matrix. In addition, time-lapse AFM revealed that podosomes harbor two types of overlapping periodic stiffness variations throughout their lifespan, which depend on F-actin and myosin II activity. This report shows that podosome biophysical properties are amenable to AFM, allowing the study of podosomes in living macrophages at nanoscale resolution and the analysis of their intimate dynamics. Such an approach opens up perspectives to better understand the mechanical functionality of podosomes under physiological and pathological contexts. PMID:21081699

  17. Revealing the intricate effect of collaboration on innovation.

    Science.gov (United States)

    Inoue, Hiroyasu; Liu, Yang-Yu

    2015-01-01

    We studied the Japan and U.S. patent records of several decades to demonstrate the effect of collaboration on innovation. We found that statistically inventor teams slightly outperform solo inventors while company teams perform equally well as solo companies. By tracking the performance record of individual teams, we found that inventor teams' performance generally degrades with more repeat collaborations. Though company teams' performance displays strongly bursty behavior, long-term collaboration does not significantly help innovation. To systematically study the effect of repeat collaboration, we defined the repeat collaboration number of a team as the average number of collaborations over all the teammate pairs. We found that mild repeat collaboration improves the performance of Japanese inventor teams and U.S. company teams. Yet, excessive repeat collaboration does not significantly help innovation at both the inventor and company levels in both countries. To control for unobserved heterogeneity, we performed a detailed regression analysis and the results were consistent with our simple observations. The presented results revealed the intricate effect of collaboration on innovation, which may also be observed in other creative projects.

  18. Mitochondrial genome sequences effectively reveal the phylogeny of Hylobates gibbons.

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    Yi-Chiao Chan

    Full Text Available BACKGROUND: Uniquely among hominoids, gibbons exist as multiple geographically contiguous taxa exhibiting distinctive behavioral, morphological, and karyotypic characteristics. However, our understanding of the evolutionary relationships of the various gibbons, especially among Hylobates species, is still limited because previous studies used limited taxon sampling or short mitochondrial DNA (mtDNA sequences. Here we use mtDNA genome sequences to reconstruct gibbon phylogenetic relationships and reveal the pattern and timing of divergence events in gibbon evolutionary history. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the mitochondrial genomes of 51 individuals representing 11 species belonging to three genera (Hylobates, Nomascus and Symphalangus using the high-throughput 454 sequencing system with the parallel tagged sequencing approach. Three phylogenetic analyses (maximum likelihood, Bayesian analysis and neighbor-joining depicted the gibbon phylogenetic relationships congruently and with strong support values. Most notably, we recover a well-supported phylogeny of the Hylobates gibbons. The estimation of divergence times using Bayesian analysis with relaxed clock model suggests a much more rapid speciation process in Hylobates than in Nomascus. CONCLUSIONS/SIGNIFICANCE: Use of more than 15 kb sequences of the mitochondrial genome provided more informative and robust data than previous studies of short mitochondrial segments (e.g., control region or cytochrome b as shown by the reliable reconstruction of divergence patterns among Hylobates gibbons. Moreover, molecular dating of the mitogenomic divergence times implied that biogeographic change during the last five million years may be a factor promoting the speciation of Sundaland animals, including Hylobates species.

  19. mTOR-sensitive translation: Cleared fog reveals more trees.

    Science.gov (United States)

    Masvidal, Laia; Hulea, Laura; Furic, Luc; Topisirovic, Ivan; Larsson, Ola

    2017-10-03

    Translation is fundamental for many biologic processes as it enables cells to rapidly respond to stimuli without requiring de novo mRNA synthesis. The mammalian/mechanistic target of rapamycin (mTOR) is a key regulator of translation. Although mTOR affects global protein synthesis, translation of a subset of mRNAs appears to be exceptionally sensitive to changes in mTOR activity. Recent efforts to catalog these mTOR-sensitive mRNAs resulted in conflicting results. Whereas ribosome-profiling almost exclusively identified 5'-terminal oligopyrimidine (TOP) mRNAs as mTOR-sensitive, polysome-profiling suggested that mTOR also regulates translation of non-TOP mRNAs. This inconsistency was explained by analytical and technical biases limiting the efficiency of ribosome-profiling in detecting mRNAs showing differential translation. Moreover, genome-wide characterization of 5'UTRs of non-TOP mTOR-sensitive mRNAs revealed 2 subsets of transcripts which differ in their requirement for translation initiation factors and biologic functions. We summarize these recent advances and their impact on the understanding of mTOR-sensitive translation.

  20. Puffy Hand Syndrome Revealed by a Severe Staphylococcal Skin Infection

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    Reyhan Amode

    2013-01-01

    Full Text Available Puffy hand syndrome develops after long-term intravenous drug addiction. It is characterized by a nonpitting edema, affecting the dorsal side of fingers and hands with puffy aspect. Frequency and severity of the complications of this syndrome are rarely reported. Local infectious complications such as cellulitis can be severe and can enable the diagnosis. Herein, we report the case of a 41-year-old man who went to the emergency department for abdominal pain, fever, and bullous lesions of legs and arms with edema. Bacteriologic examination of a closed bullous lesion evidenced a methicillin sensitive Staphylococcus aureus. The abdomen computed tomography excluded deep infections and peritoneal effusion. The patient was successfully treated by intravenous oxacillin and clindamycin. He had a previous history of intravenous heroin addiction. We retained the diagnosis of puffy hand syndrome revealed by a severe staphylococcal infection with toxic involvement mimicking a four limbs cellulitis. Puffy hand syndrome, apart from the chronic lymphedema treatment, has no specific medication available. Prophylactic measures against skin infections are essential.

  1. CRISPR loci reveal networks of gene exchange in archaea.

    Science.gov (United States)

    Brodt, Avital; Lurie-Weinberger, Mor N; Gophna, Uri

    2011-12-21

    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. 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. 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. This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).

  2. Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons.

    Science.gov (United States)

    Oddo, Calogero M; Mazzoni, Alberto; Spanne, Anton; Enander, Jonas M D; Mogensen, Hannes; Bengtsson, Fredrik; Camboni, Domenico; Micera, Silvestro; Jörntell, Henrik

    2017-04-04

    Investigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models.

  3. 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.

  4. Seismic Tremor Reveals Subglacial Discharge at Tidewater Glaciers

    Science.gov (United States)

    Bartholomaus, T. C.; Larsen, C. F.; O'Neel, S.; West, M. E.; Amundson, J. M.; Walter, J. I.; Catania, G. A.; Stearns, L. A.; Walker, R. T.; Sutherland, D.; Shroyer, E.; Nash, J. D.

    2014-12-01

    Subglacial discharge from the termini of tidewater glaciers drives submarine terminus melting, influences fjord circulation, erodes and redeposits subglacial sediment, and is a central component of proglacial marine ecosystems. The timing and variability of subglacial discharge can also exert a strong influence on the upstream flow of tidewater glaciers through hydrology-mediated changes in basal motion. However, a lack of observations of subglacial discharge at the ice-ocean interface hinders progress in understanding these processes and contributes to some of the largest uncertainties in sea level rise projections. Here we demonstrate that passive seismic observations collected adjacent to glaciers can meet this observational need. At tidewater and lake-terminating glaciers in Alaska and Greenland, we observe hourly to seasonal variations in low-amplitude, background seismic noise, termed glacio-hydraulic tremor. Variations in tremor amplitude correlate with discharge during the drainage of a glacially-dammed lake and reveal increases in discharge efficiency over the course of the melt season. Recordings of glacio-hydraulic tremor across a range of settings suggest widespread utility for our method. Reliable prediction of future sea level rise requires observations of subglacial discharge that elicit physical insight and can validate models. Our findings provide a platform for new understanding of ice-ocean interactions and related oceanographic, geologic, and ecological disciplines.

  5. Submillimeter Array reveals molecular complexity of dying stars

    Science.gov (United States)

    Tomasz

    2018-01-01

    The unique capabilities of the Submillimeter Array (SMA) have allowed unprecedented studies of cool evolved stars at submillimeter wavelengths. In particular, the SMA now offers the possibility to image multiple molecular transitions at once, owing to the 32-GHz wide instantaneous bandwidth of SWARM, the SMA’s new correlator. Molecular gas located far and very close to the photosphere of an asymptotic-giant branch (AGB) star, a red supergiant, or a pre-planetary nebula can now be examined in transitions observed simultaneously from a wide range of energy levels. This allows a very detailed quantitative investigation of physical and chemical conditions around these variable objects. Several imaging line surveys have been obtained with the SMA to reveal the beautiful complexity of these evolved systems. The surveys resulted in first submillimeter-wave identifications of molecules of prime astrophysical interest, e.g. of TiO, TiO2, and of rotational transitions at excited vibrational states of CO. An overview of recent SMA observations of cool evolved stars will be given with an emphasize on the interferometric line surveys. We will demonstrate their importance in unraveling the mass-loss phenomena, propagation of shocks in the circumstellar medium, and production of dust at elevated temperatures. The SMA studies of these molecular factories have a direct impact on our understanding of the chemical evolution of the Galaxy and stellar evolution at low and high masses.

  6. Phylogeny of the Botryosphaeriaceae reveals patterns of host association.

    Science.gov (United States)

    De Wet, Juanita; Slippers, Bernard; Preisig, Oliver; Wingfield, Brenda D; Wingfield, Michael J

    2008-01-01

    Three anamorph genera of the Botryosphaeriaceae namely Diplodia, Lasiodiplodia and Dothiorella have typically dark, ovoid conidia with thick walls, and are consequently difficult to distinguish from each other. These genera are well-known pathogens of especially pine species. We generated a multiple gene genealogy to resolve the phylogenetic relationships of Botryosphaeriaceae with dark conidial anamorphs, and mapped host associations based on this phylogeny. The multiple gene genealogy separated Diplodia, Lasiodiplodia and Dothiorella and it revealed trends in the patterns of host association. The data set was expanded to include more lineages of the Botryosphaeriaceae, and included all isolates from different host species for which ITS sequence data are available. Results indicate that Diplodia species occur mainly on gymnosperms, with a few species on both gymnosperms and angiosperms. Lasiodiplodia species occur equally on both gymnosperms and angiosperms, Dothiorella species are restricted to angiosperms and Neofusicoccum species occur mainly on angiosperms with rare reports on Southern Hemisphere gymnosperms. Botryosphaeria species with Fusicoccum anamorphs occur mostly on angiosperms with rare reports on gymnosperms. Ancestral state reconstruction suggests that a putative ancestor of the Botryosphaeriaceae most likely evolved on the angiosperms. Another interesting observation was that both host generalist and specialist species were observed in all the lineages of the Botryosphaeriaceae, with little evidence of host associated co-evolution.

  7. Kinematics of Mass Transport Deposits revealed by magnetic fabrics

    Science.gov (United States)

    Weinberger, R.; Levi, T.; Alsop, G. I.; Marco, S.

    2017-08-01

    The internal deformation and movement directions of Mass Transport Deposits (MTDs) are key factors in understanding the kinematics and dynamics of their emplacement. Although these are relatively easy to recover from well-bedded sediments, they are more difficult to deduce from massive beds without visible strain markers. In order to test the applicability of using anisotropy of magnetic susceptibility (AMS) to determine MTD movement, we compare AMS fabrics, with structural measurements of visible kinematic indicators. Our case study involves the structural analysis of slumped lake sediments extensively exposed in MTDs within the Dead Sea Basin. Structural analyses of MTDs outcropping for >100 km reveal radial transport directions toward the basin depocenter. We show that the AMS fabrics display the same transport directions as inferred from structural analyses. Based on this similarity, we outline a robust procedure to obtain the transport direction of slumped MTDs from AMS fabrics. Variations in the magnetic fabrics and anisotropies in fold-thrust systems within the slumps match the various structural domains. We therefore suggest that magnetic fabrics and anisotropy variations in drill cores may reflect internal deformation within the slumps rather than different slumps. Obtaining magnetic fabrics from MTDs provides a viable way to infer the transport directions and internal deformation of MTDs and reconstruct the basin depocenter in ancient settings. The present results also have implications beyond the kinematics of MTDs, as their geometry resembles fold-thrust systems in other geological settings, scales, and tectonic environments.

  8. Resting-state brain organization revealed by functional covariance networks.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Zhang

    Full Text Available BACKGROUND: Brain network studies using techniques of intrinsic connectivity network based on fMRI time series (TS-ICN and structural covariance network (SCN have mapped out functional and structural organization of human brain at respective time scales. However, there lacks a meso-time-scale network to bridge the ICN and SCN and get insights of brain functional organization. METHODOLOGY AND PRINCIPAL FINDINGS: We proposed a functional covariance network (FCN method by measuring the covariance of amplitude of low-frequency fluctuations (ALFF in BOLD signals across subjects, and compared the patterns of ALFF-FCNs with the TS-ICNs and SCNs by mapping the brain networks of default network, task-positive network and sensory networks. We demonstrated large overlap among FCNs, ICNs and SCNs and modular nature in FCNs and ICNs by using conjunctional analysis. Most interestingly, FCN analysis showed a network dichotomy consisting of anti-correlated high-level cognitive system and low-level perceptive system, which is a novel finding different from the ICN dichotomy consisting of the default-mode network and the task-positive network. CONCLUSION: The current study proposed an ALFF-FCN approach to measure the interregional correlation of brain activity responding to short periods of state, and revealed novel organization patterns of resting-state brain activity from an intermediate time scale.

  9. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, Bruce A.; Tanifuji, Goro; Burki, Fabien; Gruber, Ansgar; Irimia, Manuuel; Maruyama, Shinichiro; Arias, Maria C.; Ball, Steven G.; Gile, Gillian H.; Hirakawa, Yoshihisa; Hopkins, Julia F.; Kuo, Alan; Rensing, Stefan A.; Schmutz, Jeremy; Symeonidi, Aikaterini; Elias, Marek; Eveleigh, Robert J. M.; Herman, Emily K.; Klute, Mary J.; Nakayama, Takuro; Obornik, Miroslav; Reyes-Prieto, Adrian; Armbrust, E. Virginia; Aves, Stephen J.; Beiko, Robert G.; Coutinho, Pedro; Dacks, Joel B.; Durnford, Dion G.; Fast, Naomi M.; Green, Beverley R.; Grisdale, Cameron J.; Hempel, Franziska; Henrissat, Bernard; Hoppner, Marc P.; Ishida, Ken-Ichiro; Kim, Eunsoo; Koreny, Ludek; Kroth, Peter G.; Liu, Yuan; Malik, Shehre-Banoo; Maier, Uwe G.; McRose, Darcy; Mock, Thomas; Neilson, Jonathan A. D.; Onodera, Naoko T.; Poole, Anthony M.; Pritham, Ellen J.; Richards, Thomas A.; Rocap, Gabrielle; Roy, Scott W.; Sarai, Chihiro; Schaack, Sarah; Shirato, Shu; Slamovits, Claudio H.; Spencer, Davie F.; Suzuki, Shigekatsu; Worden, Alexandra Z.; Zauner, Stefan; Barry, Kerrie; Bell, Callum; Bharti, Arvind K.; Crow, John A.; Grimwood, Jane; Kramer, Robin; Lindquist, Erika; Lucas, Susan; Salamov, Asaf; McFadden, Geoffrey I.; Lane, Christopher E.; Keeling, Patrick J.; Gray, Michael W.; Grigoriev, Igor V.; Archibald, John M.

    2012-08-10

    Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

  10. Functional metabolomics reveals novel active products in the DHA metabolome

    Directory of Open Access Journals (Sweden)

    Masakazu eShinohara

    2012-04-01

    Full Text Available Endogenous mechanisms for successful resolution of an acute inflammatory response and the local return to homeostasis are of interest because excessive inflammation underlies many human diseases. In this review, we provide an update and overview of functional metabolomics that identified a new bioactive metabolome of docosahexaenoic acid (DHA. Systematic studies revealed that DHA was converted to DHEA-derived novel bioactive products as well as aspirin-triggered (AT forms of protectins. The new oxygenated DHEA derived products blocked PMN chemotaxis, reduced P-selectin expression and platelet-leukocyte adhesion, and showed organ protection in ischemia/reperfusion injury. These products activated cannabinoid receptor (CB2 receptor and not CB1 receptors. The AT-PD1 reduced neutrophil (PMN recruitment in murine peritonitis. With human cells, AT-PD1 decreased transendothelial PMN migration as well as enhanced efferocytosis of apoptotic human PMN by macrophages. The recent findings reviewed here indicate that DHEA oxidative metabolism and aspirin-triggered conversion of DHA produce potent novel molecules with anti-inflammatory and organ-protective properties, opening the DHA metabolome functional roles.

  11. Circular RNA profile in gliomas revealed by identification tool UROBORUS

    Science.gov (United States)

    Song, Xiaofeng; Zhang, Naibo; Han, Ping; Moon, Byoung-San; Lai, Rose K.; Wang, Kai; Lu, Wange

    2016-01-01

    Recent evidence suggests that many endogenous circular RNAs (circRNAs) may play roles in biological processes. However, the expression patterns and functions of circRNAs in human diseases are not well understood. Computationally identifying circRNAs from total RNA-seq data is a primary step in studying their expression pattern and biological roles. In this work, we have developed a computational pipeline named UROBORUS to detect circRNAs in total RNA-seq data. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The circRNAs expression profiling revealed more than 476 circular RNAs differentially expressed in control brain tissues and gliomas. Together with parental gene expression, we found that circRNA and its parental gene have diversified expression patterns in gliomas and control brain tissues. This study establishes an efficient and sensitive approach for predicting circRNAs using total RNA-seq data. The UROBORUS pipeline can be accessed freely for non-commercial purposes at http://uroborus.openbioinformatics.org/. PMID:26873924

  12. Scurvy revealed by difficulty walking: three cases in young children.

    Science.gov (United States)

    Kitcharoensakkul, Maleewan; Schulz, Christa G; Kassel, Rachel; Khanna, Geetika; Liang, Shannon; Ngwube, Alexander; Baszis, Kevin W; Hunstad, David A; White, Andrew J

    2014-06-01

    Scurvy is rare in developed countries but is known to cause lower-extremity pain and refusal to ambulate in children. Since the discovery of the link between scurvy and dietary deficiency of ascorbic acid, there has been a substantial decrease in its prevalence and recognition. Here we describe 3 cases of scurvy in young children presenting with difficulty walking. Only 1 of 3 patients had gingival lesions at the initial presentation. Two cases underwent an extensive evaluation for hematologic and rheumatologic diseases before the diagnosis of scurvy was made. Dietary histories eventually revealed that all 3 patients had sharply limited intake of fruits and vegetables secondary to oral aversion, and 1 patient had autism. Radiographic changes of long bones were observed in all patients. Interestingly, all patients had concomitant vitamin D deficiency. After replacement with vitamin C, all patients recovered and started to walk again with improved leg pain. These clinical manifestations and radiologic findings highlight the importance for rheumatologists to have a higher index of suspicion for scurvy in nonambulatory children.

  13. A Communal Catalogue Reveals Earth’s Multiscale Microbial Diversity

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail L.; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vazquez-Baeza, Yoshiki; Gonzalez, Antonio; Morton, James; Mirarab, Siavash; Xu, Zhenjiang Z.; Jiang, Lingjing; Haroon, Mohamed F.; Kanbar, Jad; Zhu, Qiyun; Song, Se Jin; Kosciolek, Tomasz; Bokulich, Nicholas A.; Lefler, Joshua; Brislawn, Colin J.; Humphrey, Greg C.; Owens, Sarah M.; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; Mckenzie, Valerie; Fierer, N.; Fuhrman, Jed A.; Clauset, Aaron; Stevens, Rick L.; Shade, Ashley; Pollard, Katherine S.; Goodwin, Kelly D.; Jansson, Janet K.; Gilbert, Jack A.; Knight, Rob

    2017-11-01

    Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, we find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. This dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.

  14. Elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution.

    Science.gov (United States)

    Nett, Ryan S; Montanares, Mariana; Marcassa, Ariana; Lu, Xuan; Nagel, Raimund; Charles, Trevor C; Hedden, Peter; Rojas, Maria Cecilia; Peters, Reuben J

    2017-01-01

    Gibberellins (GAs) are crucial phytohormones involved in many aspects of plant growth and development, including plant-microbe interactions, which has led to GA production by plant-associated fungi and bacteria as well. While the GA biosynthetic pathways in plants and fungi have been elucidated and found to have arisen independently through convergent evolution, little has been uncovered about GA biosynthesis in bacteria. Some nitrogen-fixing, symbiotic, legume-associated rhizobia, including Bradyrhizobium japonicum-the symbiont of soybean-and Sinorhizobium fredii-a broad-host-nodulating species-contain a putative GA biosynthetic operon, or gene cluster. Through functional characterization of five unknown genes, we demonstrate that this operon encodes the enzymes necessary to produce GA9, thereby elucidating bacterial GA biosynthesis. The distinct nature of these enzymes indicates that bacteria have independently evolved a third biosynthetic pathway for GA production. Furthermore, our results also reveal a central biochemical logic that is followed in all three convergently evolved GA biosynthetic pathways.

  15. An enzymatic atavist revealed in dual pathways for water activation.

    Directory of Open Access Journals (Sweden)

    Donghong Min

    2008-08-01

    Full Text Available Inosine monophosphate dehydrogenase (IMPDH catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a "Wang-Landau" metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme.

  16. Early Neolithic water wells reveal the world's oldest wood architecture.

    Science.gov (United States)

    Tegel, Willy; Elburg, Rengert; Hakelberg, Dietrich; Stäuble, Harald; Büntgen, Ulf

    2012-01-01

    The European Neolithization ~6000-4000 BC represents a pivotal change in human history when farming spread and the mobile style of life of the hunter-foragers was superseded by the agrarian culture. Permanent settlement structures and agricultural production systems required fundamental innovations in technology, subsistence, and resource utilization. Motivation, course, and timing of this transformation, however, remain debatable. Here we present annually resolved and absolutely dated dendroarchaeological information from four wooden water wells of the early Neolithic period that were excavated in Eastern Germany. A total of 151 oak timbers preserved in a waterlogged environment were dated between 5469 and 5098 BC and reveal unexpectedly refined carpentry skills. The recently discovered water wells enable for the first time a detailed insight into the earliest wood architecture and display the technological capabilities of humans ~7000 years ago. The timbered well constructions made of old oak trees feature an unopened tree-ring archive from which annually resolved and absolutely dated environmental data can be culled. Our results question the principle of continuous evolutionary development in prehistoric technology, and contradict the common belief that metal was necessary for complex timber constructions. Early Neolithic craftsmanship now suggests that the first farmers were also the first carpenters.

  17. Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

    Science.gov (United States)

    Dai, Fei; Chen, Zhong-Hua; Wang, Xiaolei; Li, Zefeng; Jin, Gulei; Wu, Dezhi; Cai, Shengguan; Wang, Ning; Wu, Feibo; Nevo, Eviatar; Zhang, Guoping

    2014-01-01

    The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions. PMID:25197090

  18. Metagenomics reveals flavour metabolic network of cereal vinegar microbiota.

    Science.gov (United States)

    Wu, Lin-Huan; Lu, Zhen-Ming; Zhang, Xiao-Juan; Wang, Zong-Min; Yu, Yong-Jian; Shi, Jin-Song; Xu, Zheng-Hong

    2017-04-01

    Multispecies microbial community formed through centuries of repeated batch acetic acid fermentation (AAF) is crucial for the flavour quality of traditional vinegar produced from cereals. However, the metabolism to generate and/or formulate the essential flavours by the multispecies microbial community is hardly understood. Here we used metagenomic approach to clarify in situ metabolic network of key microbes responsible for flavour synthesis of a typical cereal vinegar, Zhenjiang aromatic vinegar, produced by solid-state fermentation. First, we identified 3 organic acids, 7 amino acids, and 20 volatiles as dominant vinegar metabolites. Second, we revealed taxonomic and functional composition of the microbiota by metagenomic shotgun sequencing. A total of 86 201 predicted protein-coding genes from 35 phyla (951 genera) were involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of Metabolism (42.3%), Genetic Information Processing (28.3%), and Environmental Information Processing (10.1%). Furthermore, a metabolic network for substrate breakdown and dominant flavour formation in vinegar microbiota was constructed, and microbial distribution discrepancy in different metabolic pathways was charted. This study helps elucidating different metabolic roles of microbes during flavour formation in vinegar microbiota. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Individual differences reveal correlates of hidden hearing deficits.

    Science.gov (United States)

    Bharadwaj, Hari M; Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G

    2015-02-04

    Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of "normal hearing." Copyright © 2015 the authors 0270-6474/15/352161-12$15.00/0.

  20. Seabird movement reveals the ecological footprint of fishing vessels.

    Science.gov (United States)

    Bodey, Thomas W; Jessopp, Mark J; Votier, Stephen C; Gerritsen, Hans D; Cleasby, Ian R; Hamer, Keith C; Patrick, Samantha C; Wakefield, Ewan D; Bearhop, Stuart

    2014-06-02

    Exploitation of the seas is currently unsustainable, with increasing demand for marine resources placing intense pressure on the Earth's largest ecosystem [1]. The scale of anthropogenic effects varies from local to entire ocean basins [1-3]. For example, discards of commercial capture fisheries can have both positive and negative impacts on scavengers at the population and community-level [2-6], although this is driven by individual foraging behaviour [3,7]. Currently, we have little understanding of the scale at which individual animals initiate such behaviours. We use the known interaction between fisheries and a wide-ranging seabird, the Northern gannet Morus bassanus[3], to investigate how fishing vessels affect individual birds' behaviours in near real-time. We document the footprint of fishing vessels' (≥15 m length) influence on foraging decisions (≤11 km), and a potential underlying behavioural mechanism, by revealing how birds respond differently to vessels depending on gear type and activity. Such influences have important implications for fisheries, including the proposed discard ban [8]), and wider marine management. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. 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.

  2. Comparative metatranscriptomics reveals decline of a neustonic planktonic population

    KAUST Repository

    Mojib, Nazia

    2016-10-20

    The neuston layer in tropical seas provides a good model to study the effects of increased levels of different stressors (e.g., temperature, ultraviolet radiation and Trichodesmium blooms). Here, we use a comparative in situ metatranscriptomics approach to reveal the functional genomic composition of metabolically active neustonic mesozooplankton community in response to the summer conditions in the Red Sea. The neustonic population exhibited changes in composition and abundance with a significant decline in copepods and appendicularia in July, when Trichodesmium cells were more abundant along with high temperatures and UV-B radiation. Nearly 23,000 genes were differentially expressed at the community level when the metatranscriptomes of the neustonic zooplankton were compared in April, July, and October. On a wider Phylum level, the genes related to oxidative phosphorylation, carbon, nucleotides, amino acids, and lipids were significantly overrepresented in both arthropods and chordates in April and October. On organism level for copepods, expression of genes responsive to oxidative stress, defense against bacteria, immune response, and virus reproduction were increased along with the observed increased appearance of copepod carcasses in the samples collected during July. The differences in expression correspond either to secondary effects of the Trichodesmium bloom or more likely to the increased UV-B radiation in July. Given the dearth of information on the zooplankton gene expression in response to environmental stimuli, our study provides the first transcriptome landscape of the mesozooplankton community during a period of increased mortality of the copepod and appendicularia population.

  3. Frustration-guided motion planning reveals conformational transitions in proteins.

    Science.gov (United States)

    Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

    2017-10-01

    Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

  4. Planarian Phototactic Assay Reveals Differential Behavioral Responses Based on Wavelength.

    Science.gov (United States)

    Paskin, Taylor R; Jellies, John; Bacher, Jessica; Beane, Wendy S

    2014-01-01

    Planarians are free-living aquatic flatworms that possess a well-documented photophobic response to light. With a true central nervous system and simple cerebral eyes (ocelli), planarians are an emerging model for regenerative eye research. However, comparatively little is known about the physiology of their photoreception or how their behavior is affected by various wavelengths. Most phototactic studies have examined planarian behavior using white light. Here, we describe a novel planarian behavioral assay to test responses to small ranges of visible wavelengths (red, blue, green), as well as ultraviolet (UV) and infrared (IR) which have not previously been examined. Our data show that planarians display behavioral responses across a range of wavelengths. These responses occur in a hierarchy, with the shortest wavelengths (UV) causing the most intense photophobic responses while longer wavelengths produce no effect (red) or an apparent attraction (IR). In addition, our data reveals that planarian photophobia is comprised of both a general photophobic response (that drives planarians to escape the light source regardless of wavelength) and wavelength-specific responses that encompass specific behavioral reactions to individual wavelengths. Our results serve to improve the understanding of planarian phototaxis and suggest that behavioral studies performed with white light mask a complex behavioral interaction with the environment.

  5. Family level phylogenies reveal modes of macroevolution in RNA viruses.

    Science.gov (United States)

    Kitchen, Andrew; Shackelton, Laura A; Holmes, Edward C

    2011-01-04

    Despite advances in understanding the patterns and processes of microevolution in RNA viruses, little is known about the determinants of viral diversification at the macroevolutionary scale. In particular, the processes by which viral lineages assigned as different "species" are generated remain largely uncharacterized. To address this issue, we use a robust phylogenetic approach to analyze patterns of lineage diversification in five representative families of RNA viruses. We ask whether the process of lineage diversification primarily occurs when viruses infect new host species, either through cross-species transmission or codivergence, and which are defined here as analogous to allopatric speciation in animals, or by acquiring new niches within the same host species, analogous to sympatric speciation. By mapping probable primary host species onto family level viral phylogenies, we reveal a strong clustering among viral lineages that infect groups of closely related host species. Although this is consistent with lineage diversification within individual hosts, we argue that this pattern more likely represents strong biases in our knowledge of viral biodiversity, because we also find that better-sampled human viruses rarely cluster together. Hence, although closely related viruses tend to infect related host species, it is unlikely that they often infect the same host species, such that evolutionary constraints hinder lineage diversification within individual host species. We conclude that the colonization of new but related host species may represent the principle mode of macroevolution in RNA viruses.

  6. NMR reveals a dynamic allosteric pathway in thrombin.

    Science.gov (United States)

    Handley, Lindsey D; Fuglestad, Brian; Stearns, Kyle; Tonelli, Marco; Fenwick, R Bryn; Markwick, Phineus R L; Komives, Elizabeth A

    2017-01-06

    Although serine proteases are found ubiquitously in both eukaryotes and prokaryotes, and they comprise the largest of all of the peptidase families, their dynamic motions remain obscure. The backbone dynamics of the coagulation serine protease, apo-thrombin (S195M-thrombin), were compared to the substrate-bound form (PPACK-thrombin). R1, R2, (15)N-{(1)H}NOEs, and relaxation dispersion NMR experiments were measured to capture motions across the ps to ms timescale. The ps-ns motions were not significantly altered upon substrate binding. The relaxation dispersion data revealed that apo-thrombin is highly dynamic, with μs-ms motions throughout the molecule. The region around the N-terminus of the heavy chain, the Na(+)-binding loop, and the 170 s loop, all of which are implicated in allosteric coupling between effector binding sites and the active site, were dynamic primarily in the apo-form. Most of the loops surrounding the active site become more ordered upon PPACK-binding, but residues in the N-terminal part of the heavy chain, the γ-loop, and anion-binding exosite 1, the main allosteric binding site, retain μs-ms motions. These residues form a dynamic allosteric pathway connecting the active site to the main allosteric site that remains in the substrate-bound form.

  7. [Blasch-kolinear psoriasis revealed by infliximab therapy].

    Science.gov (United States)

    Sfia, M; Roth-Mall, B; Tortel, M-C; Guillaume, J-C; Cribier, B

    2009-12-01

    Blaschko-linear psoriasis is a rare disease about which only a few publications have appeared in the literature. This form of psoriasis poses problems of differential diagnosis with regard to other forms of inflammatory Blaschko-linear dermatoses. Herein, we report an original case, the linear nature of which was revealed by treatment with infliximab. A 29-year-old man presented chronic psoriasis present for 17 years and resistant to various forms of systemic therapy. Treatment with infliximab 5mg/kg given on D1, D15 and two-monthly, thereafter resulted in practically complete resolution of all skin lesions after the fourth infusion. The only remaining lesions were psoriatic erythematous-squamous, non-pustular lesions with a Blaschko-linear pattern, limited to one side, on the left arm and left leg. These lesions persisted after 10 courses of infliximab, although no other lesions reappeared. This case was original in terms of the revelation of Blaschko-linear lesions during treatment with infliximab, despite the complete disappearance of diffuse psoriatic plaques, thus suggesting the existence in this patient of two cell populations, each having a different response to biotherapy.

  8. Towards revealing the structure of bacterial inclusion bodies.

    Science.gov (United States)

    Wang, Lei

    2009-01-01

    Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

  9. High resolution spectroscopy reveals fibrillation inhibition pathways of insulin

    Science.gov (United States)

    Deckert-Gaudig, Tanja; Deckert, Volker

    2016-12-01

    Fibril formation implies the conversion of a protein’s native secondary structure and is associated with several neurodegenerative diseases. A better understanding of fibrillation inhibition and fibril dissection requires nanoscale molecular characterization of amyloid structures involved. Tip-enhanced Raman scattering (TERS) has already been used to chemically analyze amyloid fibrils on a sub-protein unit basis. Here, TERS in combination with atomic force microscopy (AFM), and conventional Raman spectroscopy characterizes insulin assemblies generated during inhibition and dissection experiments in the presence of benzonitrile, dimethylsulfoxide, quercetin, and β-carotene. The AFM topography indicates formation of filamentous or bead-like insulin self-assemblies. Information on the secondary structure of bulk samples and of single aggregates is obtained from standard Raman and TERS measurements. In particular the high spatial resolution of TERS reveals the surface conformations associated with the specific agents. The insulin aggregates formed under different inhibition and dissection conditions can show a similar morphology but differ in their β-sheet structure content. This suggests different aggregation pathways where the prevention of the β-sheet stacking of the peptide chains plays a major role. The presented approach is not limited to amyloid-related reasearch but can be readily applied to systems requiring extremely surface-sensitive characterization without the need of labels.

  10. CRISPR loci reveal networks of gene exchange in archaea

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    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

  11. Artificial spatiotemporal touch inputs reveal complementary decoding in neocortical neurons

    Science.gov (United States)

    Oddo, Calogero M.; Mazzoni, Alberto; Spanne, Anton; Enander, Jonas M. D.; Mogensen, Hannes; Bengtsson, Fredrik; Camboni, Domenico; Micera, Silvestro; Jörntell, Henrik

    2017-01-01

    Investigations of the mechanisms of touch perception and decoding has been hampered by difficulties in achieving invariant patterns of skin sensor activation. To obtain reproducible spatiotemporal patterns of activation of sensory afferents, we used an artificial fingertip equipped with an array of neuromorphic sensors. The artificial fingertip was used to transduce real-world haptic stimuli into spatiotemporal patterns of spikes. These spike patterns were delivered to the skin afferents of the second digit of rats via an array of stimulation electrodes. Combined with low-noise intra- and extracellular recordings from neocortical neurons in vivo, this approach provided a previously inaccessible high resolution analysis of the representation of tactile information in the neocortical neuronal circuitry. The results indicate high information content in individual neurons and reveal multiple novel neuronal tactile coding features such as heterogeneous and complementary spatiotemporal input selectivity also between neighboring neurons. Such neuronal heterogeneity and complementariness can potentially support a very high decoding capacity in a limited population of neurons. Our results also indicate a potential neuroprosthetic approach to communicate with the brain at a very high resolution and provide a potential novel solution for evaluating the degree or state of neurological disease in animal models. PMID:28374841

  12. Planarian Phototactic Assay Reveals Differential Behavioral Responses Based on Wavelength.

    Directory of Open Access Journals (Sweden)

    Taylor R Paskin

    Full Text Available Planarians are free-living aquatic flatworms that possess a well-documented photophobic response to light. With a true central nervous system and simple cerebral eyes (ocelli, planarians are an emerging model for regenerative eye research. However, comparatively little is known about the physiology of their photoreception or how their behavior is affected by various wavelengths. Most phototactic studies have examined planarian behavior using white light. Here, we describe a novel planarian behavioral assay to test responses to small ranges of visible wavelengths (red, blue, green, as well as ultraviolet (UV and infrared (IR which have not previously been examined. Our data show that planarians display behavioral responses across a range of wavelengths. These responses occur in a hierarchy, with the shortest wavelengths (UV causing the most intense photophobic responses while longer wavelengths produce no effect (red or an apparent attraction (IR. In addition, our data reveals that planarian photophobia is comprised of both a general photophobic response (that drives planarians to escape the light source regardless of wavelength and wavelength-specific responses that encompass specific behavioral reactions to individual wavelengths. Our results serve to improve the understanding of planarian phototaxis and suggest that behavioral studies performed with white light mask a complex behavioral interaction with the environment.

  13. Renal paratransplant hernia revealed: a review of the literature.

    Science.gov (United States)

    Moris, D; Bokos, J; Vailas, M; Kakavia, K; Spartalis, E; Athanasiou, A; Schizas, D; Vernadakis, S

    2017-06-01

    Renal paratransplant hernia (RPH) is an uncommon variant of internal hernias developed in renal transplant recipients. The aim of this review is to meticulously present and analyze all data coming mainly from case reports or short-case studies on this very uncommon surgical entity. The MEDLINE/PubMed database was searched for publications with the medical subject heading ''renal paratransplant hernia''. All the references from the identified articles were searched for relevant information. The end date of the literature search was set to March 2016. Our search revealed five publications, three short clinical series (three cases each) and two case reports. The total number of cases retrieved was 11. RPH should be considered as an iatrogenic surgical complication. The incidence is around 0.45%. RPH is a relatively uncommon but potentially fatal complication after renal transplantation, and its non-specific symptoms may lead to misdiagnosis. Physician awareness, prompt diagnosis, and early surgical intervention are critical. In addition, meticulous surgical technique during transplantation may help avoid this complication.

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

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    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

  15. Evolutionary pets: offspring numbers reveal speciation process in domesticated chickens.

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    Inga Tiemann

    Full Text Available Since Darwin, the nature of the relationship between evolution and domestication has been debated. Evolution offers different mechanisms of selection that lead to adaptation and may end in the origin of new species as defined by the biological species concept. Domestication has given rise to numerous breeds in almost every domesticated species, including chickens. At the same time, so-called artificial selection seems to exclude mechanisms of sexual selection by the animals themselves. We want to forward the question to the animal itself: With whom do you reproduce successfully? This study focused on the sexual behavior of the domestic chicken Gallus gallus f.dom., particularly the White Crested Polish breed. Experiments on mate choice and the observation of fertilization and hatching rates of mixed-breeding groups revealed breed-specific preferences. In breeding groups containing White Crested Polish and a comparative breed, more purebred chicks hatched than hybrids (number of eggs collected: 1059. Mating was possible in equal shares, but in relation to the number of eggs collected, purebred offspring (62.75% ± 7.10%, M ± SE hatched to a greater extend compared to hybrid offspring (28.75% ± 15.32%, M ± SE. These data demonstrate that the mechanism of sexual selection is still present in domestic chicken breeds, which includes the alteration of gene frequencies typical for domestication and evolutionary speciation. Due to selection and mate choice we state that breeding in principle can generate new species. Therefore, we see domestication as an evolutionary process that integrates human interests of animal breeding with innate mate choice by the animal.

  16. Sequence analysis reveals mosaic genome of Aichi virus

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    Han Xiaohong

    2011-08-01

    Full Text Available Abstract Aichi virus is a positive-sense and single-stranded RNA virus, which demonstrated to be related to diarrhea of Children. In the present study, phylogenetic and recombination analysis based on the Aichi virus complete genomes available in GenBank reveal a mosaic genome sequence [GenBank: FJ890523], of which the nt 261-852 region (the nt position was based on the aligned sequence file shows close relationship with AB010145/Japan with 97.9% sequence identity, while the other genomic regions show close relationship with AY747174/German with 90.1% sequence identity. Our results will provide valuable hints for future research on Aichi virus diversity. Aichi virus is a member of the Kobuvirus genus of the Picornaviridae family 12 and belongs to a positive-sense and single-stranded RNA virus. Its presence in fecal specimens of children suffering from diarrhea has been demonstrated in several Asian countries 3456, in Brazil and German 7, in France 8 and in Tunisia 9. Some reports showed the high level of seroprevalence in adults 710, suggesting the widespread exposure to Aichi virus during childhood. The genome of Aichi virus contains 8,280 nucleotides and a poly(A tail. The single large open reading frame (nt 713-8014 according to the strain AB010145 encodes a polyprotein of 2,432 amino acids that is cleaved into the typical picornavirus structural proteins VP0, VP3, VP1, and nonstructural proteins 2A, 2B, 2C, 3A, 3B, 3C and 3D 211. Based on the phylogenetic analysis of 519-bp sequences at the 3C-3D (3CD junction, Aichi viruses can be divided into two genotypes A and B with approximately 90% sequence homology 12. Although only six complete genomes of Aichi virus were deposited in GenBank at present, mosaic genomes can be found in strains from different countries.

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

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    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

  18. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

    Science.gov (United States)

    Pei, Weike; Feyerabend, Thorsten B; Rössler, Jens; Wang, Xi; Postrach, Daniel; Busch, Katrin; Rode, Immanuel; Klapproth, Kay; Dietlein, Nikolaus; Quedenau, Claudia; Chen, Wei; Sauer, Sascha; Wolf, Stephan; Höfer, Thomas; Rodewald, Hans-Reimer

    2017-08-24

    Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.

  19. Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication.

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    James A Stahl

    2013-09-01

    Full Text Available Lytic gammaherpesvirus (GHV replication facilitates the establishment of lifelong latent infection, which places the infected host at risk for numerous cancers. As obligate intracellular parasites, GHVs must control and usurp cellular signaling pathways in order to successfully replicate, disseminate to stable latency reservoirs in the host, and prevent immune-mediated clearance. To facilitate a systems-level understanding of phosphorylation-dependent signaling events directed by GHVs during lytic replication, we utilized label-free quantitative mass spectrometry to interrogate the lytic replication cycle of murine gammaherpesvirus-68 (MHV68. Compared to controls, MHV68 infection regulated by 2-fold or greater ca. 86% of identified phosphopeptides - a regulatory scale not previously observed in phosphoproteomic evaluations of discrete signal-inducing stimuli. Network analyses demonstrated that the infection-associated induction or repression of specific cellular proteins globally altered the flow of information through the host phosphoprotein network, yielding major changes to functional protein clusters and ontologically associated proteins. A series of orthogonal bioinformatics analyses revealed that MAPK and CDK-related signaling events were overrepresented in the infection-associated phosphoproteome and identified 155 host proteins, such as the transcription factor c-Jun, as putative downstream targets. Importantly, functional tests of bioinformatics-based predictions confirmed ERK1/2 and CDK1/2 as kinases that facilitate MHV68 replication and also demonstrated the importance of c-Jun. Finally, a transposon-mutant virus screen identified the MHV68 cyclin D ortholog as a viral protein that contributes to the prominent MAPK/CDK signature of the infection-associated phosphoproteome. Together, these analyses enhance an understanding of how GHVs reorganize and usurp intracellular signaling networks to facilitate infection and replication.

  20. Comparative RNA sequencing reveals substantial genetic variation in endangered primates

    Science.gov (United States)

    Perry, George H.; Melsted, Páll; Marioni, John C.; Wang, Ying; Bainer, Russell; Pickrell, Joseph K.; Michelini, Katelyn; Zehr, Sarah; Yoder, Anne D.; Stephens, Matthew; Pritchard, Jonathan K.; Gilad, Yoav

    2012-01-01

    Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success. PMID:22207615

  1. Do Dolphins’ Whistles Reveal their Age and Sex?

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    Brittany McIntosh

    2015-11-01

    Full Text Available Bottlenose dolphins (Tursiops truncatus have a complex acoustic communication system composed of a variety of sounds, including narrow-band, frequency-modulated whistles. Many past studies of dolphin whistles have focused on clarifying how dolphins use a subset of whistles for self-identification, with less attention given to other qualities that whistles may reveal about a vocalizer. Acoustic features of vocalizations provide indicators of the physical characteristics of the caller (e.g., size for many vertebrate species. To test for similar cues in dolphin whistles, we investigated whether whistles varied systematically according to the sex and age of the vocalizer. Neural networks were created to sort whistles produced by males or females, calves or adults, or from dolphins in four different age groups. Fourteen acoustic parameters of whistles were used as inputs to the networks. Results showed that neural networks were able to learn to classify whistles based on dolphin age or sex; however, networks showed relatively little ability to classify whistles other than those that they were trained to sort. No single class of acoustic cues consistently enabled networks to differentiate either males from females or older dolphins from younger dolphins. Instead, the neural networks used multiple acoustic dimensions to sort whistles. These results suggest that acoustic cues indicative of age and sex are likely present within all whistles produced by dolphins, but that these cues do not correspond to the kinds of global shifts in spectral features that would be expected from systematic age- or sex-related differences in the shape or size of sound producing membranes or acoustic resonators across individuals.

  2. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    Science.gov (United States)

    2012-01-01

    Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed. PMID:22401625

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

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    Bénédicte Coupat-Goutaland

    Full Text Available 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.

  4. 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.

  5. Acoustic terahertz graphene plasmons revealed by photocurrent nanoscopy

    Science.gov (United States)

    Alonso-González, Pablo; Nikitin, Alexey Y.; Gao, Yuanda; Woessner, Achim; Lundeberg, Mark B.; Principi, Alessandro; Forcellini, Nicolò; Yan, Wenjing; Vélez, Saül; Huber, Andreas. J.; Watanabe, Kenji; Taniguchi, Takashi; Casanova, Félix; Hueso, Luis E.; Polini, Marco; Hone, James; Koppens, Frank H. L.; Hillenbrand, Rainer

    2017-01-01

    Terahertz (THz) fields are widely used for sensing, communication and quality control. In future applications, they could be efficiently confined, enhanced and manipulated well below the classical diffraction limit through the excitation of graphene plasmons (GPs). These possibilities emerge from the strongly reduced GP wavelength, λp, compared with the photon wavelength, λ0, which can be controlled by modulating the carrier density of graphene via electrical gating. Recently, GPs in a graphene/insulator/metal configuration have been predicted to exhibit a linear dispersion (thus called acoustic plasmons) and a further reduced wavelength, implying an improved field confinement, analogous to plasmons in two-dimensional electron gases (2DEGs) near conductive substrates. Although infrared GPs have been visualized by scattering-type scanning near-field optical microscopy (s-SNOM), the real-space imaging of strongly confined THz plasmons in graphene and 2DEGs has been elusive so far—only GPs with nearly free-space wavelengths have been observed. Here we demonstrate real-space imaging of acoustic THz plasmons in a graphene photodetector with split-gate architecture. To that end, we introduce nanoscale-resolved THz photocurrent near-field microscopy, where near-field excited GPs are detected thermoelectrically rather than optically. This on-chip detection simplifies GP imaging as sophisticated s-SNOM detection schemes can be avoided. The photocurrent images reveal strongly reduced GP wavelengths (λp ≈ λ0/66), a linear dispersion resulting from the coupling of GPs with the metal gate below the graphene, and that plasmon damping at positive carrier densities is dominated by Coulomb impurity scattering.

  6. Intersubject information mapping: revealing canonical representations of complex natural stimuli

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    Nikolaus Kriegeskorte

    2015-03-01

    Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

  7. Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison.

    Directory of Open Access Journals (Sweden)

    David Forgacs

    Full Text Available Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06. Spatial analysis of these mitochondrial DNA (mtDNA haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76. However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison and Canadian wood bison (B. b. athabascae. Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions.

  8. Neural correlates of the LSD experience revealed by multimodal neuroimaging.

    Science.gov (United States)

    Carhart-Harris, Robin L; Muthukumaraswamy, Suresh; Roseman, Leor; Kaelen, Mendel; Droog, Wouter; Murphy, Kevin; Tagliazucchi, Enzo; Schenberg, Eduardo E; Nest, Timothy; Orban, Csaba; Leech, Robert; Williams, Luke T; Williams, Tim M; Bolstridge, Mark; Sessa, Ben; McGonigle, John; Sereno, Martin I; Nichols, David; Hellyer, Peter J; Hobden, Peter; Evans, John; Singh, Krish D; Wise, Richard G; Curran, H Valerie; Feilding, Amanda; Nutt, David J

    2016-04-26

    Lysergic acid diethylamide (LSD) is the prototypical psychedelic drug, but its effects on the human brain have never been studied before with modern neuroimaging. Here, three complementary neuroimaging techniques: arterial spin labeling (ASL), blood oxygen level-dependent (BOLD) measures, and magnetoencephalography (MEG), implemented during resting state conditions, revealed marked changes in brain activity after LSD that correlated strongly with its characteristic psychological effects. Increased visual cortex cerebral blood flow (CBF), decreased visual cortex alpha power, and a greatly expanded primary visual cortex (V1) functional connectivity profile correlated strongly with ratings of visual hallucinations, implying that intrinsic brain activity exerts greater influence on visual processing in the psychedelic state, thereby defining its hallucinatory quality. LSD's marked effects on the visual cortex did not significantly correlate with the drug's other characteristic effects on consciousness, however. Rather, decreased connectivity between the parahippocampus and retrosplenial cortex (RSC) correlated strongly with ratings of "ego-dissolution" and "altered meaning," implying the importance of this particular circuit for the maintenance of "self" or "ego" and its processing of "meaning." Strong relationships were also found between the different imaging metrics, enabling firmer inferences to be made about their functional significance. This uniquely comprehensive examination of the LSD state represents an important advance in scientific research with psychedelic drugs at a time of growing interest in their scientific and therapeutic value. The present results contribute important new insights into the characteristic hallucinatory and consciousness-altering properties of psychedelics that inform on how they can model certain pathological states and potentially treat others.

  9. Neural correlates of the LSD experience revealed by multimodal neuroimaging

    Science.gov (United States)

    Carhart-Harris, Robin L.; Muthukumaraswamy, Suresh; Roseman, Leor; Kaelen, Mendel; Droog, Wouter; Murphy, Kevin; Tagliazucchi, Enzo; Schenberg, Eduardo E.; Nest, Timothy; Orban, Csaba; Leech, Robert; Williams, Luke T.; Williams, Tim M.; Bolstridge, Mark; Sessa, Ben; McGonigle, John; Sereno, Martin I.; Nichols, David; Hobden, Peter; Evans, John; Singh, Krish D.; Wise, Richard G.; Curran, H. Valerie; Feilding, Amanda; Nutt, David J.

    2016-01-01

    Lysergic acid diethylamide (LSD) is the prototypical psychedelic drug, but its effects on the human brain have never been studied before with modern neuroimaging. Here, three complementary neuroimaging techniques: arterial spin labeling (ASL), blood oxygen level-dependent (BOLD) measures, and magnetoencephalography (MEG), implemented during resting state conditions, revealed marked changes in brain activity after LSD that correlated strongly with its characteristic psychological effects. Increased visual cortex cerebral blood flow (CBF), decreased visual cortex alpha power, and a greatly expanded primary visual cortex (V1) functional connectivity profile correlated strongly with ratings of visual hallucinations, implying that intrinsic brain activity exerts greater influence on visual processing in the psychedelic state, thereby defining its hallucinatory quality. LSD’s marked effects on the visual cortex did not significantly correlate with the drug’s other characteristic effects on consciousness, however. Rather, decreased connectivity between the parahippocampus and retrosplenial cortex (RSC) correlated strongly with ratings of “ego-dissolution” and “altered meaning,” implying the importance of this particular circuit for the maintenance of “self” or “ego” and its processing of “meaning.” Strong relationships were also found between the different imaging metrics, enabling firmer inferences to be made about their functional significance. This uniquely comprehensive examination of the LSD state represents an important advance in scientific research with psychedelic drugs at a time of growing interest in their scientific and therapeutic value. The present results contribute important new insights into the characteristic hallucinatory and consciousness-altering properties of psychedelics that inform on how they can model certain pathological states and potentially treat others. PMID:27071089

  10. A fifth major genetic group among honeybees revealed in Syria.

    Science.gov (United States)

    Alburaki, Mohamed; Bertrand, Bénédicte; Legout, Hélène; Moulin, Sibyle; Alburaki, Ali; Sheppard, Walter Steven; Garnery, Lionel

    2013-12-06

    Apiculture has been practiced in North Africa and the Middle-East from antiquity. Several thousand years of selective breeding have left a mosaic of Apis mellifera subspecies in the Middle-East, many uniquely adapted and survived to local environmental conditions. In this study we explore the genetic diversity of A. mellifera from Syria (n = 1258), Lebanon (n = 169) and Iraq (n = 35) based on 14 short tandem repeat (STR) loci in the context of reference populations from throughout the Old World (n = 732). Our data suggest that the Syrian honeybee Apis mellifera syriaca occurs in both Syrian and Lebanese territories, with no significant genetic variability between respective populations from Syria and Lebanon. All studied populations clustered within a new fifth independent nuclear cluster, congruent with an mtDNA Z haplotype identified in a previous study. Syrian honeybee populations are not associated with Oriental lineage O, except for sporadic introgression into some populations close to the Turkish and Iraqi borders. Southern Syrian and Lebanese populations demonstrated high levels of genetic diversity compared to the northern populations. This study revealed the effects of foreign queen importations on Syrian bee populations, especially for the region of Tartus, where extensive introgression of A. m. anatolica and/or A. m. caucasica alleles were identified. The policy of creating genetic conservation centers for the Syrian subspecies should take into consideration the influence of the oriental lineage O from the northern Syrian border and the large population of genetically divergent indigenous honeybees located in southern Syria.

  11. Local sparse bump hunting reveals molecular heterogeneity of colon tumors.

    Science.gov (United States)

    Dazard, Jean-Eudes; Rao, J Sunil; Markowitz, Sanford

    2012-05-20

    The question of molecular heterogeneity and of tumoral phenotype in cancer remains unresolved. To understand the underlying molecular basis of this phenomenon, we analyzed genome-wide expression data of colon cancer metastasis samples, as these tumors are the most advanced and hence would be anticipated to be the most likely heterogeneous group of tumors, potentially exhibiting the maximum amount of genetic heterogeneity. Casting a statistical net around such a complex problem proves difficult because of the high dimensionality and multicollinearity of the gene expression space, combined with the fact that genes act in concert with one another and that not all genes surveyed might be involved. We devise a strategy to identify distinct subgroups of samples and determine the genetic/molecular signature that defines them. This involves use of the local sparse bump hunting algorithm, which provides a much more optimal and biologically faithful transformed space within which to search for bumps. In addition, thanks to the variable selection feature of the algorithm, we derived a novel sparse gene expression signature, which appears to divide all colon cancer patients into two populations: a population whose expression pattern can be molecularly encompassed within the bump and an outlier population that cannot be. Although all patients within any given stage of the disease, including the metastatic group, appear clinically homogeneous, our procedure revealed two subgroups in each stage with distinct genetic/molecular profiles. We also discuss implications of such a finding in terms of early detection, diagnosis and prognosis. Copyright © 2011 John Wiley & Sons, Ltd.

  12. Complete mitochondrial genomes reveal neolithic expansion into Europe.

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    Qiaomei Fu

    Full Text Available The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.

  13. Environmental barcoding reveals massive dinoflagellate diversity in marine environments.

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    Rowena F Stern

    Full Text Available BACKGROUND: Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we assembled a large cytochrome c oxidase 1 (COI barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean, including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. CONCLUSIONS/SIGNIFICANCE: COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a

  14. Training reveals the sources of Stroop and Flanker interference effects.

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    Antao Chen

    Full Text Available In the field of cognitive control, dimensional overlap and pathway automaticity are generally believed to be critical for the generation of congruency effects. However, their specific roles in the generation of congruency effects are unclear. In two experiments, with the 4:2 mapping design, we investigated this issue by examining the training-related effects on congruency effects (the Stroop interference effect and the Flanker interference effect in Experiments 1 and 2, respectively normally expressed as incongruent minus congruent difference and on their subcomponents (the stimulus interference and response interference. Experiment 1 revealed that the stimulus interference in the Stroop task, wherein the task-relevant (printed color of word and the task-irrelevant (semantics of word dimensions of the stimuli were processed in different pathways, was present during early training but was virtually eliminated at the late stage of training. This indicates that the two dimensions overlap at the early stage but separate at the late stage. In contrast, Experiment 2 showed that the response interference in a variant of the Flanker task, wherein the task-relevant (central color word printed in black font and the task-irrelevant (flanking color words printed in black font dimensions of the stimuli were processed in the same pathway, was enhanced after training. This indicates that the enhanced automaticity of irrelevant-dimension processing induces stronger response competition, which therefore results in the larger response interference. Taken together, the present study demonstrates that (1 dimensional overlap is necessary for the generation of congruency effects, (2 pathway automaticity can affect the size of congruency effects, and (3 training enhances the degree of automatic processing in a given pathway.

  15. Antarctic krill 454 pyrosequencing reveals chaperone and stress transcriptome.

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    Melody S Clark

    Full Text Available BACKGROUND: The Antarctic krill Euphausia superba is a keystone species in the Antarctic food chain. Not only is it a significant grazer of phytoplankton, but it is also a major food item for charismatic megafauna such as whales and seals and an important Southern Ocean fisheries crop. Ecological data suggest that this species is being affected by climate change and this will have considerable consequences for the balance of the Southern Ocean ecosystem. Hence, understanding how this organism functions is a priority area and will provide fundamental data for life history studies, energy budget calculations and food web models. METHODOLOGY/PRINCIPAL FINDINGS: The assembly of the 454 transcriptome of E. superba resulted in 22,177 contigs with an average size of 492bp (ranging between 137 and 8515bp. In depth analysis of the data revealed an extensive catalogue of the cellular chaperone systems and the major antioxidant proteins. Full length sequences were characterised for the chaperones HSP70, HSP90 and the super-oxide dismutase antioxidants, with the discovery of potentially novel duplications of these genes. The sequence data contained 41,470 microsatellites and 17,776 Single Nucleotide Polymorphisms (SNPs/INDELS, providing a resource for population and also gene function studies. CONCLUSIONS: This paper details the first 454 generated data for a pelagic Antarctic species or any pelagic crustacean globally. The classical "stress proteins", such as HSP70, HSP90, ferritin and GST were all highly expressed. These genes were shown to be over expressed in the transcriptomes of Antarctic notothenioid fish and hypothesized as adaptations to living in the cold, with the associated problems of decreased protein folding efficiency and increased vulnerability to damage by reactive oxygen species. Hence, these data will provide a major resource for future physiological work on krill, but in particular a suite of "stress" genes for studies understanding

  16. Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison

    Science.gov (United States)

    Derr, James N.

    2016-01-01

    Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions. PMID:27880780

  17. Revealing cell assemblies at multiple levels of granularity.

    Science.gov (United States)

    Billeh, Yazan N; Schaub, Michael T; Anastassiou, Costas A; Barahona, Mauricio; Koch, Christof

    2014-10-30

    Current neuronal monitoring techniques, such as calcium imaging and multi-electrode arrays, enable recordings of spiking activity from hundreds of neurons simultaneously. Of primary importance in systems neuroscience is the identification of cell assemblies: groups of neurons that cooperate in some form within the recorded population. We introduce a simple, integrated framework for the detection of cell-assemblies from spiking data without a priori assumptions about the size or number of groups present. We define a biophysically-inspired measure to extract a directed functional connectivity matrix between both excitatory and inhibitory neurons based on their spiking history. The resulting network representation is analyzed using the Markov Stability framework, a graph theoretical method for community detection across scales, to reveal groups of neurons that are significantly related in the recorded time-series at different levels of granularity. Using synthetic spike-trains, including simulated data from leaky-integrate-and-fire networks, our method is able to identify important patterns in the data such as hierarchical structure that are missed by other standard methods. We further apply the method to experimental data from retinal ganglion cells of mouse and salamander, in which we identify cell-groups that correspond to known functional types, and to hippocampal recordings from rats exploring a linear track, where we detect place cells with high fidelity. We present a versatile method to detect neural assemblies in spiking data applicable across a spectrum of relevant scales that contributes to understanding spatio-temporal information gathered from systems neuroscience experiments. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  18. Sequence analysis reveals mosaic genome of Aichi virus.

    Science.gov (United States)

    Han, Xiaohong; Zhang, Wen; Xue, Yanjun; Shao, Shihe

    2011-08-05

    Aichi virus is a positive-sense and single-stranded RNA virus, which demonstrated to be related to diarrhea of Children. In the present study, phylogenetic and recombination analysis based on the Aichi virus complete genomes available in GenBank reveal a mosaic genome sequence [GenBank: FJ890523], of which the nt 261-852 region (the nt position was based on the aligned sequence file) shows close relationship with AB010145/Japan with 97.9% sequence identity, while the other genomic regions show close relationship with AY747174/German with 90.1% sequence identity. Our results will provide valuable hints for future research on Aichi virus diversity.Aichi virus is a member of the Kobuvirus genus of the Picornaviridae family 12 and belongs to a positive-sense and single-stranded RNA virus. Its presence in fecal specimens of children suffering from diarrhea has been demonstrated in several Asian countries 3456, in Brazil and German 7, in France 8 and in Tunisia 9. Some reports showed the high level of seroprevalence in adults 710, suggesting the widespread exposure to Aichi virus during childhood.The genome of Aichi virus contains 8,280 nucleotides and a poly(A) tail. The single large open reading frame (nt 713-8014 according to the strain AB010145) encodes a polyprotein of 2,432 amino acids that is cleaved into the typical picornavirus structural proteins VP0, VP3, VP1, and nonstructural proteins 2A, 2B, 2C, 3A, 3B, 3C and 3D 211. Based on the phylogenetic analysis of 519-bp sequences at the 3C-3D (3CD) junction, Aichi viruses can be divided into two genotypes A and B with approximately 90% sequence homology 12. Although only six complete genomes of Aichi virus were deposited in GenBank at present, mosaic genomes can be found in strains from different countries.

  19. Heterogeneity in Neutrophil Microparticles Reveals Distinct Proteome and Functional Properties*

    Science.gov (United States)

    Dalli, Jesmond; Montero-Melendez, Trinidad; Norling, Lucy V; Yin, Xiaoke; Hinds, Charles; Haskard, Dorian; Mayr, Manuel; Perretti, Mauro

    2013-01-01

    Altered plasma neutrophil microparticle levels have recently been implicated in a number of vascular and inflammatory diseases, yet our understanding of their actions is very limited. Herein, we investigate the proteome of neutrophil microparticles in order to shed light on their biological actions. Stimulation of human neutrophils, either in suspension or adherent to an endothelial monolayer, led to the production of microparticles containing >400 distinct proteins with only 223 being shared by the two subsets. For instance, postadherent microparticles were enriched in alpha-2 macroglobulin and ceruloplasmin, whereas microparticles produced by neutrophils in suspension were abundant in heat shock 70 kDa protein 1. Annexin A1 and lactotransferrin were expressed in both microparticle subsets. We next determined relative abundance of these proteins in three types of human microparticle samples: healthy volunteer plasma, plasma of septic patients and skin blister exudates finding that these proteins were differentially expressed on neutrophil microparticles from these samples reflecting in part the expression profiles we found in vitro. Functional assessment of the neutrophil microparticles subsets demonstrated that in response to direct stimulation neutrophil microparticles produced reactive oxygen species and leukotriene B4 as well as locomoted toward a chemotactic gradient. Finally, we investigated the actions of the two neutrophil microparticles subsets described herein on target cell responses. Microarray analysis with human primary endothelial cells incubated with either microparticle subset revealed a discrete modulation of endothelial cell gene expression profile. These findings demonstrate that neutrophil microparticles are heterogenous and can deliver packaged information propagating the activation status of the parent cell, potentially exerting novel and fundamental roles both under homeostatic and disease conditions. PMID:23660474

  20. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition

    Science.gov (United States)

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G.; Mpourmpakis, Giannis; Asplin, John R.; Rimer, Jeffrey D.

    2016-08-01

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization—citrate and hydroxycitrate—exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation

  1. Fish mucus metabolome reveals fish life-history traits

    Science.gov (United States)

    Reverter, M.; Sasal, P.; Banaigs, B.; Lecchini, D.; Lecellier, G.; Tapissier-Bontemps, N.

    2017-06-01

    Fish mucus has important biological and ecological roles such as defense against fish pathogens and chemical mediation among several species. A non-targeted liquid chromatography-mass spectrometry metabolomic approach was developed to study gill mucus of eight butterflyfish species in Moorea (French Polynesia), and the influence of several fish traits (geographic site and reef habitat, species taxonomy, phylogeny, diet and parasitism levels) on the metabolic variability was investigated. A biphasic extraction yielding two fractions (polar and apolar) was used. Fish diet (obligate corallivorous, facultative corallivorous or omnivorous) arose as the main driver of the metabolic differences in the gill mucus in both fractions, accounting for 23% of the observed metabolic variability in the apolar fraction and 13% in the polar fraction. A partial least squares discriminant analysis allowed us to identify the metabolites (variable important in projection, VIP) driving the differences between fish with different diets (obligate corallivores, facultative corallivores and omnivorous). Using accurate mass data and fragmentation data, we identified some of these VIP as glycerophosphocholines, ceramides and fatty acids. Level of monogenean gill parasites was the second most important factor shaping the gill mucus metabolome, and it explained 10% of the metabolic variability in the polar fraction and 5% in the apolar fraction. A multiple regression tree revealed that the metabolic variability due to parasitism in the polar fraction was mainly due to differences between non-parasitized and parasitized fish. Phylogeny and butterflyfish species were factors contributing significantly to the metabolic variability of the apolar fraction (10 and 3%, respectively) but had a less pronounced effect in the polar fraction. Finally, geographic site and reef habitat of butterflyfish species did not influence the gill mucus metabolome of butterflyfishes.

  2. Nucleotide substitutions revealing specific functions of Polycomb group genes.

    Science.gov (United States)

    Bajusz, Izabella; Sipos, László; Pirity, Melinda K

    2015-04-01

    POLYCOMB group (PCG) proteins belong to the family of epigenetic regulators of genes playing important roles in differentiation and development. Mutants of PcG genes were isolated first in the fruit fly, Drosophila melanogaster, resulting in spectacular segmental transformations due to the ectopic expression of homeotic genes. Homologs of Drosophila PcG genes were also identified in plants and in vertebrates and subsequent experiments revealed the general role of PCG proteins in the maintenance of the repressed state of chromatin through cell divisions. The past decades of gene targeting experiments have allowed us to make significant strides towards understanding how the network of PCG proteins influences multiple aspects of cellular fate determination during development. Being involved in the transmission of specific expression profiles of different cell lineages, PCG proteins were found to control wide spectra of unrelated epigenetic processes in vertebrates, such as stem cell plasticity and renewal, genomic imprinting and inactivation of X-chromosome. PCG proteins also affect regulation of metabolic genes being important for switching programs between pluripotency and differentiation. Insight into the precise roles of PCG proteins in normal physiological processes has emerged from studies employing cell culture-based systems and genetically modified animals. Here we summarize the findings obtained from PcG mutant fruit flies and mice generated to date with a focus on PRC1 and PRC2 members altered by nucleotide substitutions resulting in specific alleles. We also include a compilation of lessons learned from these models about the in vivo functions of this complex protein family. With multiple knockout lines, sophisticated approaches to study the consequences of peculiar missense point mutations, and insights from complementary gain-of-function systems in hand, we are now in a unique position to significantly advance our understanding of the molecular basis of

  3. Phenotypic mismatches reveal escape from arms-race coevolution.

    Directory of Open Access Journals (Sweden)

    Charles T Hanifin

    2008-03-01

    Full Text Available Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts and predator traits (tetrodotoxin resistance of snakes to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were "ahead" of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race.

  4. A parts list for fungal cellulosomes revealed by comparative genomics

    Energy Technology Data Exchange (ETDEWEB)

    Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K.; Solomon, Kevin V.; de Groot, Randall; Kuo, Alan; Mondo, Stephen J.; Salamov, Asaf A.; LaButti, Kurt; Zhao, Zhiying; Chiniquy, Jennifer; Barry, Kerrie; Brewer, Heather M.; Purvine, Samuel O.; Wright, Aaron T.; Hainaut, Matthieu; Boxma, Brigitte; van Alen, Theo; Hackstein, Johannes H. P.; Henrissat, Bernard; Baker, Scott E.; Grigoriev, Igor V.; O' Malley, Michelle A.

    2017-05-26

    Cellulosomes are large, multi-protein complexes that tether plant biomass degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria where species specific dockerin domains mediate assembly of enzymes onto complementary cohesin motifs interspersed within non-catalytic protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic protein-scale pathways2,3. For decades, analogous structures have been reported in the early branching anaerobic fungi, which are known to assemble by sequence divergent non-catalytic dockerin domains (NCDD)4. However, the enzyme components, modular assembly mechanism, and functional role of fungal cellulosomes remain unknown5,6. Here, we describe the comprehensive set of proteins critical to fungal cellulosome assembly, including novel, conserved scaffolding proteins unique to the Neocallimastigomycota. High quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single molecule technology to overcome their repeat-richness and extremely low GC content. Genomic analysis coupled with proteomic validation revealed an average 320 NCDD-containing proteins per fungal strain that were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across 4 genera that contain a conserved amino acid sequence repeat that binds to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. Though many catalytic domains are shared with bacteria, the biocatalytic activity of anaerobic fungi is expanded by the inclusion of GH3, GH6, and GH45 enzymes in the enzyme complexes. Collectively, these findings suggest that the fungal cellulosome is an evolutionarily

  5. Global considerations in hierarchical clustering reveal meaningful patterns in data.

    Directory of Open Access Journals (Sweden)

    Roy Varshavsky

    Full Text Available BACKGROUND: A hierarchy, characterized by tree-like relationships, is a natural method of organizing data in various domains. When considering an unsupervised machine learning routine, such as clustering, a bottom-up hierarchical (BU, agglomerative algorithm is used as a default and is often the only method applied. METHODOLOGY/PRINCIPAL FINDINGS: We show that hierarchical clustering that involve global considerations, such as top-down (TD, divisive, or glocal (global-local algorithms are better suited to reveal meaningful patterns in the data. This is demonstrated, by testing the correspondence between the results of several algorithms (TD, glocal and BU and the correct annotations provided by experts. The correspondence was tested in multiple domains including gene expression experiments, stock trade records and functional protein families. The performance of each of the algorithms is evaluated by statistical criteria that are assigned to clusters (nodes of the hierarchy tree based on expert-labeled data. Whereas TD algorithms perform better on global patterns, BU algorithms perform well and are advantageous when finer granularity of the data is sought. In addition, a novel TD algorithm that is based on genuine density of the data points is presented and is shown to outperform other divisive and agglomerative methods. Application of the algorithm to more than 500 protein sequences belonging to ion-channels illustrates the potential of the method for inferring overlooked functional annotations. ClustTree, a graphical Matlab toolbox for applying various hierarchical clustering algorithms and testing their quality is made available. CONCLUSIONS: Although currently rarely used, global approaches, in particular, TD or glocal algorithms, should be considered in the exploratory process of clustering. In general, applying unsupervised clustering methods can leverage the quality of manually-created mapping of proteins families. As demonstrated, it can

  6. Global considerations in hierarchical clustering reveal meaningful patterns in data.

    Science.gov (United States)

    Varshavsky, Roy; Horn, David; Linial, Michal

    2008-05-21

    A hierarchy, characterized by tree-like relationships, is a natural method of organizing data in various domains. When considering an unsupervised machine learning routine, such as clustering, a bottom-up hierarchical (BU, agglomerative) algorithm is used as a default and is often the only method applied. We show that hierarchical clustering that involve global considerations, such as top-down (TD, divisive), or glocal (global-local) algorithms are better suited to reveal meaningful patterns in the data. This is demonstrated, by testing the correspondence between the results of several algorithms (TD, glocal and BU) and the correct annotations provided by experts. The correspondence was tested in multiple domains including gene expression experiments, stock trade records and functional protein families. The performance of each of the algorithms is evaluated by statistical criteria that are assigned to clusters (nodes of the hierarchy tree) based on expert-labeled data. Whereas TD algorithms perform better on global patterns, BU algorithms perform well and are advantageous when finer granularity of the data is sought. In addition, a novel TD algorithm that is based on genuine density of the data points is presented and is shown to outperform other divisive and agglomerative methods. Application of the algorithm to more than 500 protein sequences belonging to ion-channels illustrates the potential of the method for inferring overlooked functional annotations. ClustTree, a graphical Matlab toolbox for applying various hierarchical clustering algorithms and testing their quality is made available. Although currently rarely used, global approaches, in particular, TD or glocal algorithms, should be considered in the exploratory process of clustering. In general, applying unsupervised clustering methods can leverage the quality of manually-created mapping of proteins families. As demonstrated, it can also provide insights in erroneous and missed annotations.

  7. 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

  8. Revealing electronic structure in atomically-engineered manganite thin films

    Science.gov (United States)

    Monkman, Eric Justin

    Semiconductor technology is based on tuning the properties of devices by manipulating thin films and interfaces. Recently, this approach has been extended to complex oxides, where quantum many-body interactions give rise to emergent ground states not present in the parent materials. Rationally controlling and engineering correlated electronic phases has the potential to revolutionize modern electronics, but is hindered by the inability of current theory to account for the effects of many-body interactions on the underlying electronic structure. Manganites provide a particularly model system for studying many-body effects due to their complex electronic and magnetic phase diagrams, which give rise to many potentially useful properties. Despite extensive work on manganite films demonstrating numerous electronic phase transitions, little is directly known about how the electronic structure responds to the 'control parameters' accessible in thin films. This dissertation presents direct measurements of the electronic structure in La1-- xSrxMnO3 based thin films and interfaces through several phase transitions using a unique integrated oxide molecular-beam epitaxy and angle-resolved photoemission spectroscopy system. We observe the full Fermi surface and near-EF electronic structure of the ferromagnetic and A-type antiferromagnetic metallic phases, reconciling first-principles calculations with experiment for the first time. Furthermore, our results provide key insights into the polaronic nature of the metallic charge carriers. We then explore the mechanism underlying the insulating ground state for La2/3Sr1/3MnO3 under strong tensile strain. Our measurements rule out the scenarios of bandwidth or localization-driven metal-insulator transitions, and reveal an instability of the strongly interacting metal towards an ordered insulating phase that can be accessed through epitaxial strain. By next studying atomically precise interfaces in (LaMnO3)2n/(SrMnO 3)n superlattices

  9. Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal.

    Science.gov (United States)

    Sharma, Prashant P; Kaluziak, Stefan T; Pérez-Porro, Alicia R; González, Vanessa L; Hormiga, Gustavo; Wheeler, Ward C; Giribet, Gonzalo

    2014-11-01

    Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicerate phylogeny. The monophyly of Arachnida, the terrestrial chelicerates, is generally accepted, but has garnered little support from molecular data, which have been limited either in breadth of taxonomic sampling or in depth of sequencing. To address the internal phylogeny of this group, we employed a phylogenomic approach, generating transcriptomic data for 17 species in combination with existing data, including two complete genomes. We analyzed multiple data sets containing up to 1,235,912 sites across 3,644 loci, using alternative approaches to optimization of matrix composition. Here, we show that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the data set. Accelerated evolutionary rates in Acariformes, Pseudoscorpiones, and Parasitiformes potentially engender long-branch attraction artifacts, yielding nonmonophyly of Arachnida with increasing support upon incrementing the number of concatenated genes. Mutually exclusive hypotheses are supported by locus groups of variable evolutionary rate, revealing significant conflicts in phylogenetic signal. Analyses of gene-tree discordance indicate marked incongruence in relationships among chelicerate orders, whereas derived relationships are demonstrably robust. Consistently recovered and supported relationships include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and all orders represented by multiple terminals. Relationships supported by subsets of slow-evolving genes include Ricinulei + Solifugae; a clade comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of Tetrapulmonata

  10. Revealing Invisible Water: Moisture Recycling as an Ecosystem Service.

    Directory of Open Access Journals (Sweden)

    Patrick W Keys

    Full Text Available An ecosystem service is a benefit derived by humanity that can be traced back to an ecological process. Although ecosystem services related to surface water have been thoroughly described, the relationship between atmospheric water and ecosystem services has been mostly neglected, and perhaps misunderstood. Recent advances in land-atmosphere modeling have revealed the importance of terrestrial ecosystems for moisture recycling. In this paper, we analyze the extent to which vegetation sustains the supply of atmospheric moisture and precipitation for downwind beneficiaries, globally. We simulate land-surface evaporation with a global hydrology model and track changes to moisture recycling using an atmospheric moisture budget model, and we define vegetation-regulated moisture recycling as the difference in moisture recycling between current vegetation and a hypothetical desert world. Our results show that nearly a fifth of annual average precipitation falling on land is from vegetation-regulated moisture recycling, but the global variability is large, with many places receiving nearly half their precipitation from this ecosystem service. The largest potential impacts for changes to this ecosystem service are land-use changes across temperate regions in North America and Russia. Likewise, in semi-arid regions reliant on rainfed agricultural production, land-use change that even modestly reduces evaporation and subsequent precipitation, could significantly affect human well-being. We also present a regional case study in the Mato Grosso region of Brazil, where we identify the specific moisture recycling ecosystem services associated with the vegetation in Mato Grosso. We find that Mato Grosso vegetation regulates some internal precipitation, with a diffuse region of benefit downwind, primarily to the south and east, including the La Plata River basin and the megacities of Sao Paulo and Rio de Janeiro. We synthesize our global and regional results

  11. Dynamics of the Wulong landslide revealed by broadband seismic records

    Science.gov (United States)

    Li, Zhengyuan; Huang, Xinghui; Xu, Qiang; Yu, Dan; Fan, Junyi; Qiao, Xuejun

    2017-02-01

    The catastrophic Wulong landslide occurred at 14:51 (Beijing time, UTC+8) on 5 June 2009, in Wulong Prefecture, Southwest China. This rockslide occurred in a complex topographic environment. Seismic signals generated by this event were recorded by the seismic network deployed in the surrounding area, and long-period signals were extracted from 8 broadband seismic stations within 250 km to obtain source time functions by inversion. The location of this event was simultaneously acquired using a stepwise refined grid search approach, with an error of 2.2 km. The estimated source time functions reveal that, according to the movement parameters, this landslide could be divided into three stages with different movement directions, velocities, and increasing inertial forces. The sliding mass moved northward, northeastward and northward in the three stages, with average velocities of 6.5, 20.3, and 13.8 m/s, respectively. The maximum movement velocity of the mass reached 35 m/s before the end of the second stage. The basal friction coefficients were relatively small in the first stage and gradually increasing; large in the second stage, accompanied by the largest variability; and oscillating and gradually decreasing to a stable value, in the third stage. Analysis shows that the movement characteristics of these three stages are consistent with the topography of the sliding zone, corresponding to the northward initiation, eastward sliding after being stopped by the west wall, and northward debris flowing after collision with the east slope of the Tiejianggou valley. The maximum movement velocity of the sliding mass results from the largest height difference of the west slope of the Tiejianggou valley. The basal friction coefficients of the three stages represent the thin weak layer in the source zone, the dramatically varying topography of the west slope of the Tiejianggou valley, and characteristics of the debris flow along the Tiejianggou valley. Based on the above

  12. Seismic tomography reveals magma chamber location beneath Uturuncu volcano (Bolivia)

    Science.gov (United States)

    Kukarina, Ekaterina; West, Michael; Koulakov, Ivan

    2014-05-01

    reveal the paths of the ascending fluids and melts, feeding the magma chamber. This work was partly supported by Project #7.3 of BES RAS and Project #14-05-31176 mola of RFBR.

  13. PRIVATE INFORMATION REVEALED BY ROMANIAN FACEBOOK USERS - AN EXPLORATORY ASSESSMENT

    Directory of Open Access Journals (Sweden)

    VEGHES Calin

    2013-07-01

    Full Text Available The use of online social networks has become part of our lives. More and more people join networks, create their online profile, add pictures with themselves, add personal information about them, find people they know and connect with them, share and like posts, comments, pictures or movies and many more. The social networks allow more and more features and people are open and willing to try them. In this context, it is important for those who own such a profile to be aware of how their personal information is handled, who can view the data they publish in the social network and how they can protect the information they post, by granting access to it only to those persons they want to. The objective of this research was to study what type of information Romanian Facebook users are revealing on their profiles. We have conducted an empirical research, based on an online questionnaire which was available to be accessed in March 2013. 42,5% of the respondents, aged between 21 and 40, formed mostly my employees, managers and students, have not shared on their profiles neither their phone number, their home address, nor their messenger ID. Even though we have considered that the email address was also considered personal and very private information, our assumption did not confirmed, about 30% of the respondents have their email address shown on their profile. At the opposite side, it was confirmed that the gender, real name, personal pictures, birthday and current town are information published by more than 80% the respondents. The respondents do know and do make a difference between having their profile shown when searched on Facebook and allowing their profile to be visualised by whomever they want. Even though most of the respondents have their profile public when searched for it, the great majority have set that only their friends to be able to see the information they post online. Only about 10% of the respondents have added or have accepted

  14. Genome size analyses of Pucciniales reveal the largest fungal genomes

    Directory of Open Access Journals (Sweden)

    Silvia eTavares

    2014-08-01

    Full Text Available Rust fungi (Basidiomycota, Pucciniales are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 151.5 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi. In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1,800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp. Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94 %. The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7,000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  15. 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

  16. 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

  17. Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns.

    Science.gov (United States)

    Wang, Linhai; Li, Donghua; Zhang, Yanxin; Gao, Yuan; Yu, Jingyin; Wei, Xin; Zhang, Xiurong

    2016-01-01

    Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive

  18. Landsat 7 Reveals Large-scale Fractal Motion of Clouds

    Science.gov (United States)

    2002-01-01

    get carried along within the vortices, but these are soon mixed into the surrounding clouds. Landsat is unique in its ability to image both the small-scale eddies that mix clear and cloudy air, down to the 30 meter pixel size of Landsat, but also having a wide enough field-of-view, 180 km, to reveal the connection of the turbulence to large-scale flows such as the subtropical oceanic gyres. Landsat 7, with its new onboard digital recorder, has extended this capability away from the few Landsat ground stations to remote areas such as Alejandro Island, and thus is gradually providing a global dynamic picture of evolving human-scale phenomena. (For more details on von Karman vortices, refer to http://climate.gsfc.nasa.gov/cahalan) Image and caption courtesy Bob Cahalan, NASA GSFC

  19. 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

  20. 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

  1. "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

  2. Origin of Enigmatic Galactic-center Filaments Revealed

    Science.gov (United States)

    2004-06-01

    were oriented perpendicular to the plane of the Galaxy, which would have aligned them with the Galaxy’s own magnetic field. "The problem with this hypothesis is that more recent images have revealed a population of weaker filaments oriented randomly in relation to the plane of the Galaxy," said Yusef-Zadeh. "This makes it difficult to explain the origin of the filaments by an organized Galactic magnetic field." In March and June of 2004, a team of astronomers using the GBT made images of the Galactic center at various wavelengths. The purpose of these surveys was to help identify radio features produced by hot gas (thermal emission) and those produced in magnetic fields (non-thermal emission). In general, thermal features radiate more strongly at shorter wavelengths and non-thermal at longer wavelengths. By comparing the GBT images with earlier VLA data taken of the same region, Yusef-Zadeh determined that a number of the non-thermal filaments seemed to connect to concentrated areas of thermal emission, which identify pockets of star formation. Galatic Center Combined radio image from the Very Large Array and Green Bank Telescope. The linear filaments near the top are some of the nonthermal radio filaments (NRFs) studied by the researchers. Other features, such as supernova remnants (SNRs) and the area surrounding our Galaxy's supermassive black hole (Sgr A) are shown. CREDIT: NRAO/AUI/NSF Yusef-Zadeh, et.al. (Click on Image for Larger Version) "What this showed us is that two seemingly disparate processes, thermal and non-thermal radio emission, can be created by the very same phenomenon," said Yusef-Zadeh. "In this case, that phenomenon is pockets of starburst activity." Yusef-Zadeh notes that the exact mechanism for how the areas of starburst generate the magnetic fields is still being investigated. "There are many ideas about the mechanism that generates these filaments," added Yusef-Zadeh, "but one possibility is that they are produced by the collision of winds

  3. Tremendous Mass Concentration in Strange Galaxy Revealed by VLBA

    Science.gov (United States)

    1995-01-01

    A dense whirling mass orbiting what almost certainly is a black hole of truly Brobdingnagian proportions has been discovered at the heart of an active galaxy some 21 million light years from Earth. The astronomical observations were made by an international team of Japanese and American astronomers using a continent-wide radio telescope funded by the National Science Foundation. The work is reported in the January 12th issue of Nature. The tremendous concentration of mass, equivalent to 40 million suns, in the center of the galaxy NGC4258 in the constellation Canes Venatici, was revealed by the apparent rotation of a molecular disk that surrounds it. The observations showed that the disk of dense material is orbiting within the galaxy's nucleus at velocities -- up to 650 miles per second -- that require the gravitational pull of such a massive object. The high angular resolution and sensitivity of the Very Long Baseline Array of the National Radio Astronomy Observatory allowed precise measurements of the differential rotation of the material in the disk, which provides the most direct and definitive evidence to date for the presence of a supermassive black hole in the center of another galaxy. Black holes, so dense that nothing -- not even light -- can escape their gravitational fields, have long been thought to be present in the centers of active galaxies, where they would act as central engines driving a variety of exotic and energetic phenomena that are seen on much larger scales, such as jets and powerful X ray emission. NGC 4258, a spiral some 90,000 light-years across, is known to have jets of gas that are twisted into the shape of a helix emerging from the nucleus at speeds of 400 miles per second. Makoto Miyoshi of Japan's Mizusawa Astrogeodymanics Observatory; James Moran, James Herrnstein and Lincoln Greenhill of the Harvard-Smithsonian Center for Astrophysics in Cambridge, MA; Naomasa Nakai of Japan's Nobeyama Radio Observatory; Philip Diamond of the

  4. SOHO reveals how sunspots take a stranglehold on the Sun

    Science.gov (United States)

    2001-11-01

    what order the contestants arrive at the finish. Here the runners are packets of sound waves, and the obstacles are local variations in temperature, magnetic fields and gas flows beneath the Sun's surface. "We needed better mathematical tricks," comments Duvall. "So we put together ideas from classical and quantum physics, and also from a recent advance in seismology on the Earth." In an earlier application of solar tomography, the team examined in detail the ante-natal events for an important group of sunspots born on 12 January 1998. They found sound waves beginning to travel faster and faster through the region where sunspots were about to form. Less than half a day elapsed between signs of unusual magnetic activity in the Sun's interior and the appearance of the dark spots on a previously unblemished surface. "Sunspots form when intense magnetic fields break through the visible surface," says Alexander Kosovichev of Stanford. "We could see the magnetic field shooting upwards like a fountain, faster than we expected." Even late on the previous day there was little hint of anything afoot, either at the surface or in the interior. By midnight (Universal Time) a region of strong magnetic field had risen from a depth of 18 000 kilometres and was already half way to the surface, travelling at 4500 km/hr. Sound speeds were increasing above the perturbed zone. By 8:00 a.m. an intense, rope-like magnetic field was in possession of a column of gas 20 000 kilometres wide and reaching almost to the visible surface. In the uppermost layer beneath the surface, the magnetic rope divided itself into strands that made the individual sunspots of the group. Under a large, well-established sunspot, in June 1998, the sound waves revealed a persistent column of hot, magnetised gas rising from deep in the interior. At a depth of 4000 kilometres it spread fingers towards neighbouring parts of the surface where it sustained some smaller sunspots. The magnetic column was not connected to

  5. DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera

    National Research Council Canada - National Science Library

    Bello, Abubakar; Daru, Barnabas H; Stirton, Charles H; Chimphango, Samson B M; van der Bank, Michelle; Maurin, Olivier; Muasya, A Muthama

    2015-01-01

    ... (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae...

  6. Aspirin revealed

    Science.gov (United States)

    Lacey, D.; Hu, X. K.; Loboda, A. V.; Mosey, N. J.; Lipson, R. H.

    2007-03-01

    Experiments are described where the experimental conditions have been optimized to detect aspirin by MALDI mass spectrometry. Although protonated aspirin was not observed by MALDI, sodium and potassium aspirin adducts could be found. Significantly better signals could be obtained by using Rb and Cs salts as cationization sources. Quantum calculations were carried out to determine the structure and energetics of the Li, K, Rb, and Cs alkali--aspirin adducts.

  7. CREST Revealed

    DEFF Research Database (Denmark)

    Rapp, Hermann; Parisi, Cristiana; Bridgeman, Alfia

    This report covers the period from 1993 when the CREST project was initiated, to its launch in 1996, and considers the environment that prompted its instigation. The report looks at the massive cooperation of Government, industry and a range of different service providers that all came together......, under the central control of the CREST project team. It proposes five reasons why the CREST project was successful and examines why the CREST system continues to be at the heart of UK settlement, 20 years on....

  8. Revealing roads

    DEFF Research Database (Denmark)

    Pinder, David

    2017-01-01

    against the motorway’s grain. Based on moving with selected walkers who conduct ‘deliberately slow travelling’, and tracing the narratives of time-based civic art projects, the chapter explores the spectral dimensions of motorways in the UK. The chapter ends by positioning their streams of traffic as much...

  9. Revealing Hearts

    DEFF Research Database (Denmark)

    Saghaug, Kristin Falck; Pattison, George; Lindgren, Peter

    2014-01-01

    Some small business owners want to balance personal values as well as economic values. “I have to follow my heart” or “it must be meaningful” some of them say. But how might they be able to know what gives meaning to the heart? The philosophical theologian Paul Tillich finds that the problem...

  10. On combining revealed and stated preferences to forecast customer behaviour: three case studies

    OpenAIRE

    Franses, Philip Hans; Verhoef, Peter

    2002-01-01

    textabstractMany companies collect stated preference data (SP) like intentions and satisfaction as well as revealed preference data (RP) like actual purchasing behavior. It seems relevant to examine the predictive usefulness of this information for future revealed preferences, that is, customer behavior. In this paper we address this issue by considering three case studies.

  11. Eye lens radiocarbon reveals centuries of longevity in the Greenland shark (Somniosus microcephalus)

    DEFF Research Database (Denmark)

    Nielsen, Julius; Hedeholm, Rasmus B; Heinemeier, Jan

    2016-01-01

    in total length) revealed a life span of at least 272 years. Only the smallest sharks (220 cm or less) showed signs of the radiocarbon bomb pulse, a time marker of the early 1960s. The age ranges of prebomb sharks (reported as midpoint and extent of the 95.4% probability range) revealed the age at sexual...

  12. Deciding to Reveal Sexual Information and Sexuality Education in Mother-Daughter Relationships

    Science.gov (United States)

    Coffelt, Tina A.

    2017-01-01

    Communication privacy management theory informed this study of nine mothers and their 18- or 19-year-old daughters who were interviewed to understand privacy rule foundations that influence their decisions to reveal or conceal sexual information. Findings reveal the salience of motivation and the risk-benefit ratio when making decisions about…

  13. Sperm whale long-range echolocation sounds revealed by ANTARES, a deep-sea neutrino telescope

    National Research Council Canada - National Science Library

    ...; M André; A Caballé; M Van Der Schaar; A Solsona; L Houégnigan; S Zaugg; A M Sánchez; J V Castell; M Solé; F Vila; D Djokic; S Adrián-martínez; A Albert; M Anghinolfi; G Anton; M Ardid; J-j Aubert; T Avgitas; B Baret; J Barrios-martí; S Basa; V Bertin; S Biagi; R Bormuth; M C Bouwhuis; R Bruijn; J Brunner; J Busto; A Capone; L Caramete; J Carr; S Celli; T Chiarusi; M Circella; A Coleiro; R Coniglione; H Costantini; P Coyle; A Creusot; A Deschamps; G De Bonis; C Distefano; I Di Palma; C Donzaud; D Dornic; D Drouhin; T Eberl; I El Bojaddaini; D Elsässer; A Enzenhöfer; K Fehn; I Felis; L A Fusco; S Galatà; P Gay; S Geißelsöder; K Geyer; V Giordano; A Gleixner; H Glotin; R Gracia-ruiz; K Graf; S Hallmann; H Van Haren; A J Heijboer; Y Hello; J J Hernandez-rey; J Hößl; J Hofestädt; C Hugon; G Illuminati; C W James; M De Jong; M Jongen; M Kadler; O Kalekin; U Katz; D Kießling; A Kouchner; M Kreter; I Kreykenbohm; V Kulikovskiy; C Lachaud; R Lahmann; D Lefèvre; E Leonora; S Loucatos; M Marcelin; A Margiotta; A Marinelli; J A Martínez-mora; A Mathieu; K Melis; T Michael; P Migliozzi; A Moussa; C Mueller; E Nezri; G E Pavalas; C Pellegrino

    2017-01-01

    ... is still presently uncertain. The analysis of two years of continuous acoustic data provided by the ANTARES neutrino telescope revealed the year-round presence of sperm whales in the Ligurian Sea, probably associated...

  14. DNA Barcoding Reveals High Cryptic Diversity of the Freshwater Halfbeak Genus Hemirhamphodon from Sundaland

    National Research Council Canada - National Science Library

    Lim, HongChiun; Zainal Abidin, Muchlisin; Pulungan, Chaidir Parlindungan; de Bruyn, Mark; Mohd Nor, Siti Azizah

    2016-01-01

    .... A total of 201 individuals from 46 locations in Peninsular Malaysia, north Borneo (Sarawak) and Sumatra were successfully amplified for 616 base pairs of the COI gene revealing 231 variable and 213 parsimony informative sites...

  15. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

    National Research Council Canada - National Science Library

    Mitchell, Kieren J; Llamas, Bastien; Soubrier, Julien; Rawlence, Nicolas J; Worthy, Trevor H; Wood, Jamie; Lee, Michael S Y; Cooper, Alan

    2014-01-01

    ...) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant...

  16. Principal component analysis of ensemble recordings reveals cell assemblies at high temporal resolution

    NARCIS (Netherlands)

    Peyrache, A.; Benchenane, K.; Khamassi, M.; Wiener, S.I.; Battaglia, F.P.

    2010-01-01

    Simultaneous recordings of many single neurons reveals unique insights into network processing spanning the timescale from single spikes to global oscillations. Neurons dynamically self-organize in subgroups of coactivated elements referred to as cell assemblies. Furthermore, these cell assemblies

  17. Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression

    National Research Council Canada - National Science Library

    Putluri, Nagireddy; Shojaie, Ali; Vasu, Vihas T; Vareed, Shaiju K; Nalluri, Srilatha; Putluri, Vasanta; Thangjam, Gagan Singh; Panzitt, Katrin; Tallman, Christopher T; Butler, Charles; Sana, Theodore R; Fischer, Steven M; Sica, Gabriel; Brat, Daniel J; Shi, Huidong; Palapattu, Ganesh S; Lotan, Yair; Weizer, Alon Z; Terris, Martha K; Shariat, Shahrokh F; Michailidis, George; Sreekumar, Arun

    2011-01-01

    .... Subsequent enrichment-based bioprocess mapping revealed alterations in phase I/II metabolism and suggested a possible role for DNA methylation in perturbing xenobiotic metabolism in bladder cancer...

  18. Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae

    National Research Council Canada - National Science Library

    Jing Li; Danxiang Han; Dongmei Wang; Kang Ning; Jing Jia; Li Wei; Xiaoyan Jing; Shi Huang; Jie Chen; Yantao Li; Qiang Hu; Jian Xu

    2014-01-01

    To reveal the molecular mechanisms of oleaginousness in microalgae, transcriptomic and lipidomic dynamics of the oleaginous microalga Nannochloropsis oceanica IMET1 under nitrogen-replete (N+) and N-depleted (N...

  19. Genome sequencing of Ewing sarcoma patients reveals genetic predisposition | Center for Cancer Research

    Science.gov (United States)

    The largest and most comprehensive genomic analysis of individuals with Ewing sarcoma performed to date reveals that some patients are genetically predisposed to developing the cancer.  Learn more...

  20. The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, Steve

    2010-03-24

    Francis Martin from the French agricultural research institute INRA talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  1. A Filtering Method to Reveal Crystalline Patterns from Atom Probe Microscopy Desorption Maps

    Science.gov (United States)

    2016-03-26

    reveal crystalline patterns from atom probe microscopy desorption maps Lan Yao Department of Materials Science and Engineering, University of Michigan, Ann...reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. Themethod filters atoms based on the time difference...between their evaporation and the evaporation of the previous atom . Since this time difference correlates with the location and the local structure of

  2. Unitary Root Music and Unitary Music with Real-Valued Rank Revealing Triangular Factorization

    Science.gov (United States)

    2010-06-01

    AFRL-RY-WP-TP-2010-1213 UNITARY ROOT MUSIC AND UNITARY MUSIC WITH REAL-VALUED RANK REVEALING TRIANGULAR FACTORIZATION (Postprint) Nizar...DATES COVERED (From - To) June 2010 Journal Article Postprint 08 September 2006 – 31 August 2009 4. TITLE AND SUBTITLE UNITARY ROOT MUSIC AND...UNITARY MUSIC WITH REAL-VALUED RANK REVEALING TRIANGULAR FACTORIZATION (Postprint) 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA8650-05-D-1912-0007 5c

  3. Revealed Comparative Advantage and the Alternatives as Measures of International Specialization

    DEFF Research Database (Denmark)

    Laursen, Keld

    2015-01-01

    This paper provides an analysis of Balassa's 'revealed comparative advantage' (RCA). It shows that when using RCA, it should be adjusted such that it becomes symmetric around its neutral value. The proposed adjusted index is called 'revealed symmetric comparative advantage' (RSCA). The theoretical...... Balance, Chi Square, and Bowen's Net Trade Index. The result of the analysis is that RSCA-on balance-is the best measure of comparative advantage....

  4. Gene expression profiling in equine polysaccharide storage myopathy revealed inflammation, glycogenesis inhibition, hypoxia and mitochondrial dysfunctions

    Directory of Open Access Journals (Sweden)

    Benech Philippe

    2009-08-01

    Full Text Available Abstract Background Several cases of myopathies have been observed in the horse Norman Cob breed. Muscle histology examinations revealed that some families suffer from a polysaccharide storage myopathy (PSSM. It is assumed that a gene expression signature related to PSSM should be observed at the transcriptional level because the glycogen storage disease could also be linked to other dysfunctions in gene regulation. Thus, the functional genomic approach could be conducted in order to provide new knowledge about the metabolic disorders related to PSSM. We propose exploring the PSSM muscle fiber metabolic disorders by measuring gene expression in relationship with the histological phenotype. Results Genotypying analysis of GYS1 mutation revealed 2 homozygous (AA and 5 heterozygous (GA PSSM horses. In the PSSM muscles, histological data revealed PAS positive amylase resistant abnormal polysaccharides, inflammation, necrosis, and lipomatosis and active regeneration of fibers. Ultrastructural evaluation revealed a decrease of mitochondrial number and structural disorders. Extensive accumulation of an abnormal polysaccharide displaced and partially replaced mitochondria and myofibrils. The severity of the disease was higher in the two homozygous PSSM horses. Gene expression analysis revealed 129 genes significantly modulated (p Conclusion The main disorders observed in PSSM muscles could be related to mitochondrial dysfunctions, glycogenesis inhibition and the chronic hypoxia of the PSSM muscles.

  5. Virtually naked: virtual environment reveals sex-dependent nature of skin disclosure.

    Directory of Open Access Journals (Sweden)

    Anna M Lomanowska

    Full Text Available The human tendency to reveal or cover naked skin reflects a competition between the individual propensity for social interactions related to sexual appeal and interpersonal touch versus climatic, environmental, physical, and cultural constraints. However, due to the ubiquitous nature of these constraints, isolating on a large scale the spontaneous human tendency to reveal naked skin has remained impossible. Using the online 3-dimensional virtual world of Second Life, we examined spontaneous human skin-covering behavior unhindered by real-world climatic, environmental, and physical variables. Analysis of hundreds of avatars revealed that virtual females disclose substantially more naked skin than virtual males. This phenomenon was not related to avatar hypersexualization as evaluated by measurement of sexually dimorphic body proportions. Furthermore, analysis of skin-covering behavior of a population of culturally homogeneous avatars indicated that the propensity of female avatars to reveal naked skin persisted despite explicit cultural norms promoting less revealing attire. These findings have implications for further understanding how sex-specific aspects of skin disclosure influence human social interactions in both virtual and real settings.

  6. [Revealing of tuberculosis in an infectious diseases hospital of a megalopolis].

    Science.gov (United States)

    Malashenkov, E A; Ivanovskiĭ, V B

    2007-01-01

    The advisory work of the phthisiatrician in an infectious diseases hospital was analyzed; the analysis revealed that in 2005 tuberculose changes of various degrees of activity had been revealed in 42.5% of examined patients, and 32.1% of them were subjects in whom tuberculosis of diferent localizations had been revealed for the first time. In 43.2% of the latter subjects, the reasons for hospitalization were "clinical masks" of tuberculose process (influenza, acute respiratory viral disease), while 48.6% were hospitalized for gastrointestinal infections and viral hepatitis. In 20.7% of cases tuberculosis was combined with HIV infection. In the infectious diseases hospital, 16.2% of patients with active tuberculosis died. Among the patients treated in the infectious diseases hospital during one year, the proportion of patients with active tuberculosis was 1.44%, the proportion of those in whom the process was revealed for the first time, was 0.75%. In Botkin infectious diseases hospital, there were approximately 6% of patients in whom tuberculose process was revealed for the first time in Saint Petersburg. The peculiarities of this group of patients in an infectious diseases hospital require not only tuberculose alertness, but also reinforcement of phthisiatric, radiological, and laboratory services.

  7. Ancient biomolecules: their origins, fossilization, and role in revealing the history of life.

    Science.gov (United States)

    Briggs, Derek E G; Summons, Roger E

    2014-05-01

    The discovery of traces of a blood meal in the abdomen of a 50-million-year-old mosquito reminds us of the insights that the chemistry of fossils can provide. Ancient DNA is the best known fossil molecule. It is less well known that new fossil targets and a growing database of ancient gene sequences are paralleled by discoveries on other classes of organic molecules. New analytical tools, such as the synchrotron, reveal traces of the original composition of arthropod cuticles that are more than 400 my old. Pigments such as melanin are readily fossilized, surviving virtually unaltered for ∼200 my. Other biomarkers provide evidence of microbial processes in ancient sediments, and have been used to reveal the presence of demosponges, for example, more than 635 mya, long before their spicules appear in the fossil record. Ancient biomolecules are a powerful complement to fossil remains in revealing the history of life. © 2014 WILEY Periodicals, Inc.

  8. 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.

  9. Self-disclosure on Facebook: How much do we really reveal?

    Directory of Open Access Journals (Sweden)

    Stephanie Day

    Full Text Available This paper investigates the use of the social networking site Facebook to self-disclose and analyses the responses of a small group of Facebook users surveyed about their own willingness to self-disclose. An online survey was used to ask Facebook users about their level of Facebook use, what types of personal information they are willing to reveal and the frequency of these personal revelations. The survey also asked the participants to take a look at their publicly viewable profile and the types of information revealed there. Results indicated that overall, most people tended to be cautious about the types of information they revealed, posted mainly positive statements about themselves and were aware of personal privacy issues.

  10. Papillary Renal Cell Carcinoma Revealed by Renal Traumatism: A Case Report in Lomé

    Directory of Open Access Journals (Sweden)

    Tchilabalo Matchonna Kpatcha

    2017-07-01

    Full Text Available This study is a report on a case of papillary carcinoma of the kidney revealed by an abdominal contusion. The results of radiological investigations were discordant with the low intensity of the shock. The treatment consisted of radical nephrectomy because of the suspicion of a pre-existing malignancy. Histological analysis revealed a papillary carcinoma pT3N0M0. We focus on the need for performing diagnostic tests in order to avoid missing a pre-existing anomaly to the kidney trauma.

  11. REVEAL II: Seasonality and spatial variability of particle and visibility conditions in the Fraser Valley

    DEFF Research Database (Denmark)

    Pryor, S.C.; Barthelmie, R.J.

    2000-01-01

    This paper presents data collected during a year-long field experiment (REVEAL II) in the Fraser Valley, British Columbia. The data are used to provide information regarding ambient visibility conditions and fine particle concentrations in the valley. Although average fine mass measured during...... taken at a number of sites during REVEAL II are used to evaluate a simple method for obtaining (classed) quantitative estimates of visual range from this medium without requiring access to specialized instrumentation. (C) 2000 Elsevier Science B.V. All rights reserved....

  12. Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

    DEFF Research Database (Denmark)

    Frelat, Romain; Lindegren, Martin; Dencker, Tim Spaanheden

    2017-01-01

    it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered......) reveal external drivers of change. Our results revealed a strong spatial structure in fish assemblages persistent over time and linked to differences in depth, primary production and seasonality. Furthermore, we simultaneously characterized important temporal distribution changes related to the low...

  13. Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

    DEFF Research Database (Denmark)

    Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia

    2014-01-01

    these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach......, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large...

  14. High rates of hybridisation reveal fragile reproductive barriers between endangered Australian sea snakes

    DEFF Research Database (Denmark)

    Sanders, Kate L; Redsted Rasmussen, Arne; Guinea, Michael L.

    2014-01-01

    The viviparous sea snakes include 62 ecologically diverse species, many of which are of very recent evolutionary origin and have overlapping distributions. Peak sea snake diversity and endemism is recorded from the isolated emergent reefs of the Timor Sea in Northwest Australia. However, nine...... designations, but revealed high frequencies of hybrids on all four reefs and individuals of pure A. fuscus ancestry only at Scott and (historically) Ashmore. Most unexpectedly, 95% of snakes sampled at Hibernia were hybrids that resembled A. laevis in phenotype, revealing a collapse of reproductive barriers...

  15. Survey reveals public open to ban on hand-held cell phone use and texting.

    Science.gov (United States)

    2013-01-01

    A study performed by the Bureau of Transportation Statistics : (BTS) reveals that the public is open to a ban on : hand-held cell phone use while driving. The study is based : on data from 2009s Omnibus Household Survey (OHS), : which is administe...

  16. Revealing structural and dynamical properties of high density lipoproteins through molecular simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vattulainen, I.

    2012-01-01

    The structure and function of high density lipoprotein (HDL) particles have intrigued the scientific community for decades because of their crucial preventive role in coronary heart disease. However, it has been a taunting task to reveal the precise molecular structure and dynamics of HDL. Further...

  17. Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

    DEFF Research Database (Denmark)

    Zelezniak, Aleksej; Pers, Tune Hannes; Pinho Soares, Simao Pedro

    2010-01-01

    Type 2 diabetes mellitus (T2DM) is a disorder characterized by both insulin resistance and impaired insulin secretion. Recent transcriptomics studies related to T2DM have revealed changes in expression of a large number of metabolic genes in a variety of tissues. Identification of the molecular...

  18. The Streptococcus milleri population of a cystic fibrosis clinic reveals patient specificity and intraspecies diversity.

    Science.gov (United States)

    Sibley, Christopher D; Sibley, Kristen A; Leong, Tara A; Grinwis, Margot E; Parkins, Michael D; Rabin, Harvey R; Surette, Michael G

    2010-07-01

    The genetic relatedness of Streptococcus milleri group isolates from the airways of cystic fibrosis patients was determined by using pulsed-field gel electrophoresis. This study reveals no evidence for patient-to-patient transmission in our patient population; however, within individual patients, complex inter- and intraspecies diversity and dynamics can be observed.

  19. Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Ligare, Marshall R.; Baker, Erin S.; Laskin, Julia; Johnson, Grant E.

    2017-01-01

    Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

  20. Puzzles in modern biology. I. Male sterility, failure reveals design [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Steven A. Frank

    2016-09-01

    Full Text Available Many human males produce dysfunctional sperm. Various plants frequently abort pollen. Hybrid matings often produce sterile males. Widespread male sterility is puzzling. Natural selection prunes reproductive failure. Puzzling failure implies something that we do not understand about how organisms are designed. Solving the puzzle reveals the hidden processes of design.

  1. Homogeneous vs heterogeneous polymerization catalysis revealed by single-particle fluorescence microscopy.

    Science.gov (United States)

    Esfandiari, N Melody; Blum, Suzanne A

    2011-11-16

    A high-sensitivity and high-resolution single-particle fluorescence microscopy technique differentiated between homogeneous and heterogeneous metathesis polymerization catalysis by imaging the location of the early stages of polymerization. By imaging single polymers and single crystals of Grubbs II, polymerization catalysis was revealed to be solely homogeneous rather than heterogeneous or both.

  2. Revealing School Counselors' Perspectives on Using Physical Activity and Consulting with Coaches

    Science.gov (United States)

    Hayden, Laura; Silva, Meghan Ray; Gould, Kaitlin

    2018-01-01

    This study reveals school counselors' perspectives on using physical activity and a consultative process with coaches to provide school-based support for youth. Emerging from this exploration are ways that school-based physical activity might be used to help students develop life skills and to remove barriers to systemic integration of…

  3. Improvising in music: A learning biography study to reveal skill acquisition

    NARCIS (Netherlands)

    Wopereis, Iwan; Van Merriënboer, Jeroen; Kirschner, Paul A.

    2010-01-01

    Wopereis, I. G. J. H., Van Merriënboer, J. J. G., & Kirschner, P. A. (2010). Improvising in music: A learning biography study to reveal skill acquisition. In K. Gomez, L. Lyons, & J. Radinsky (Eds.), Proceedings of the 9th International Conference of the Learning Sciences: Vol. 2 (pp. 419-420).

  4. Revealing Ozgur's Thoughts of a Quadratic Function with a Clinical Interview: Concepts and Their Underlying Reasons

    Science.gov (United States)

    Ozaltun Celik, Aytug; Bukova Guzel, Esra

    2017-01-01

    The quadratic function is an important concept for calculus but the students at high school have many difficulties related to this concept. It is important that the teaching of the quadratic function is realized considering the students' thinking. In this context, the aim of this study conducted through a qualitative case study is to reveal the…

  5. ICT-Based Dynamic Assessment to Reveal Special Education Students' Potential in Mathematics

    Science.gov (United States)

    Peltenburg, Marjolijn; van den Heuvel-Panhuizen, Marja; Robitzsch, Alexander

    2010-01-01

    This paper reports on a research project on information and communication technology (ICT)-based dynamic assessment. The project aims to reveal the mathematical potential of students in special education. The focus is on a topic that is generally recognised as rather difficult for weak students: subtraction up to 100 with crossing the ten. The…

  6. Lack of tissue renewal in human adult Achilles tendon is revealed by nuclear bomb C

    DEFF Research Database (Denmark)

    Heinemeier, Katja Maria; Schjerling, Peter; Heinemeier, J.

    2013-01-01

    the 14C bomb-pulse method. This method takes advantage of the dramatic increase in atmospheric levels of 14C, produced by nuclear bomb tests in 1955-1963, which is reflected in all living organisms. Levels of 14C were measured in 28 forensic samples of Achilles tendon core and 4 skeletal muscle samples...... is revealed by nuclear bomb 14C....

  7. Host?pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies

    OpenAIRE

    Streicker, Daniel G.; Winternitz, Jamie C.; Satterfield, Dara A.; Condori-Condori, Rene Edgar; Broos, Alice; Tello, Carlos; Recuenco, Sergio; Velasco-Villa, Andr?s; Altizer, Sonia; Valderrama, William

    2016-01-01

    Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared complete...

  8. Linguistic Landscape in Singapore: What Shop Names Reveal about Singapore's Multilingualism

    Science.gov (United States)

    Shang, Guowen; Guo, Libo

    2017-01-01

    The visibility and salience of specific languages in public spaces are important parameters of their ethnolinguistic vitality in a society. Drawing upon data from first-hand fieldwork, this paper explores the display of multiple languages in shop names presented in Singapore's neighbourhood centres in order to reveal how local shop owners address…

  9. Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building

    Directory of Open Access Journals (Sweden)

    Chen Shaotian

    2012-04-01

    Full Text Available Abstract Background Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM in 705 individuals from 47 localities. Results A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST = 0.975, P  Conclusions The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.

  10. Gene co-expression networks and profiles reveal potential biomarkers of boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Skinkyté-Juskiené, Rúta; Do, Duy Ngoc

    Boar taint (BT) is an offensive odour or taste of porcine meat which may occur in entire male pigs due to skatole and androstenone accumulation. To avoid BT, castration of young piglets is performed but this strategy is under debate due to animal welfare concerns. The study aimed to reveal potent...

  11. Predator-prey interaction reveals local effects of high-altitude insect migration

    Science.gov (United States)

    High-altitude nocturnal insect migrations represent significant pulses of resources, yet are difficult to study and poorly understood. Predator-prey interactions, specifically migratory moth consumption by high-flying bats, potentially reveal flows of migratory insects across a landscape. In North...

  12. Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage

    NARCIS (Netherlands)

    van der Reijden, Wil A.; Brunner, Jorg; Bosch-Tijhof, Carolien J.; van Trappen, Stefanie; Rijnsburger, Martine C.; de Graaff, Marcel P. W.; van Winkelhoff, Arie J.; Cleenwerck, Ilse; de Vos, Paul

    2010-01-01

    The periodontal pathogen Aggregatibacter actinomycetemcomitans that comprises six serotypes (a-f), is often identified by PCR-based techniques targeting the 16S rRNA gene. In this study, 16S rRNA gene sequence analysis revealed an aberrant cluster of 19 strains within serotype e, denoted as serotype

  13. Meaning Making: What Reflective Essays Reveal about Biology Students' Conceptions about Natural Selection

    Science.gov (United States)

    Balgopal, Meena M.; Montplaisir, Lisa M.

    2011-01-01

    The process of reflective writing can play a central role in making meaning as learners process new information and connect it to prior knowledge. An examination of the written discourse can therefore be revealing of learners' cognitive understanding and affective (beliefs, feelings, motivation to learn) responses to concepts. Despite reflective…

  14. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  15. Toward accountable land use mapping: Using geocomputation to improve classification accuracy and reveal uncertainty

    NARCIS (Netherlands)

    Beekhuizen, J.; Clarke, K.C.

    2010-01-01

    The classification of satellite imagery into land use/cover maps is a major challenge in the field of remote sensing. This research aimed at improving the classification accuracy while also revealing uncertain areas by employing a geocomputational approach. We computed numerous land use maps by

  16. Hyperspectral imaging technology for revealing the original handwritings covered by the same inks

    Directory of Open Access Journals (Sweden)

    Yuanyuan Lian

    2017-01-01

    Full Text Available This manuscript presents a preliminary investigation on the applicability of hyperspectral imaging technology for nondestructive and rapid analysis to reveal covered original handwritings. The hyperspectral imager Nuance-Macro was used to collect the reflected light signature of inks from the overlapping parts. The software Nuance1p46 was used to analyze the reflected light signature of inks which shows the covered original handwritings. Different types of black/blue ballpoint pen inks and black/blue gel pen inks were chosen for sample preparation. From the hyperspectral images examined, the covered original handwritings of application were revealed in 90.5%, 69.1%, 49.5%, and 78.6% of the cases. Further, the correlation between the revealing effect and spectral characteristics of the reflected light of inks at the overlapping parts was interpreted through theoretical analysis and experimental verification. The results indicated that when the spectral characteristics of the reflected light of inks at the overlapping parts were the same or very similar to that of the ink that was used to cover the original handwriting, the original handwriting could not be shown. On the contrary, when the spectral characteristics of the reflected light of inks at the overlapping parts were different to that of the ink that was used to cover the original handwriting, the original handwriting was revealed.

  17. Opening the Big Black Box: European study reveals visitors' impressions of science laboratories

    CERN Multimedia

    2004-01-01

    "On 29 - 30 March the findings of 'Inside the Big Black Box'- a Europe-wide science and society project - will be revealed during a two-day seminar hosted by CERN*. The principle aim of Inside the Big Black Box (IN3B) is to determine whether a working scientific laboratory can capture the curiosity of the general public through visits" (1 page)

  18. Revealing Learner Interests through Topic Mining from Question-Answering Data

    Science.gov (United States)

    Dun, Yijie; Wang, Na; Wang, Min; Hao, Tianyong

    2017-01-01

    In a question-answering system, learner generated content including asked and answered questions is a meaningful resource to capture learning interests. This paper proposes an approach based on question topic mining for revealing learners' concerned topics in real community question-answering systems. The authors' approach firstly preprocesses all…

  19. Prostate cancer revealed by skin metastasis: A case report in black ...

    African Journals Online (AJOL)

    K. Tengue

    2016-11-23

    Nov 23, 2016 ... Uro-Oncology. Case report. Prostate cancer revealed by skin metastasis: A case report in black African man. K. Tenguea,∗. , T. Kpatchaa, E. Sewaa, ... Production and hosting by Elsevier B.V. This is an open access article under the CC ... So the patient has been referred to urology for management. He pre-.

  20. Genomewide analysis of MATE-type gene family in maize reveals ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 95; Issue 3. Genomewide analysis of MATE-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment. HUASHENG ZHU JIANDONG WU YINGLI JIANG JING JIN WEI ZHOU YU WANG GUOMIN HAN YANG ZHAO BEIJIU CHENG.

  1. Naturally death-resistant precursor cells revealed as the origin of retinoblastoma

    DEFF Research Database (Denmark)

    Trinh, Emmanuelle; Lazzerini Denchi, Eros; Helin, Kristian

    2004-01-01

    The molecular mechanisms and the cell-of-origin leading to retinoblastoma are not well defined. In this issue of Cancer Cell, Bremner and colleagues describe the first inheritable model of retinoblastoma, revealing that loss of the pocket proteins pRb and p107 deregulates cell cycle exit in retinal...

  2. Chronotopes and Timespace Contexts: Academic Identity Work Revealed in Narrative Fiction

    Science.gov (United States)

    Pick, David; Symons, Christine; Teo, Stephen T. T.

    2017-01-01

    In this paper, academic identity work is explored through an examination of its portrayal in a work of narrative fiction using a conceptual tool from literary studies. It is found that such an approach provides insights that would otherwise be difficult to uncover by more conventional methods. The analysis reveals academic identity work as an…

  3. Radio tagging technology reveals extreme nest drifting behavior in a eusocial insect

    DEFF Research Database (Denmark)

    Sumner, Seirian; Lucas, Eric; Barker, Jessie

    2007-01-01

    is less closely related. Here we reveal nest drifting as a strategy by which workers may maximize their indirect fitness by helping on several related nests, preferring those where the marginal return from their help is greatest. By using a novel monitoring technique, radio frequency identification (RFID...

  4. Using risk analysis to reveal opportunities for the management of unplanned ignitions in wilderness

    Science.gov (United States)

    Kevin Barnett; Carol Miller; Tyron J. Venn

    2016-01-01

    A goal of fire management in wilderness is to allow fire to play its natural ecological role without intervention. Unfortunately, most unplanned ignitions in wilderness are suppressed, in part because of the risk they might pose to values outside of the wilderness. We capitalize on recent advances in fire risk analysis to demonstrate a risk-based approach for revealing...

  5. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

    Science.gov (United States)

    Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

  6. 78 FR 55772 - Culturally Significant Object Imported for Exhibition Determinations: “Beauty Revealed: Images of...

    Science.gov (United States)

    2013-09-11

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF STATE Culturally Significant Object Imported for Exhibition Determinations: ``Beauty Revealed: Images of Women in...: Images of Women in Qing Dynasty Chinese Painting,'' imported from abroad for temporary exhibition within...

  7. Investigation of pancreas indocrine function in order to reveal subclinical insulin resistence in women with acne

    OpenAIRE

    Filippova, T.; Rudykh, N.; Shevchuk, A

    2008-01-01

    Changed glycemic curves and indices of insulin resistance, the increase of insulin basal level in comparison with healthy persons, presence of antibodies to insulin antigen, decrease of level sex hormone bilding globulin were revealed in patients with acne. It can be considered as sign of formation of subclinical insulin resistance.

  8. Working in Separate Silos? What Citation Patterns Reveal about Higher Education Research Internationally

    Science.gov (United States)

    Tight, Malcolm

    2014-01-01

    Higher education research is a growing, inter-disciplinary and increasingly international field of study. This article examines the citation patterns of articles published in six leading higher education journals--three published in the United States and three published elsewhere in the world--for what they reveal about the development of this…

  9. Revealing the Mind of the Sage: The Narrative Rhetoric of the "Chuang Tzu."

    Science.gov (United States)

    Kirkwood, William G.

    1992-01-01

    Argues that one of the formative texts of Taoism, the "Chuang Tzu," is worthy of study by rhetoric scholars because it reveals a unique approach to rhetoric in its attempt to disclose the mind of the sage not through logic but through intuition, and it shows how storytelling can acquaint people with previously unsuspected possibilities of thought…

  10. Automatic sleep classification using a data-driven topic model reveals latent sleep states

    DEFF Research Database (Denmark)

    Koch, Henriette; Christensen, Julie Anja Engelhard; Frandsen, Rune

    2014-01-01

    Background: The golden standard for sleep classification uses manual scoring of polysomnography despite points of criticism such as oversimplification, low inter-rater reliability and the standard being designed on young and healthy subjects. New method: To meet the criticism and reveal the laten...

  11. Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    DEFF Research Database (Denmark)

    Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

    2016-01-01

    by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

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

    Science.gov (United States)

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

    2016-01-01

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

  13. Plasma metabolomics combined with personalized diagnosis guided by Chinese medicine reveals subtypes of chronic heart failure

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2015-04-01

    Conclusion: This study suggests that combining metabolomics with traditional Chinese medicine diagnosis can reveal metabolic signatures for CHF syndrome subtypes. The plasma metabolites identified might be of special clinical relevance for subtypes of CHF, which could lead to further understanding of mechanisms involved and an improvement in personalized treatment for CHF.

  14. ‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Albertsen, Mads; Andresen, Eva Kammer

    2014-01-01

    as for denitrification, nitrogen fixation, fermentation, trehalose synthesis and utilisation of glucose and lactate. Genetic comparison of P metabolism pathways with sequenced PAOs revealed the absence of the Pit phosphate transporter in the Competibacter-lineage genomes—identifying a key metabolic difference...

  15. Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

    DEFF Research Database (Denmark)

    de Fine Licht, Henrik Hjarvard; Jensen, Annette Bruun; Eilenberg, Jørgen

    2017-01-01

    of toxins that interfere with the host immune response. Phylogenetic comparison with the nonobligate generalist insect-pathogenic fungus Conidiobolus coronatus revealed a gene-family expansion of trehalase enzymes in E. muscae. The main sugar in insect haemolymph is trehalose, and efficient sugar...

  16. Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species

    NARCIS (Netherlands)

    Thompson, S.M.; Tan, Y.P.; Young, A.J.; Neate, S.M.; Aitken, E.A.B.; Shivas, R.G.

    2012-01-01

    The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are

  17. The Health Challenges of Urban Latino College Students as Revealed through Student Journaling

    Science.gov (United States)

    Rowland, Amy L.

    2008-01-01

    Because of the unique health risks faced by the Hispanic population and the notoriously poor health habits of college students, this study examines the health challenges faced by Latino college students enrolled at an urban commuter institution. A thematic analysis reveals the top themes for males and females as healthy eating, weight management,…

  18. Revealing the Transformatory Moment of Learning Technology: The Place of Critical Social Theory

    Science.gov (United States)

    Hall, Richard

    2011-01-01

    In revealing the transformatory moment of learning technology, a holistic and ongoing critique that is related to a range of socio-cultural factors is required. This critique further uncovers the social relations that frame the place of learning technology in bourgeois capitalist work and the development of the knowledge economy. This article…

  19. Eye Movements Reveal the Influence of Event Structure on Reading Behavior

    Science.gov (United States)

    Swets, Benjamin; Kurby, Christopher A.

    2016-01-01

    When we read narrative texts such as novels and newspaper articles, we segment information presented in such texts into discrete events, with distinct boundaries between those events. But do our eyes reflect this event structure while reading? This study examines whether eye movements during the reading of discourse reveal how readers respond…

  20. On the galactic spiral arms nature as revealed by the kinematics of the stellar component

    NARCIS (Netherlands)

    Roca-Fàbrega, S.; Valenzuela, O.; Figueras, F.; Romero-Gómez, M.; Velázquez, H.; Antoja, T.; Pichardo, B.; Guirado, J.C.; Lara, L.M.; Quilis, V.; Gorgas, J.

    N-body simulations conducted for kinematic analysis of stellar disk component -high number of disk particles, small time step and few parsecs spatial resolution - reveal two different behaviors for the spiral arm angular velocity. Whereas subdominant disk cases present transient spiral arm features

  1. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

  2. Humor Ability Reveals Intelligence, Predicts Mating Success, and Is Higher in Males

    Science.gov (United States)

    Greengross, Gil; Miller, Geoffrey

    2011-01-01

    A good sense of humor is sexually attractive, perhaps because it reveals intelligence, creativity, and other "good genes" or "good parent" traits. If so, intelligence should predict humor production ability, which in turn should predict mating success. In this study, 400 university students (200 men and 200 women) completed…

  3. Shape-independent object category responses revealed by MEG and fMRI decoding.

    Science.gov (United States)

    Kaiser, Daniel; Azzalini, Damiano C; Peelen, Marius V

    2016-04-01

    Neuroimaging research has identified category-specific neural response patterns to a limited set of object categories. For example, faces, bodies, and scenes evoke activity patterns in visual cortex that are uniquely traceable in space and time. It is currently debated whether these apparently categorical responses truly reflect selectivity for categories or instead reflect selectivity for category-associated shape properties. In the present study, we used a cross-classification approach on functional MRI (fMRI) and magnetoencephalographic (MEG) data to reveal both category-independent shape responses and shape-independent category responses. Participants viewed human body parts (hands and torsos) and pieces of clothing that were closely shape-matched to the body parts (gloves and shirts). Category-independent shape responses were revealed by training multivariate classifiers on discriminating shape within one category (e.g., hands versus torsos) and testing these classifiers on discriminating shape within the other category (e.g., gloves versus shirts). This analysis revealed significant decoding in large clusters in visual cortex (fMRI) starting from 90 ms after stimulus onset (MEG). Shape-independent category responses were revealed by training classifiers on discriminating object category (bodies and clothes) within one shape (e.g., hands versus gloves) and testing these classifiers on discriminating category within the other shape (e.g., torsos versus shirts). This analysis revealed significant decoding in bilateral occipitotemporal cortex (fMRI) and from 130 to 200 ms after stimulus onset (MEG). Together, these findings provide evidence for concurrent shape and category selectivity in high-level visual cortex, including category-level responses that are not fully explicable by two-dimensional shape properties. Copyright © 2016 the American Physiological Society.

  4. Monkeys choose as if maximizing utility compatible with basic principles of revealed preference theory.

    Science.gov (United States)

    Pastor-Bernier, Alexandre; Plott, Charles R; Schultz, Wolfram

    2017-03-07

    Revealed preference theory provides axiomatic tools for assessing whether individuals make observable choices "as if" they are maximizing an underlying utility function. The theory evokes a tradeoff between goods whereby individuals improve themselves by trading one good for another good to obtain the best combination. Preferences revealed in these choices are modeled as curves of equal choice (indifference curves) and reflect an underlying process of optimization. These notions have far-reaching applications in consumer choice theory and impact the welfare of human and animal populations. However, they lack the empirical implementation in animals that would be required to establish a common biological basis. In a design using basic features of revealed preference theory, we measured in rhesus monkeys the frequency of repeated choices between bundles of two liquids. For various liquids, the animals' choices were compatible with the notion of giving up a quantity of one good to gain one unit of another good while maintaining choice indifference, thereby implementing the concept of marginal rate of substitution. The indifference maps consisted of nonoverlapping, linear, convex, and occasionally concave curves with typically negative, but also sometimes positive, slopes depending on bundle composition. Out-of-sample predictions using homothetic polynomials validated the indifference curves. The animals' preferences were internally consistent in satisfying transitivity. Change of option set size demonstrated choice optimality and satisfied the Weak Axiom of Revealed Preference (WARP). These data are consistent with a version of revealed preference theory in which preferences are stochastic; the monkeys behaved "as if" they had well-structured preferences and maximized utility.

  5. Analyses of Genomic tRNA Reveal Presence of Novel tRNAs in Oryza sativa

    Science.gov (United States)

    Mohanta, Tapan K.; Bae, Hanhong

    2017-01-01

    Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNASer found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O. sativa and to our knowledge, this is the smallest gene of eukaryotic lineage reported so far. Analyses revealed the presence of several novel/pseudo tRNA genes in O. sativa which are reported for the first time. Multiple sequence alignment of tRNAs revealed the presence of family specific conserved consensus sequences. Functional study of these novel tRNA and family specific conserved consensus sequences will be crucial to decipher their importance in biological events. The rate of transition of O. sativa tRNA was found to be higher than the rate of transversion. Evolutionary study revealed, O. sativa tRNAs were evolved from the lineages of multiple common ancestors. Duplication and loss study of tRNAs genes revealed, majority of the O. sativa tRNA were duplicated and 17 of them were found to be undergone loss during the evolution. Orthology and paralogy study showed, the majority of O. sativa tRNA were paralogous and only a few of tRNASer were found to contain orthologous tRNAs. PMID:28713421

  6. Quantitative gradient of subsidies reveals a threshold in community-level trophic cascades.

    Science.gov (United States)

    Klemmer, Amanda J; Richardson, John S

    2013-09-01

    Evidence varies on how subsidies affect trophic cascades within recipient food webs. This could be due to complex nonlinearities being masked by single-level manipulations (presence/absence) of subsidies in past studies. We predicted that trophic cascade strength would increase nonlinearly across a gradient of subsidies. We set out to reveal these complex, nonlinear relationships through manipulating a quantitative gradient of detrital subsidies to lake benthic food webs along with the presence/absence of trout. Contrary to our prediction, we found that trophic cascades only occurred at low subsidy levels, disappearing as subsidies increased. This threshold in trophic cascade strength may be due to an increase in intermediate predators in the absence of top predators, as well as changes in the proportion of armored vs. un-armored primary consumers. Future studies on the effect of subsidies on trophic cascade strength need to incorporate naturally occurring gradients to reveal the complex direct and indirect interactions within food webs.

  7. Revealing the hyperdiverse mite fauna of subarctic Canada through DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Monica R Young

    Full Text Available Although mites are one of the most abundant and diverse groups of arthropods, they are rarely targeted for detailed biodiversity surveys due to taxonomic constraints. We address this gap through DNA barcoding, evaluating acarine diversity at Churchill, Manitoba, a site on the tundra-taiga transition. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species of mites with high species turnover between substrates and between forested and non-forested sites. Accumulation curves have not reached an asymptote for any of the three mite orders investigated, and estimates suggest that more than 1200 species of Acari occur at this locality. The coupling of DNA barcode results with taxonomic assignments revealed that Trombidiformes compose 49% of the fauna, a larger fraction than expected based on prior studies. This investigation demonstrates the efficacy of DNA barcoding in facilitating biodiversity assessments of hyperdiverse taxa.

  8. Multispectral imaging reveals biblical-period inscription unnoticed for half a century.

    Directory of Open Access Journals (Sweden)

    Shira Faigenbaum-Golovin

    Full Text Available Most surviving biblical period Hebrew inscriptions are ostraca-ink-on-clay texts. They are poorly preserved and once unearthed, fade rapidly. Therefore, proper and timely documentation of ostraca is essential. Here we show a striking example of a hitherto invisible text on the back side of an ostracon revealed via multispectral imaging. This ostracon, found at the desert fortress of Arad and dated to ca. 600 BCE (the eve of Judah's destruction by Nebuchadnezzar, has been on display for half a century. Its front side has been thoroughly studied, while its back side was considered blank. Our research revealed three lines of text on the supposedly blank side and four "new" lines on the front side. Our results demonstrate the need for multispectral image acquisition for both sides of all ancient ink ostraca. Moreover, in certain cases we recommend employing multispectral techniques for screening newly unearthed ceramic potsherds prior to disposal.

  9. Proteomic and genomic analysis reveals novel Campylobacter jejuni outer membrane proteins and potential heterogeneity

    Directory of Open Access Journals (Sweden)

    Eleanor Watson

    2014-09-01

    Full Text Available Gram-negative bacterial outer membrane proteins play important roles in the interaction of bacteria with their environment including nutrient acquisition, adhesion and invasion, and antibiotic resistance. In this study we identified 47 proteins within the Sarkosyl-insoluble fraction of Campylobacter jejuni 81-176, using LC–ESI-MS/MS. Comparative analysis of outer membrane protein sequences was visualised to reveal protein distribution within a panel of Campylobacter spp., identifying several C. jejuni-specific proteins. Smith–Waterman analyses of C. jejuni homologues revealed high sequence conservation amongst a number of hypothetical proteins, sequence heterogeneity of other proteins and several proteins which are absent in a proportion of strains.

  10. Cambrian spiral-plated echinoderms from Gondwana reveal the earliest pentaradial body plan.

    Science.gov (United States)

    Smith, Andrew B; Zamora, Samuel

    2013-08-22

    Echinoderms are unique among animal phyla in having a pentaradial body plan, and their fossil record provides critical data on how this novel organization came about by revealing intermediate stages. Here, we report a spiral-plated animal from the early Cambrian of Morocco that is the most primitive pentaradial echinoderm yet discovered. It is intermediate between helicoplacoids (a bizarre group of spiral-bodied echinoderms) and crown-group pentaradiate echinoderms. By filling an important gap, this fossil reveals the common pattern that underpins the body plans of the two major echinoderm clades (pelmatozoans and eleutherozoans), showing that differential growth played an important role in their divergence. It also adds to the striking disparity of novel body plans appearing in the Cambrian explosion.

  11. Practice effects reveal visuomotor vulnerability in school and university rugby players.

    Science.gov (United States)

    Shuttleworth-Edwards, Ann B; Radloff, Sarah E; Whitefield-Alexander, Victoria J; Smith, Ian P; Horsman, Mark

    2014-02-01

    This article reports on three pre- versus post-season prospective studies in which male university and high school contact sport players predominantly of Rugby Union (hereafter rugby) were compared with age, education, and IQ equivalent non-contact sport controls on the ImPACT (Immediate Postconcussion Assessment and Cognitive Testing) test. All analyses revealed a relative absence of practice effects on the Visual Motor Speed (VMS) composite for contact sport groups compared with controls. The VMS data for rugby players from each study were pooled and subjected to additional analysis (Rugby, n = 145; Controls, n = 106). Controls revealed significant improvement over the season (p rugby players whose performance remained the same (interaction effect, p = .028). It is apparent that practice effects have diagnostic potential in this context, implicating vulnerability on speeded visuomotor processing in association with participation in rugby. Pointers for further research and concussion management in the individual case are explored.

  12. Boudin trafficking reveals the dynamic internalisation of specific septate junction components in Drosophila

    Science.gov (United States)

    Tempesta, Camille; Hijazi, Assia; Moussian, Bernard

    2017-01-01

    The maintenance of paracellular barriers in invertebrate epithelia depends on the integrity of specific cell adhesion structures known as septate junctions (SJ). Multiple studies in Drosophila have revealed that these junctions have a stereotyped architecture resulting from the association in the lateral membrane of a large number of components. However, little is known about the dynamic organisation adopted by these multi-protein complexes in living tissues. We have used live imaging techniques to show that the Ly6 protein Boudin is a component of these adhesion junctions and can diffuse systemically to associate with the SJ of distant cells. We also observe that this protein and the claudin Kune-kune are endocytosed in epidermal cells during embryogenesis. Our data reveal that the SJ contain a set of components exhibiting a high membrane turnover, a feature that could contribute in a tissue-specific manner to the morphogenetic plasticity of these adhesion structures. PMID:28977027

  13. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.

    Science.gov (United States)

    Long, Yuchen; Stahl, Yvonne; Weidtkamp-Peters, Stefanie; Postma, Marten; Zhou, Wenkun; Goedhart, Joachim; Sánchez-Pérez, María-Isabel; Gadella, Theodorus W J; Simon, Rüdiger; Scheres, Ben; Blilou, Ikram

    2017-08-03

    During multicellular development, specification of distinct cell fates is often regulated by the same transcription factors operating differently in distinct cis-regulatory modules, either through different protein complexes, conformational modification of protein complexes, or combinations of both. Direct visualization of different transcription factor complex states guiding specific gene expression programs has been challenging. Here we use in vivo FRET-FLIM (Förster resonance energy transfer measured by fluorescence lifetime microscopy) to reveal spatial partitioning of protein interactions in relation to specification of cell fate. We show that, in Arabidopsis roots, three fully functional fluorescently tagged cell fate regulators establish cell-type-specific interactions at endogenous expression levels and can form higher order complexes. We reveal that cell-type-specific in vivo FRET-FLIM distributions reflect conformational changes of these complexes to differentially regulate target genes and specify distinct cell fates.

  14. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Xueling; Zhou, Tongqing; Zhu, Jiang; Zhang, Baoshan; Georgiev, Ivelin; Wang, Charlene; Chen, Xuejun; Longo, Nancy S.; Louder, Mark; McKee, Krisha; O’Dell, Sijy; Perfetto, Stephen; Schmidt, Stephen D.; Shi, Wei; Wu, Lan; Yang, Yongping; Yang, Zhi-Yong; Yang, Zhongjia; Zhang, Zhenhai; Bonsignori, Mattia; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Haynes, Barton F.; Simek, Melissa; Burton, Dennis R.; Koff, Wayne C.; Doria-Rose, Nicole A.; Connors, Mark; Mullikin, James C.; Nabel, Gary J.; Roederer, Mario; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R. (Tumaini); (NIH); (Duke); (Kilimanjaro Repro.); (IAVI)

    2013-03-04

    Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

  15. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

    Directory of Open Access Journals (Sweden)

    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  16. Master stability functions reveal diffusion-driven instabilities in multi-layer networks

    CERN Document Server

    Brechtel, Andreas; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

    2016-01-01

    Many systems in science and technology can be described as multilayer networks, which are known to exhibit phenomena such as catastrophic failure cascades and pattern-forming instabilities. A particular class of multilayer networks describes systems where different interacting copies of a local network exist in different spatial locations, including for instance regulatory and metabolic networks of identical cells and interacting habitats of ecological populations. Here, we show that such systems can be analyzed by a master stability function (MSF) approach, which reveals conditions for diffusion-driven instabilities (DDIs). We demonstrate the methodology on the example of state-of-the-art meta-foodweb models, where it reveals diffusion-driven instabilities that lead to localized dynamics and spatial patterns. This type of approach can be applied to a variety of systems from nature, science and engineering to aid the understanding and design of complex self-organizing systems.

  17. Gender Stereotypes and Gender Roles Revealed in the Students Written Work

    Directory of Open Access Journals (Sweden)

    Gonca Ekşi

    2009-04-01

    Full Text Available Masculinity and femininity are two words that entail two opposite images with distinct sets of behaviour and personal attributes. Regardless of how well these definitions fit to each individual man and woman in society, these gender stereotypes are maintained and transmitted within the society throughout years. In return, gender stereotypes and roles affect men and women in society. In this study, 96 English Language Teaching (ELT junior students are given a questionnaire to get socio-economic information about them and their families. Later, the samples of their process writing work in Advanced Reading and Writing Course I are scanned to find expressions revealing their ideas about gender stereotypes and gender roles. These expressions and their frequency are listed. It is thought that this study will reveal gender stereotypes and roles shared by the average language students at universities.Key Words: Gender stereotypes, gender roles, socialization,

  18. New signatures of underground nuclear tests revealed by satellite radar interferometry

    Science.gov (United States)

    Vincent, P.; Larsen, S.; Galloway, D.; Laczniak, R.J.; Walter, W.R.; Foxall, W.; Zucca, J.J.

    2003-01-01

    New observations of surface displacement caused by past underground nuclear tests at the Nevada Test Site (NTS) are presented using interferometric synthetic aperture radar (InSAR). The InSAR data reveal both coseismic and postseismic subsidence signals that extend one kilometer or more across regardless of whether or not a surface crater was formed from each test. While surface craters and other coseismic surface effects (ground cracks, etc.) may be detectable using high resolution optical or other remote sensing techniques, these broader, more subtle subsidence signals (one to several centimeters distributed over an area 1-2 kilometers across) are not detectable using other methods [Barker et al., 1998]. A time series of interferograms reveal that the postseismic signals develop and persist for months to years after the tests and that different rates and styles of deformation occur depending on the geologic and hydrologic setting and conditions of the local test area.

  19. Germline organization in Strongyloides nematodes reveals alternative differentiation and regulation mechanisms.

    Science.gov (United States)

    Kulkarni, Arpita; Lightfoot, James W; Streit, Adrian

    2016-09-01

    Nematodes of the genus Strongyloides are important parasites of vertebrates including man. Currently, little is known about their germline organization or reproductive biology and how this influences their parasitic life strategies. Here, we analyze the structure of the germline in several Strongyloides and closely related species and uncover striking differences in the development, germline organization, and fluid dynamics compared to the model organism Caenorhabditis elegans. With a focus on Strongyloides ratti, we reveal that the proliferation of germ cells is restricted to early and mid-larval development, thus limiting the number of progeny. In order to understand key germline events (specifically germ cell progression and the transcriptional status of the germline), we monitored conserved histone modifications, in particular H3Pser10 and H3K4me3. The evolutionary significance of these events is subsequently highlighted through comparisons with six other nematode species, revealing underlying complexities and variations in the development of the germline among nematodes.

  20. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

    Science.gov (United States)

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

    2012-01-01

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans. PMID:23012415