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Sample records for species-specific x-ray-induced inflammation

  1. X-ray-induced changes in the expression of inflammation-related genes in human peripheral blood.

    PubMed

    Wang, Ping; Guo, Fei; Han, Lin; Wang, Xi'ai; Li, Jie; Guo, Yan; Lü, Yumin

    2014-10-27

    Using quantitative real-time polymerase chain reaction (PCR) array, we explored and compared the expression changes of inflammation-related genes in human peripheral blood irradiated with 0.5, 3, and 10 Gy doses of X-rays 24 h after exposure. Results indicated that the expression of 62 out of 84 genes was significantly altered after X-ray radiation. Among these 62 genes, 35 (such as TNFSF4) are known to be associated with radiation response, but others are novel. At a low radiation dose (0.5 Gy), 9 genes were up-regulated and 19 were down-regulated. With further increased dose to 3 Gy, 8 unique genes were up-regulated and 19 genes were down-regulated. We also identified 48 different genes that were differentially expressed significantly after 10 Gy of irradiation, and among these transcripts, up-regulated genes accounted for only one-third (16 genes) of the total. Of the 62 genes, 31 were significantly altered only at a specific dose, and a total of 10 genes were significantly expressed at all 3 doses. The dose- and time-dependent expression of CCL2 was confirmed by quantitative real-time reverse-transcription PCR. A number of candidate genes reported herein may be useful molecular biomarkers of radiation exposure in human peripheral blood.

  2. X-ray-induced water vaporization

    SciTech Connect

    Weon, B. M.; Lee, J. S.; Je, J. H.; Fezzaa, K.

    2011-09-15

    We present quantitative evidence for x-ray-induced water vaporization: water is vaporized at a rate of 5.5 pL/s with the 1-A-wavelength x-ray irradiation of {approx}0.1 photons per A{sup 2}; moreover, water vapor is reversibly condensed during pauses in irradiation. This result fundamentally suggests that photoionization induces vaporization. This phenomenon is attributed to surface-tension reduction by ionization and would be universally important in radiological and electrohydrodynamic situations.

  3. X-ray induced photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Xiang, Liangzhong; Han, Bin; Carpenter, Colin; Pratx, Guillem; Kuang, Yu; Xing, Lei

    2013-03-01

    X-ray induced photoacoustic tomography, also called X-ray acoustic computer tomography (XACT) is investigated in this paper. Short pulsed (μs-range) X-ray beams from a medical linear accelerator were used to generate ultrasound. The ultrasound signals were collected with an ultrasound transducer (500 KHz central frequency) positioned around an object. The transducer, driven by a computer-controlled step motor to scan around the object, detected the resulting acoustic signals in the imaging plane at each scanning position. A pulse preamplifier, with a bandwidth of 20 KHz-2 MHz at -3 dB, and switchable gains of 40 and 60 dB, received the signals from the transducer and delivered the amplified signals to a secondary amplifier. The secondary amplifier had bandwidth of 20 KHz-30 MHz at -3 dB, and a gain range of 10-60 dB. Signals were recorded and averaged 128 times by an oscilloscope. A sampling rate of 100 MHz was used to record 2500 data points at each view angle. One set of data incorporated 200 positions as the receiver moved 360°. The x-ray generated acoustic image was then reconstructed with the filtered back projection algorithm. The twodimensional XACT images of the lead rod embedded in chicken breast tissue were found to be in good agreement with the shape of the object. This new modality may be useful for a number of applications, such as providing the location of a fiducial, or monitoring x-ray dose distribution during radiation therapy.

  4. High Resolution X-ray-Induced Acoustic Tomography

    PubMed Central

    Xiang, Liangzhong; Tang, Shanshan; Ahmad, Moiz; Xing, Lei

    2016-01-01

    Absorption based CT imaging has been an invaluable tool in medical diagnosis, biology, and materials science. However, CT requires a large set of projection data and high radiation dose to achieve superior image quality. In this letter, we report a new imaging modality, X-ray Induced Acoustic Tomography (XACT), which takes advantages of high sensitivity to X-ray absorption and high ultrasonic resolution in a single modality. A single projection X-ray exposure is sufficient to generate acoustic signals in 3D space because the X-ray generated acoustic waves are of a spherical nature and propagate in all directions from their point of generation. We demonstrate the successful reconstruction of gold fiducial markers with a spatial resolution of about 350 μm. XACT reveals a new imaging mechanism and provides uncharted opportunities for structural determination with X-ray. PMID:27189746

  5. X-ray induced photoconductivity in Vanadium Dioxide samples

    NASA Astrophysics Data System (ADS)

    Dietze, Sebastian; Mohanty, Jyoti; Marsh, Moses; Kim, Jong Woo; West, Kevin; Schuller, Ivan K.; Shpyrko, Oleg G.

    2011-03-01

    Vanadium Dioxide (VO2) goes through a first-order phase transition at approximately 340K, exhibiting both an insulator to metal transition (IMT) and a structural phase transition (SPT), with a monoclinic (M1) insulating phase at low temperatures and a rutile (R) metallic phase at high temperatures. We show an anomalous behavior of x-ray induced persistent photoconductivity (PPC) well below the temperature induced phase transition in VO2 devices. We present conductivity and X-ray Diffraction (XRD) measurements, revealing a large enhancement of conductivity due to photo-induced carriers. Moreover, with the addition of nominal electric fields, we are able to fully transition into the rutile metallic phase at room temperature. This effect is completely reversible, allowing the monoclinic insulating phase to be recovered via annealing.

  6. High Resolution X-ray-Induced Acoustic Tomography.

    PubMed

    Xiang, Liangzhong; Tang, Shanshan; Ahmad, Moiz; Xing, Lei

    2016-05-18

    Absorption based CT imaging has been an invaluable tool in medical diagnosis, biology, and materials science. However, CT requires a large set of projection data and high radiation dose to achieve superior image quality. In this letter, we report a new imaging modality, X-ray Induced Acoustic Tomography (XACT), which takes advantages of high sensitivity to X-ray absorption and high ultrasonic resolution in a single modality. A single projection X-ray exposure is sufficient to generate acoustic signals in 3D space because the X-ray generated acoustic waves are of a spherical nature and propagate in all directions from their point of generation. We demonstrate the successful reconstruction of gold fiducial markers with a spatial resolution of about 350 μm. XACT reveals a new imaging mechanism and provides uncharted opportunities for structural determination with X-ray.

  7. High Resolution X-ray-Induced Acoustic Tomography

    NASA Astrophysics Data System (ADS)

    Xiang, Liangzhong; Tang, Shanshan; Ahmad, Moiz; Xing, Lei

    2016-05-01

    Absorption based CT imaging has been an invaluable tool in medical diagnosis, biology, and materials science. However, CT requires a large set of projection data and high radiation dose to achieve superior image quality. In this letter, we report a new imaging modality, X-ray Induced Acoustic Tomography (XACT), which takes advantages of high sensitivity to X-ray absorption and high ultrasonic resolution in a single modality. A single projection X-ray exposure is sufficient to generate acoustic signals in 3D space because the X-ray generated acoustic waves are of a spherical nature and propagate in all directions from their point of generation. We demonstrate the successful reconstruction of gold fiducial markers with a spatial resolution of about 350 μm. XACT reveals a new imaging mechanism and provides uncharted opportunities for structural determination with X-ray.

  8. Studies in useful hard x-ray induced chemistry

    NASA Astrophysics Data System (ADS)

    Pravica, Michael; Bai, Ligang; Sneed, Daniel; Park, Changyong

    2013-06-01

    The observed rapid decomposition of potassium chlorate (via 2KClO3 + h ν --> 2KCl +3O2) via synchrotron hard x-ray irradiation (>10 keV) has enabled experiments that are developing novel and useful hard x-ray chemistry. We have observed a number of radiation-induced in situ decomposition reactions in various substances which release O2, H2, N2, NH3, and H2O in a diamond anvil cell (DAC) at ambient and high pressures. These novel acatalytic and isothermal reactions represent a highly controllable, penetrating, and focused method to initiate chemistry (including x-ray induced combustion) in sealed and/or isolated chambers which maintain matter under extreme conditions. During our studies, we have typically observed a slowing of decomposition with pressure including phase dependent decomposition of KClO3. Energy dependent studies have observed an apparent resonance near 15 keV at which the decomposition rate is maximized. This may enable use of much lower flux and portable x-ray sources (e.g. x-ray tubes) in larger scale experiments. These developments support novel means to load DACs and control chemical reactions providing novel routes of synthesis of novel materials under extreme conditions.

  9. X-ray-induced changes in growth of Mozambique tilapia

    SciTech Connect

    Jana, B.B.; Basu, M.

    1995-01-01

    Early fry (30 d postfertilization) and 7-8-week-old Mozambique tilapias (Tilapia mossambica) were exposed to X rays in dosages of 50, 100, 200, 300, 400 or 500 roentgens and reared in outdoor culture tanks between May 1981 and October 1988. Fish of either sex that were irradiated as fry grew faster than controls at all test X-ray doses. Among fish irradiated at 7-8 weeks, males grew significantly faster, but females grew significantly slower, than controls at all test doses. X-ray-induced changes in growth were dose-dependent: growth rates of fry (both sexes) and of juvenile males rose relative to those of controls with increased radiation dose. The growth increase per unit of radiation dose was higher for fry than for older juveniles. The length-weight regression was steeper for irradiated males than for controls. The average weights of F{sub 1} offspring of irradiated fish were greatly reduced as compared with controls, which suggests the transfer of the detrimental effects of X rays from irradiated parents to their offspring. 39 refs., 3 figs., 3 tabs.

  10. X-ray-induced cell death: Apoptosis and necrosis

    SciTech Connect

    Nakano, Hisako; Shinohara, Kunio

    1994-10-01

    X-ray-induced cell death in MOLT-4N1, a subclone of MOLT-4 cells, and M10 cells was studied with respect to their modes of cell death, apoptosis and necrosis. MOLT-4N1 cells showed radiosensitivity similar to that of M10 cells, a radiosensitive mutant of L5178Y, as determined by the colony formation assay. Analysis of cell size demonstrated that MOLT-4N1 cells increased in size at an early stage after irradiation and then decreased to a size smaller than that of control cells, whereas the size of irradiated M10 cells increased continuously. Apoptosis detected by morphological changes and DNA ladder formation (the cleavage of DNA into oligonucleosomal fragments) occurred in X-irradiated MOLT-4N1 cells but not in M10 cells. Pulsed-field gel electrophoresis showed that the ladder formation involved an intermediate-sized DNA (about 20 kbp). Most of the DNA was detected at the origin in both methods of electrophoresis in the case of M10 cells, though a trace amount of ladder formation was observed. Heat treatment of M10 cells induced apoptosis within 30 min after treatment, in contrast to MOLT-4N1 cells. The results suggest that apoptosis and necrosis are induced by X rays in a manner which is dependent on the cell line irrespective of the capability of the cells to develop apoptosis. DNA fragmentation was the earliest change observed in the development of apoptosis. 27 refs., 8 figs., 1 tab.

  11. A room-temperature X-ray-induced photochromic material for X-ray detection.

    PubMed

    Wang, Ming-Sheng; Yang, Chen; Wang, Guan-E; Xu, Gang; Lv, Xiang-Ying; Xu, Zhong-Ning; Lin, Rong-Guang; Cai, Li-Zhen; Guo, Guo-Cong

    2012-04-02

    A color change: X-ray-induced photochromic species are rare and can be used for detection of X-rays. A highly robust X-ray-sensitive material with the discrete structure of a metal-organic complex has been found to show both soft and hard X-ray-induced photochromism at room temperature. A new ligand-to-ligand electron-transfer mechanism was proposed to elucidate this photochromic phenomenon.

  12. Bisdemethoxycurcumin enhances X-ray-induced apoptosis possibly through p53/Bcl-2 pathway.

    PubMed

    Enomoto, Atsushi; Yamada, Junko; Morita, Akinori; Miyagawa, Kiyoshi

    2017-03-01

    Bisdemethoxycurcumin (BDMC), which is isolated from the rhizomes of Curcuma longa, has anti-inflammatory and anti-carcinogenic activities. Here we found that BDMC enhanced X-ray-induced apoptosis in human T-cell leukemia MOLT-4 cells. Knockdown of p53 significantly attenuated the radiosensitizing effect of BDMC. However, BDMC did not enhance X-ray-mediated activation of the p53 signaling pathway via p53's transactivation or mitochondrial translocation. On the other hand, BDMC promoted the X-ray-induced dephosphorylation at Ser 70 in Bcl-2's flexible loop regulatory domain and Bcl-2 binding to p53. Overexpressing Bcl-2 completely blocked the BDMC's radiosensitization effect. Our results indicate that BDMC stimulates the dephosphorylation and p53-binding activity of Bcl-2 and suggest that BDMC may induce a neutralization of Bcl-2's anti-apoptotic function, thereby enhancing X-ray-induced apoptosis.

  13. DNA sequence analysis of X-ray induced Adh null mutations in Drosophila melanogaster

    SciTech Connect

    Mahmoud, J.; Fossett, N.G.; Arbour-Reily, P.; McDaniel, M.; Tucker, A.; Chang, S.H.; Lee, W.R. )

    1991-01-01

    The mutational spectrum for 28 X-ray induced mutations and 2 spontaneous mutations, previously determined by genetic and cytogenetic methods, consisted of 20 multilocus deficiencies (19 induced and 1 spontaneous) and 10 intragenic mutations (9 induced and 1 spontaneous). One of the X-ray induced intragenic mutations was lost, and another was determined to be a recombinant with the allele used in the recovery scheme. The DNA sequence of two X-ray induced intragenic mutations has been published. This paper reports the results of DNA sequence analysis of the remaining intragenic mutations and a summary of the X-ray induced mutational spectrum. The combination of DNA sequence analysis with genetic complementation analysis shows a continuous distribution in size of deletions rather than two different types of mutations consisting of deletions and point mutations'. Sequencing is shown to be essential for detecting intragenic deletions. Of particular importance for future studies is the observation that all of the intragenic deletions consist of a direct repeat adjacent to the breakpoint with one of the repeats deleted.

  14. Surface studies of solids using integral x-ray-induced photoemission yield

    DOE PAGES

    Stoupin, Stanislav; Zhernenkov, Mikhail; Shi, Bing

    2016-11-22

    X-ray induced photoemission yield contains structural information complementary to that provided by X-ray Fresnel reflectivity, which presents an advantage to a wide variety of surface studies if this information is made easily accessible. Photoemission in materials research is commonly acknowledged as a method with a probing depth limited by the escape depth of the photoelectrons. Here we show that the integral hard-X-ray-induced photoemission yield is modulated by the Fresnel reflectivity of a multilayer structure and carries structural information that extends well beyond the photoelectron escape depth. A simple electric self-detection of the integral photoemission yield and Fourier data analysis permitmore » extraction of thicknesses of individual layers. The approach does not require detection of the reflected radiation and can be considered as a framework for non-invasive evaluation of buried layers with hard X-rays under grazing incidence.« less

  15. Surface studies of solids using integral x-ray-induced photoemission yield

    SciTech Connect

    Stoupin, Stanislav; Zhernenkov, Mikhail; Shi, Bing

    2016-11-22

    X-ray induced photoemission yield contains structural information complementary to that provided by X-ray Fresnel reflectivity, which presents an advantage to a wide variety of surface studies if this information is made easily accessible. Photoemission in materials research is commonly acknowledged as a method with a probing depth limited by the escape depth of the photoelectrons. Here we show that the integral hard-X-ray-induced photoemission yield is modulated by the Fresnel reflectivity of a multilayer structure and carries structural information that extends well beyond the photoelectron escape depth. A simple electric self-detection of the integral photoemission yield and Fourier data analysis permit extraction of thicknesses of individual layers. The approach does not require detection of the reflected radiation and can be considered as a framework for non-invasive evaluation of buried layers with hard X-rays under grazing incidence.

  16. Surface studies of solids using integral X-ray-induced photoemission yield

    PubMed Central

    Stoupin, Stanislav; Zhernenkov, Mikhail; Shi, Bing

    2016-01-01

    X-ray induced photoemission yield contains structural information complementary to that provided by X-ray Fresnel reflectivity, which presents an advantage to a wide variety of surface studies if this information is made easily accessible. Photoemission in materials research is commonly acknowledged as a method with a probing depth limited by the escape depth of the photoelectrons. Here we show that the integral hard-X-ray-induced photoemission yield is modulated by the Fresnel reflectivity of a multilayer structure and carries structural information that extends well beyond the photoelectron escape depth. A simple electric self-detection of the integral photoemission yield and Fourier data analysis permit extraction of thicknesses of individual layers. The approach does not require detection of the reflected radiation and can be considered as a framework for non-invasive evaluation of buried layers with hard X-rays under grazing incidence. PMID:27874041

  17. Pump–probe spectrometer for measuring x-ray induced strain

    DOE PAGES

    Loether, A.; Adams, B. W.; DiCharia, A.; ...

    2016-04-20

    A hard x-ray pump–probe spectrometer using a multi-crystal Bragg reflector is demonstrated at a third generation synchrotron source. This device derives both broadband pump and monochromatic probe pulses directly from a single intense, broadband x-ray pulse centered at 8.767 keV. In conclusion, we present a proof-of-concept experiment which directly measures x-ray induced crystalline lattice strain.

  18. Ultraintense X-Ray Induced Ionization, Dissociation, and Frustrated Absorption in Molecular Nitrogen

    SciTech Connect

    Hoener, M.; Fang, L.; Murphy, B.; Berrah, N.; Kornilov, O.; Gessner, O.; Pratt, S. T.; Kanter, E. P.; Guehr, M.; Bucksbaum, P. H.; Cryan, J.; Glownia, M.; McFarland, B.; Petrovic, V.; Blaga, C.; DiMauro, L.; Bostedt, C.; Bozek, J. D.; Coffee, R.; Messerschmidt, M.

    2010-06-25

    Sequential multiple photoionization of the prototypical molecule N{sub 2} is studied with femtosecond time resolution using the Linac Coherent Light Source (LCLS). A detailed picture of intense x-ray induced ionization and dissociation dynamics is revealed, including a molecular mechanism of frustrated absorption that suppresses the formation of high charge states at short pulse durations. The inverse scaling of the average target charge state with x-ray peak brightness has possible implications for single-pulse imaging applications.

  19. Ultraintense x-ray induced ionization, dissociation and frustrated absorption in molecular nitrogen.

    SciTech Connect

    Hoener, M.; Fang, L.; Kornilov, O.; Gessner, O.; Pratt, S. T.; Guhr, M.; Kanter, E. P.; Blaga, C.; Bostedt, C.; Bozek, J. D.; Bucksbaum, P. H.; Buth, C.; Chen, M.; Coffee, R.; Cryan, J.; DiMauro, L.; Glownia, M.; Hosler, E.; Kukk, E.; Leone, S. R.; McFarland, B.; Messerschmidt, M.; Murphy, B.; Petrovic, V.; Rolles, D.; Berrah, N.; Chemical Sciences and Engineering Division; Western Michigan Univ.; LBNL; Ohio State Univ.; Louisiana State Univ.; LLNL; Univ. of Turku; Univ. of California at Berkeley; Max Planck Advanced Study Group, CFEL; LCLS

    2010-06-23

    Sequential multiple photoionization of the prototypical molecule N2 is studied with femtosecond time resolution using the Linac Coherent Light Source (LCLS). A detailed picture of intense x-ray induced ionization and dissociation dynamics is revealed, including a molecular mechanism of frustrated absorption that suppresses the formation of high charge states at short pulse durations. The inverse scaling of the average target charge state with x-ray peak brightness has possible implications for single-pulse imaging applications.

  20. Measurement of the energy dependence of X-ray-induced decomposition of potassium chlorate.

    PubMed

    Pravica, Michael; Bai, Ligang; Sneed, Daniel; Park, Changyong

    2013-03-21

    We report the first measurements of the X-ray induced decomposition of KClO3 as a function of energy in two experiments. KClO3 was pressurized to 3.5 GPa and irradiated with monochromatic synchrotron X-rays ranging in energy from 15 to 35 keV in 5 keV increments. A systematic increase in the decomposition rate as the energy was decreased was observed, which agrees with the 1/E(3) trend for the photoelectric process, except at the lowest energy studied. A second experiment was performed to access lower energies (10 and 12 keV) using a beryllium gasket; suggesting an apparent resonance near 15 keV or 0.83 Ǻ maximizing the chemical decomposition rate. A third experiment was performed using KIO3 to ascertain the anionic dependence of the decomposition rate, which was observed to be far slower than in KClO3, suggesting that the O-O distance is the critical factor in chemical reactions. These results will be important for more efficiently initiating chemical decomposition in materials using selected X-ray wavelengths that maximize decomposition to aid useful hard X-ray-induced chemistry and contribute understanding of the mechanism of X-ray-induced decomposition of the chlorates.

  1. Principles of femtosecond X-ray/optical cross-correlation with X-ray induced transient optical reflectivity in solids

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Beye, M.; Pietzsch, A.; Quevedo, W.; Hantschmann, M.; Ochmann, M.; Ross, M.; Minitti, M. P.; Turner, J. J.; Moeller, S. P.; Schlotter, W. F.; Dakovski, G. L.; Khalil, M.; Huse, N.; Föhlisch, A.

    2015-02-01

    The discovery of ultrafast X-ray induced optical reflectivity changes enabled the development of X-ray/optical cross correlation techniques at X-ray free electron lasers worldwide. We have now linked through experiment and theory the fundamental excitation and relaxation steps with the transient optical properties in finite solid samples. Therefore, we gain a thorough interpretation and an optimized detection scheme of X-ray induced changes to the refractive index and the X-ray/optical cross correlation response.

  2. Principles of femtosecond X-ray/optical cross-correlation with X-ray induced transient optical reflectivity in solids

    SciTech Connect

    Eckert, S. E-mail: martin.beye@helmholtz-berlin.de; Beye, M. E-mail: martin.beye@helmholtz-berlin.de; Pietzsch, A.; Quevedo, W.; Hantschmann, M.; Ochmann, M.; Huse, N.; Ross, M.; Khalil, M.; Minitti, M. P.; Turner, J. J.; Moeller, S. P.; Schlotter, W. F.; Dakovski, G. L.; Föhlisch, A.

    2015-02-09

    The discovery of ultrafast X-ray induced optical reflectivity changes enabled the development of X-ray/optical cross correlation techniques at X-ray free electron lasers worldwide. We have now linked through experiment and theory the fundamental excitation and relaxation steps with the transient optical properties in finite solid samples. Therefore, we gain a thorough interpretation and an optimized detection scheme of X-ray induced changes to the refractive index and the X-ray/optical cross correlation response.

  3. X-ray Methods in High-Intensity Discharges and Metal-Halide Lamps: X-ray Induced Fluorescence

    SciTech Connect

    Curry, John J.; Lapatovich, Walter P.; Henins, Albert

    2011-12-09

    We describe the use of x-ray induced fluorescence to study metal-halide high-intensity discharge lamps and to measure equilibrium vapor pressures of metal-halide salts. The physical principles of metal-halide lamps, relevant aspects of x-ray-atom interactions, the experimental method using synchrotron radiation, and x-ray induced fluorescence measurements relevant to metal-halide lamps are covered.

  4. Roles of oxidative stress in synchrotron radiation X-ray-induced testicular damage of rodents

    PubMed Central

    Ma, Yingxin; Nie, Hui; Sheng, Caibin; Chen, Heyu; Wang, Ban; Liu, Tengyuan; Shao, Jiaxiang; He, Xin; Zhang, Tingting; Zheng, Chaobo; Xia, Weiliang; Ying, Weihai

    2012-01-01

    Synchrotron radiation (SR) X-ray has characteristic properties such as coherence and high photon flux, which has excellent potential for its applications in medical imaging and cancer treatment. However, there is little information regarding the mechanisms underlying the damaging effects of SR X-ray on biological tissues. Oxidative stress plays an important role in the tissue damage induced by conventional X-ray, while the role of oxidative stress in the tissue injury induced by SR X-ray remains unknown. In this study we used the male gonads of rats as a model to study the roles of oxidative stress in SR X-ray-induced tissue damage. Exposures of the testes to SR X-ray at various radiation doses did not significantly increase the lipid peroxidation of the tissues, assessed at one day after the irradiation. No significant decreases in the levels of GSH or total antioxidation capacity were found in the SR X-ray-irradiated testes. However, the SR X-ray at 40 Gy induced a marked increase in phosphorylated H2AX – a marker of double-strand DNA damage, which was significantly decreased by the antioxidant N-acetyl cysteine (NAC). NAC also attenuated the SR X-ray-induced decreases in the cell layer number of seminiferous tubules. Collectively, our observations have provided the first characterization of SR X-ray-induced oxidative damage of biological tissues: SR X-ray at high doses can induce DNA damage and certain tissue damage during the acute phase of the irradiation, at least partially by generating oxidative stress. However, SR X-ray of various radiation doses did not increase lipid peroxidation. PMID:22837810

  5. Note: A novel method for in situ loading of gases via x-ray induced chemistry

    SciTech Connect

    Pravica, Michael; Bai, Ligang; Park, Changyong; Liu, Yu; Galley, Martin; Robinson, John; Bhattacharya, Neelanjan

    2011-12-14

    We have developed and demonstrated a novel method to load oxygen in a sealed diamond anvil cell via the x-ray induced decomposition of potassium chlorate. By irradiating a pressurized sample of an oxidizer (KClO{sub 3}) with either monochromatic or white beam x-rays from the Advanced Photon Source at ambient temperature and variable pressure, we succeeded in creating a localized region of molecular oxygen surrounded by unreacted sample which was confirmed via Raman spectroscopy. We anticipate that this technique will be useful in loading even more challenging, difficult-to-load gases such as hydrogen and also to load multiple gases.

  6. Note: A novel method for in situ loading of gases via x-ray induced chemistry

    NASA Astrophysics Data System (ADS)

    Pravica, Michael; Bai, Ligang; Park, Changyong; Liu, Yu; Galley, Martin; Robinson, John; Bhattacharya, Neelanjan

    2011-10-01

    We have developed and demonstrated a novel method to load oxygen in a sealed diamond anvil cell via the x-ray induced decomposition of potassium chlorate. By irradiating a pressurized sample of an oxidizer (KClO3) with either monochromatic or white beam x-rays from the Advanced Photon Source at ambient temperature and variable pressure, we succeeded in creating a localized region of molecular oxygen surrounded by unreacted sample which was confirmed via Raman spectroscopy. We anticipate that this technique will be useful in loading even more challenging, difficult-to-load gases such as hydrogen and also to load multiple gases.

  7. X-ray-induced shortwave infrared biomedical imaging using rare-earth nanoprobes.

    PubMed

    Naczynski, Dominik Jan; Sun, Conroy; Türkcan, Silvan; Jenkins, Cesare; Koh, Ai Leen; Ikeda, Debra; Pratx, Guillem; Xing, Lei

    2015-01-14

    Shortwave infrared (SWIR or NIR-II) light provides significant advantages for imaging biological structures due to reduced autofluorescence and photon scattering. Here, we report on the development of rare-earth nanoprobes that exhibit SWIR luminescence following X-ray irradiation. We demonstrate the ability of X-ray-induced SWIR luminescence (X-IR) to monitor biodistribution and map lymphatic drainage. Our results indicate X-IR imaging is a promising new modality for preclinical applications and has potential for dual-modality molecular disease imaging.

  8. X-ray-Induced Shortwave Infrared Biomedical Imaging Using Rare-Earth Nanoprobes

    PubMed Central

    2015-01-01

    Shortwave infrared (SWIR or NIR-II) light provides significant advantages for imaging biological structures due to reduced autofluorescence and photon scattering. Here, we report on the development of rare-earth nanoprobes that exhibit SWIR luminescence following X-ray irradiation. We demonstrate the ability of X-ray-induced SWIR luminescence (X-IR) to monitor biodistribution and map lymphatic drainage. Our results indicate X-IR imaging is a promising new modality for preclinical applications and has potential for dual-modality molecular disease imaging. PMID:25485705

  9. Influence of caffeine on X-ray-induced killing and mutation in V79 cells

    SciTech Connect

    Bhattacharjee, S.B.; Bhattacharyya, N.; Chatterjee, S.

    1987-02-01

    Effects produced by caffeine on X-irradiated Chinese hamster V79 cells depended on the growth conditions of the cells. For exponentially growing cells, nontoxic concentrations of caffeine decreased the shoulder width from the survival curve, but the slope remained unchanged. The yield of mutants under the same conditions also remained unaffected. In case of density-inhibited cells, delaying trypsinization for 24 h after X irradiation increased the survival and decreased the yield of mutants. The presence of caffeine during this incubation period inhibited such recovery and significantly increased the yield of X-ray-induced mutants.

  10. X-ray Induced Effects on Photocurrents in Amorphous Se Films

    NASA Astrophysics Data System (ADS)

    Shimakawa, Koichi; Fukami, Kenji; Kishi, Hiroki; Belev, George; Kasap, Safa

    2007-03-01

    Amorphous selenium (a-Se) is one of the X-ray photoconductors that is available for use in recently developed direct conversion flat panel X-ray image detectors for medical imaging. To obtain a better understanding of trapping and recombination effects in a-Se, we have studied light and X-ray induced photocurrents in a-Se films. The residual photocurrent, after X-ray exposure, decreases in sandwich cells whereas it increases in coplanar cells. These effects are recovered over a time scale of hours. We show that the results can be interpreted by using valence alternation pair (VAP) type charged defects.

  11. Differential effects of radical scavengers on X-ray-induced mutation and cytotoxicity in human cells

    SciTech Connect

    Corn, B.W.; Liber, H.L.; Little, J.B.

    1987-01-01

    The cytotoxic and mutagenic effects of X irradiation on a human lymphoblast cell line were examined in the presence of two radioprotective agents which modulate damage to DNA. The cells were treated with X rays alone or in the presence of either dimethyl sulfoxide or cysteamine. Surviving fraction and mutation to trifluorothymidine resistance (tk locus) and to 6-thioguanine resistance (hgprt locus) were measured. Survival was enhanced when the cells were irradiated in the presence of dimethyl sulfoxide; the D0 rose from 58 to 107 rad. However, at both genetic loci the induced mutant fractions were identical in the presence or absence of dimethyl sulfoxide. Survival was enhanced to a greater degree when the cells were irradiated in the presence of cysteamine; the D0 rose from 58 to 200 rad. Cysteamine also protected the cells from X-ray-induced mutation; the frequencies of X-ray-induced mutation at both the tk and hgprt loci were reduced by 50-75%. No protective effects were observed unless dimethyl sulfoxide or cysteamine was present during irradiation. These findings are discussed in terms of the hypothesis that, unlike for cell killing, radiation-induced mutagenesis in human lymphoblast cells is not mediated by the actions of aqueous free radicals, but rather by the direct effects of ionizing radiation.

  12. Characterization of X-ray-induced immunostaining of proliferating cell nuclear antigen in human diploid fibroblasts

    SciTech Connect

    Miura, Masahiko; Sasaki, Takehito; Takasaki, Yoshinari

    1996-01-01

    The repair of X-ray-induced DNA damage related to the proliferating cell nuclear antigen (PCNA) was characterized in human diploid fibroblasts by an indirect immunofluorescence method. PCNA staining induced by X rays was lost after DNase I treatment but not after RNase treatment. The staining was not induced when ATP was depleted or the temperature was lowered to 0{degrees}C during the X irradiation. When cells were incubated at 37{degrees}C after X irradiation, PCNA staining diminished gradually and was almost entirely absent 12-15 h later. On the other hand, PCNA staining persisted during aphidicolin treatment even 20 h after X irradiation. Induction of PCNA staining was not affected by the aphidicolin treatment. Cycloheximide treatment did not affect induction of the staining either, but did inhibit the disappearance of the staining. There was no difference in the staining pattern and time course of PCNA staining after X irradiation between normal and xeroderma pigmentosum group A (XP-A) cells. These results imply that PCNA-dependent, aphidicolin-sensitive DNA polymerases may be involved in repair of X-ray-induced DNA damage in vivo, but the repair initiation step could be different from that of nucleotide excision repair initiated by XP proteins. 39 refs., 6 figs.

  13. Dose-rate plays a significant role in synchrotron radiation X-ray-induced damage of rodent testes

    PubMed Central

    Chen, Heyu; Wang, Ban; Wang, Caixia; Cao, Wei; Zhang, Jie; Ma, Yingxin; Hong, Yunyi; Fu, Shen; Wu, Fan; Ying, Weihai

    2016-01-01

    Synchrotron radiation (SR) X-ray has significant potential for applications in medical imaging and cancer treatment. However, the mechanisms underlying SR X-ray-induced tissue damage remain unclear. Previous studies on regular X-ray-induced tissue damage have suggested that dose-rate could affect radiation damage. Because SR X-ray has exceedingly high dose-rate compared to regular X-ray, it remains to be determined if dose-rate may affect SR X-ray-induced tissue damage. We used rodent testes as a model to investigate the role of dose-rate in SR X-ray-induced tissue damage. One day after SR X-ray irradiation, we determined the effects of the irradiation of the same dosage at two different dose-rates, 0.11 Gy/s and 1.1 Gy/s, on TUNEL signals, caspase-3 activation and DNA double-strand breaks (DSBs) of the testes. Compared to those produced by the irradiation at 0.11 Gy/s, irradiation at 1.1 Gy/s produced higher levels of DSBs, TUNEL signals, and caspase-3 activation in the testes. Our study has provided the first evidence suggesting that dose-rate could be a significant factor in SR X-ray-induced tissue damage, which may establish a valuable base for utilizing this factor to manipulate the tissue damage in SR X-ray-based medical applications. PMID:28078052

  14. Dose-rate plays a significant role in synchrotron radiation X-ray-induced damage of rodent testes.

    PubMed

    Chen, Heyu; Wang, Ban; Wang, Caixia; Cao, Wei; Zhang, Jie; Ma, Yingxin; Hong, Yunyi; Fu, Shen; Wu, Fan; Ying, Weihai

    2016-01-01

    Synchrotron radiation (SR) X-ray has significant potential for applications in medical imaging and cancer treatment. However, the mechanisms underlying SR X-ray-induced tissue damage remain unclear. Previous studies on regular X-ray-induced tissue damage have suggested that dose-rate could affect radiation damage. Because SR X-ray has exceedingly high dose-rate compared to regular X-ray, it remains to be determined if dose-rate may affect SR X-ray-induced tissue damage. We used rodent testes as a model to investigate the role of dose-rate in SR X-ray-induced tissue damage. One day after SR X-ray irradiation, we determined the effects of the irradiation of the same dosage at two different dose-rates, 0.11 Gy/s and 1.1 Gy/s, on TUNEL signals, caspase-3 activation and DNA double-strand breaks (DSBs) of the testes. Compared to those produced by the irradiation at 0.11 Gy/s, irradiation at 1.1 Gy/s produced higher levels of DSBs, TUNEL signals, and caspase-3 activation in the testes. Our study has provided the first evidence suggesting that dose-rate could be a significant factor in SR X-ray-induced tissue damage, which may establish a valuable base for utilizing this factor to manipulate the tissue damage in SR X-ray-based medical applications.

  15. X-ray-induced lysis of the Fe-CO bond in carbonmonoxy-myoglobin.

    PubMed

    Della Longa, Stefano; Arcovito, Alessandro

    2010-11-01

    By using X-ray absorption near edge structure (XANES) spectroscopy, we show that under prolonged exposure to Synchrotron X-rays, at T < 10 K, the Fe-heme in carbonmonoxy-myoglobin (MbCO) undergoes a slow two-state transition process. The final spectrum is nearly identical to that of the classical photoproduct (Mb*CO) obtained by UV-visible light illumination at 15 K. By increasing the temperature, the starting spectrum of MbCO is recovered at T > 100 K, demonstrating that the process is reversible and no damage occurred at the heme site in the time course of the experiment. Thus, the overall X-ray-induced process at low temperature is identical to the well-known (light-induced) photolysis of CO-hemeproteins.

  16. Note: Loading method of molecular fluorine using x-ray induced chemistry

    SciTech Connect

    Pravica, Michael Sneed, Daniel; White, Melanie; Wang, Yonggang

    2014-08-15

    We have successfully loaded molecular fluorine into a diamond anvil cell at high pressure using the synchrotron x-ray induced decomposition of perfluorohexane (C{sub 6}F{sub 14}). “White” x-ray radiation from the Advanced Photon Source was used to initiate the chemical decomposition of C{sub 6}F{sub 14}, which resulted in the in situ production of F{sub 2} as verified via Raman spectroscopy. Due to the toxic nature of fluorine, this method will offer significant advantages in the ability to easily load a relatively nontoxic and inert substance into a chamber (such as a diamond anvil cell) that, when sealed with other reactants and irradiate with hard x-rays (>7 keV), releases highly reactive and toxic fluorine into the sample/reaction chamber to enable novel chemical synthesis under isolated and/or extreme conditions.

  17. Time-resolved x-ray spectroscopy for x-ray-induced phenomena

    NASA Astrophysics Data System (ADS)

    Picón, Antonio

    2017-05-01

    X-ray-pump/x-ray-probe spectroscopy allows investigation of ultrafast x-ray induced molecular dynamics. X-ray absorption and Auger decay leave molecules in manifolds of transient intermediate states in the femtosecond time scale. By using an x-ray probe pulse, we can image nuclear wavepackets as a function of time using ion-ion coincidence spectroscopy to record ion momentum distributions and kinetic energy releases (KERs). Numerical simulations, a timedependent approach that includes both K-shell photoionization and Auger decay, show how the transient intermediate states are projected onto the KERs. At short time delays, the measurements are sensitive to interatomic interactions, whereas at longer delays the contribution from separated ions due to dissociative intermediate states becomes observable. We present simulations for the nitrogen molecule. These simulations have the potential to be extended to more complex molecules.

  18. Note: Loading method of molecular fluorine using x-ray induced chemistry

    NASA Astrophysics Data System (ADS)

    Pravica, Michael; Sneed, Daniel; White, Melanie; Wang, Yonggang

    2014-08-01

    We have successfully loaded molecular fluorine into a diamond anvil cell at high pressure using the synchrotron x-ray induced decomposition of perfluorohexane (C6F14). "White" x-ray radiation from the Advanced Photon Source was used to initiate the chemical decomposition of C6F14, which resulted in the in situ production of F2 as verified via Raman spectroscopy. Due to the toxic nature of fluorine, this method will offer significant advantages in the ability to easily load a relatively nontoxic and inert substance into a chamber (such as a diamond anvil cell) that, when sealed with other reactants and irradiate with hard x-rays (>7 keV), releases highly reactive and toxic fluorine into the sample/reaction chamber to enable novel chemical synthesis under isolated and/or extreme conditions.

  19. Note: Loading method of molecular fluorine using x-ray induced chemistry.

    PubMed

    Pravica, Michael; Sneed, Daniel; White, Melanie; Wang, Yonggang

    2014-08-01

    We have successfully loaded molecular fluorine into a diamond anvil cell at high pressure using the synchrotron x-ray induced decomposition of perfluorohexane (C6F14). "White" x-ray radiation from the Advanced Photon Source was used to initiate the chemical decomposition of C6F14, which resulted in the in situ production of F2 as verified via Raman spectroscopy. Due to the toxic nature of fluorine, this method will offer significant advantages in the ability to easily load a relatively nontoxic and inert substance into a chamber (such as a diamond anvil cell) that, when sealed with other reactants and irradiate with hard x-rays (>7 keV), releases highly reactive and toxic fluorine into the sample/reaction chamber to enable novel chemical synthesis under isolated and/or extreme conditions.

  20. Effect of caffeine on the expression of a major X-ray induced protein in human tumor cells

    SciTech Connect

    Hughes, E.N.; Boothman, D.A. )

    1991-03-01

    We have examined the effect of caffeine on the concomitant processes of the repair of potentially lethal damage (PLD) and the synthesis of X-ray-induced proteins in the human malignant melanoma cell line, Ul-Mel. Caffeine administered at a dose of 5mM after X radiation not only inhibited PLD repair but also markedly reduced the level of XIP269, a major X-ray-induced protein whose expression has been shown to correlate with the capacity to repair PLD. The expression of the vast majority of other cellular proteins, including seven other X-ray-induced proteins, remained unchanged following caffeine treatment. A possible role for XIP269 in cell cycle delay following DNA damage by X irradiation is discussed.

  1. Isochronal annealing study of X-ray induced defects in single- and double-walled carbon nanotubes

    SciTech Connect

    Murakami, Toshiya; Yamamoto, Yuki; Itoh, Chihiro; Kisoda, Kenji

    2013-09-21

    X-ray induced defects in single-walled (SWCNTs) and double-walled carbon nanotubes (DWCNTs) were characterized by Raman scattering spectroscopy. Frenkel defects, interstitial-vacancy pairs, were revealed to form in both SWCNTs and DWCNTs after X-ray irradiation because these defects were entirely healed by thermal annealing. In order to clarify the structure of the X-ray induced defect in SWCNT and DWCNT, isochronal-annealing experiments were performed on the irradiated samples and the activation energy for defect healing was estimated. The intensity of D band (defect induced band) on Raman spectra was used as a measure of the density of X-ray induced defects. The experimental results were in good agreement with the simulated values using second order reaction model, which indicated that the defect healing was determined by the migration energy of interstitials on the carbon layer. We also found that the activation energy for defect healing of SWCNT and DWCNT were around 0.5 eV and 0.32 eV, respectively. The X-ray induced defects in SWCNTs were more stable than those in DWCNTs. Compared these estimated activation energies to previous theoretical reports, we concluded that bridge and/or dumbbell interstitials are formed in both SWCNT and DWCNT by X-ray irradiation.

  2. NAD+ administration significantly attenuates synchrotron radiation X-ray-induced DNA damage and structural alterations of rodent testes

    PubMed Central

    Sheng, Caibin; Chen, Heyu; Wang, Ban; Liu, Tengyuan; Hong, Yunyi; Shao, Jiaxiang; He, Xin; Ma, Yingxin; Nie, Hui; Liu, Na; Xia, Weiliang; Ying, Weihai

    2012-01-01

    Synchrotron radiation (SR) X-ray has great potential for its applications in medical imaging and cancer treatment. In order to apply SR X-ray in clinical settings, it is necessary to elucidate the mechanisms underlying the damaging effects of SR X-ray on normal tissues, and to search for the strategies to reduce the detrimental effects of SR X-ray on normal tissues. However, so far there has been little information on these topics. In this study we used the testes of rats as a model to characterize SR X-ray-induced tissue damage, and to test our hypothesis that NAD+ administration can prevent SR X-ray-induced injury of the testes. We first determined the effects of SR X-ray at the doses of 0, 0.5, 1.3, 4 and 40 Gy on the biochemical and structural properties of the testes one day after SR X-ray exposures. We found that 40 Gy of SR X-ray induced a massive increase in double-strand DNA damage, as assessed by both immunostaining and Western blot of phosphorylated H2AX levels, which was significantly decreased by intraperitoneally (i.p.) administered NAD+ at doses of 125 and 625 mg/kg. Forty Gy of SR X-ray can also induce marked increases in abnormal cell nuclei as well as significant decreases in the cell layers of the seminiferous tubules one day after SR X-ray exposures, which were also ameliorated by the NAD+ administration. In summary, our study has shown that SR X-ray can produce both molecular and structural alterations of the testes, which can be significantly attenuated by NAD+ administration. These results have provided not only the first evidence that SR X-ray-induced tissue damage can be ameliorated by certain approaches, but also a valuable basis for elucidating the mechanisms underlying SR X-ray-induced tissue injury. PMID:22518270

  3. X-Ray Induced Photodynamic Therapy: A Combination of Radiotherapy and Photodynamic Therapy

    PubMed Central

    Wang, Geoffrey D.; Nguyen, Ha T.; Chen, Hongmin; Cox, Phillip B.; Wang, Lianchun; Nagata, Koichi; Hao, Zhonglin; Wang, Andrew; Li, Zibo; Xie, Jin

    2016-01-01

    Conventional photodynamic therapy (PDT)'s clinical application is limited by depth of penetration by light. To address the issue, we have recently developed X-ray induced photodynamic therapy (X-PDT) which utilizes X-ray as an energy source to activate a PDT process. In addition to breaking the shallow tissue penetration dogma, our studies found more efficient tumor cell killing with X-PDT than with radiotherapy (RT) alone. The mechanisms behind the cytotoxicity, however, have not been elucidated. In the present study, we investigate the mechanisms of action of X-PDT on cancer cells. Our results demonstrate that X-PDT is more than just a PDT derivative but is essentially a PDT and RT combination. The two modalities target different cellular components (cell membrane and DNA, respectively), leading to enhanced therapy effects. As a result, X-PDT not only reduces short-term viability of cancer cells but also their clonogenecity in the long-run. From this perspective, X-PDT can also be viewed as a unique radiosensitizing method, and as such it affords clear advantages over RT in tumor therapy, especially for radioresistant cells. This is demonstrated not only in vitro but also in vivo with H1299 tumors that were either subcutaneously inoculated or implanted into the lung of mice. These findings and advances are of great importance to the developments of X-PDT as a novel treatment modality against cancer. PMID:27877235

  4. Protective role of Aloe vera against X-ray induced testicular dysfunction.

    PubMed

    Bala, S; Chugh, N A; Bansal, S C; Garg, M L; Koul, A

    2017-09-01

    The present investigation was carried out to evaluate the possible radioprotective potential of an Aloe vera extract against whole-body X-ray irradiation-induced testicular alterations in mice. Male balb/c mice were divided into four groups: control, A. vera, X-ray and A. vera pre-treated + X-ray irradiated. Histopathological examination revealed significant structural alterations in testes after X-ray exposure, which was also associated with the presence of apoptotic cells as assessed by TUNEL assay. X-ray irradiation resulted in elevation in the levels of reactive oxygen species, lipid peroxidation, a reduction in glutathione concentration and enhanced activities of antioxidant enzymes such as glutathione reductase, glutathione peroxidase, catalase, superoxide dismutase and glutathione-S-transferase. Sperm count/motility and testosterone levels were significantly decreased in the irradiated group. Irradiated animals pre-treated with A. vera extract revealed an improvement in antioxidant status, inhibition of lipid peroxides, apoptotic cell formation and enhanced testicular parameters when compared to the X-ray-exposed group. These findings suggest that A. vera extract could ameliorate X-ray-induced damage due to its free radical scavenging properties and its potential to boost cellular antioxidant defence machinery. © 2016 Blackwell Verlag GmbH.

  5. Establishment of a Dose-response Curve for X-ray-Induced Micronuclei in Human Lymphocytes

    PubMed Central

    Lusiyanti, Yanti; Alatas, Zubaidah; Syaifudin, Mukh; Purnami, Sofiati

    2016-01-01

    The cytokinesis-block micronucleus assay in peripheral blood lymphocytes is an established technique for biodosimetry. The aim of this project was to generate a X-ray induced micronuclei (MN) curve for peripheral blood lymphocytes taken from five healthy donors. The blood samples were irradiated with X-rays of 122 KeV at a dose rate of 0.652 Gy/min to doses of 0.5, 1, 2, 3, and 4 Gy. The blood samples were then cultured for 72 h at 37°C and processed following the International Atomic Energy Agency standard procedure with slight modifications. The result showed that the yields of MN frequencies were increased with the increase of radiation dose. Reconstruction of the relationship of MN with dose was fitted to a linear-quadratic model using Chromosome Aberration Calculation Software version 2.0. Due to their advantages, mainly, the dependence on radiation dose and dose rate, despite their limitation, these curves will be useful as alternative method for in vitro dose reconstruction and can support the preparedness for public or occupational radiation overexposure and protection. The results reported here also give us confidence to apply the obtained calibration curve of MN for future biological dosimetry requirements in Indonesia. PMID:28217283

  6. Establishment of a Dose-response Curve for X-ray-Induced Micronuclei in Human Lymphocytes.

    PubMed

    Lusiyanti, Yanti; Alatas, Zubaidah; Syaifudin, Mukh; Purnami, Sofiati

    2016-01-01

    The cytokinesis-block micronucleus assay in peripheral blood lymphocytes is an established technique for biodosimetry. The aim of this project was to generate a X-ray induced micronuclei (MN) curve for peripheral blood lymphocytes taken from five healthy donors. The blood samples were irradiated with X-rays of 122 KeV at a dose rate of 0.652 Gy/min to doses of 0.5, 1, 2, 3, and 4 Gy. The blood samples were then cultured for 72 h at 37°C and processed following the International Atomic Energy Agency standard procedure with slight modifications. The result showed that the yields of MN frequencies were increased with the increase of radiation dose. Reconstruction of the relationship of MN with dose was fitted to a linear-quadratic model using Chromosome Aberration Calculation Software version 2.0. Due to their advantages, mainly, the dependence on radiation dose and dose rate, despite their limitation, these curves will be useful as alternative method for in vitro dose reconstruction and can support the preparedness for public or occupational radiation overexposure and protection. The results reported here also give us confidence to apply the obtained calibration curve of MN for future biological dosimetry requirements in Indonesia.

  7. X-ray-induced mutations in mouse embryonic stem cells

    PubMed Central

    Thomas, James W.; LaMantia, Christian; Magnuson, Terry

    1998-01-01

    Deletion complexes consisting of multiple chromosomal deletions induced at single loci can provide a means for functional analysis of regions spanning several centimorgans in model genetic systems. A strategy to identify and map deletions at any cloned locus in the mouse is described here. First, a highly polymorphic, germ-line competent F1(129/Sv-+Tyr+p × CAST/Ei) mouse embryonic stem cell line was established. Then, x-ray and UV-induced mutagenesis was performed to determine the feasibility of generating deletion complexes throughout the mouse genome. Reported here are the selection protocols, induced mutation frequencies, cytogenetic and extensive molecular analysis of mutations at the X-chromosome-linked hypoxanthine phosphoribosyltransferase (Hprt) locus and at the neural cell adhesion molecule (Ncam) locus located on chromosome 9. Mutation analysis with PCR-based polymorphic microsatellite markers revealed deletions of <3 cM at the Hprt locus, whereas results consistent with deletions covering >28 cM were observed at the Ncam locus. Fluorescence in situ hybridization with a chromosome 9 paint revealed that some of the Ncam deletions were accompanied by complex chromosome rearrangements. In addition, deletion mapping in combination with loss of heterozygosity of microsatellite markers revealed a putative haploinsufficient region distal to Ncam. These data indicate that it is feasible to generate x-ray-induced deletion complexes in mouse embryonic stem cells. PMID:9448294

  8. The role of metal ions in X-ray-induced photochemistry.

    PubMed

    Stumpf, V; Gokhberg, K; Cederbaum, L S

    2016-03-01

    Metal centres in biomolecules are recognized as being particularly sensitive to radiation damage by X-ray photons. This results in such molecules being both susceptible to an effective X-ray-induced loss of function and problematic to study using X-ray diffraction methods, with reliable structures of the metal centres difficult to obtain. Despite the abundance of experimental evidence, the mechanistic details of radiation damage at metal centres are unclear. Here, using ab initio calculations, we show that the absorption of X-rays by microsolvated Mg(2+) results in a complicated chain of ultrafast electronic relaxation steps that comprise both intra- and intermolecular processes and last for a few hundred femtoseconds. At the end of this cascade the metal reverts to its original charge state, the immediate environment becomes multiply ionized and large concentrations of radicals and slow electrons build up in the metal's vicinity. We conclude that such cascades involving metal ions are essential to our understanding of radiation chemistry and radiation damage in biological environments.

  9. Protective effect of ethanol on X-ray-induced mitotic recombination in drosophilia melanogaster

    SciTech Connect

    Palermo, A.M.; Rey, M.; Munoz, E.R.

    1994-12-31

    The effect of ethanol treatment on X-ray-induced mitotic recombination in D. melanogaster females was investigated by means of the white/white{sup +} w/w{sup +} spot test. White females inseminated by yellow males were allowed to oviposit for 8 hr on medium containing 5%, 7.5% and 10% (v/v) ethanol and submitted to 10 Gy of X-rays 52 hr after the beginning of the egg laying period (chronic treatments). For acute treatments 56 {+-}4-hr-old larvae grown in regular medium were held in petri dishes containing filter paper soaked with 50% (v/v) ethanol for 30 min before being irradiated with 10 Gy. The emerging heterozygous w/w{sup +} females were inspected for the presence of white spots (LS) in their eyes. Acute ethanol pretreatments lead to a significant reduction in the frequency of LS. This is suggested to be due to the scavenging by ethanol of free radicals originating during irradiation. If so, the contribution of the indirect action of radiation to mitotic recombination induced by X-rays must be significant. Chronic ethanol pretreatments also resulted in a decrease of LS, though impairment of larval development by ethanol may have partly contributed to the effect observed. At the concentrations tested, ethanol by itself did not modify the frequency of LS observed in the control. 29 refs., 4 tabs.

  10. Role of x-ray-induced transcripts in adaptive responses following x-rays

    SciTech Connect

    Boothman, D.A.

    1992-01-01

    Potentially lethal damage repair (PLDR) and sublethal damage repair, may be the same manifestations of a series of common enzymatic steps. PLDR, has two distinct phases based upon DNA lesion repair and survival recovery studies. The first phase of PLDR occurs very quickly (t{sub {1/2}}:2--20 mins) to increase the survival of X-irradiated cells by mending the vast array of DNA lesions created by ionizing radiation. The second slower phase of PLDR proceeds much later (i.e., >1--2 hrs) following X-irradiation, during which the remaining double-stranded DNA breaks are completely repaired. This second phase of repair closely corresponds to the restructuring of gross chromosomal damage, and can be partially blocked in some human cells by inhibiting protein synthesis. This slower phase of PLDR correlated with a rapid decline in X-ray-induced transformation of normal cells. The fast component of PLDR may be due to constitutively synthesized DNA ligases, topoisomerases, or polymerases, which act immediately to repair damaged, DNA. In contrast, the slow phase of PLDR in human cells may require the induction of specific genes and gene product's involved in the repair of potentially lethal or carcinogenic DNA lesions. Induced gene products (i.e., proteins) specifically synthesized in response to physiological doses of ionizing radiation in radioresistant human melanoma (U1-Mel) cells, and in a variety of other human normal and cancer-prone cells, were identified using two-dimensional gel electrophoresis. We identified and partially characterized ten proteins synthesized by U1-Mel cells. The synthesis of eight of these proteins were specifically induced by ionizing radiation and two proteins were repressed Neither heat shock, UV-irradiation, nor bifunctional alkylating agent treatments resulted in the induction of these proteins. The expression of one protein, XIP269, correlated very well with PLDR capacity.

  11. Genetics of x-ray induced double strand break repair in saccharomyces cerevisiae

    SciTech Connect

    Budd, M.E.

    1982-07-01

    The possible fates of x-ray-induced double-strand breaks in Saccharomyces cerevisiae were examined. One possible pathway which breaks can follow, the repair pathway, was studied by assaying strains with mutations in the RAD51, RAD54, and RAD57 loci for double-strand break repair. In order of increasing radiation sensitivity one finds: rad57-1(23/sup 0/)> rad51-1(30/sup 0/)> rad54-3(36/sup 0/). At 36/sup 0/, rad54-3 cells cannot repair double-strand breaks, while 23/sup 0/, they can. Strains with the rad57-1 mutation can rejoin broken chromosomes at both temperatures. However, the low survival at 36/sup 0/ shows that the assay is not distinguishing large DNA fragments which allow cell survival from those which cause cell death. A rad51-1 strain could also rejoin broken chromosomes, and was thus capable of incomplete repair. The data can be explained with the hypothesis that rad54-3 cells are blocked in an early step of repair, while rad51-1 and rad57-1 strains are blocked in a later step of repair. The fate of double-strand breaks when they are left unrepaired was investigated with the rad54-3 mutation. If breaks are prevented from entering the RAD54 repair pathway they become uncommitted lesions. These lesions are repaired slower than the original breaks. One possible fate for an uncommitted lesion is conversion into a fixed lesion, which is likely to be an unrepairable or misrepaired double-strand break. The presence of protein synthesis after irradiation increases the probability that a break will enter the repair pathway. Evidence shows that increased probability of repair results from enhanced synthesis of repair proteins shortly after radiation. (ERB)

  12. Free radical scavenger edaravone suppresses x-ray-induced apoptosis through p53 inhibition in MOLT-4 cells.

    PubMed

    Sasano, Nakashi; Enomoto, Atsushi; Hosoi, Yoshio; Katsumura, Yosuke; Matsumoto, Yoshihisa; Shiraishi, Kenshiro; Miyagawa, Kiyoshi; Igaki, Hiroshi; Nakagawa, Keiichi

    2007-11-01

    Edaravone, a clinical drug used widely for the treatment of acute cerebral infarction, is reported to scavenge free radicals. In the present study, we investigated the radioprotective effect of edaravone on X-ray-induced apoptosis in MOLT-4 cells. Apoptosis was determined by the dye exclusion test, Annexin V binding assay, cleavage of caspase, and DNA fragmentation. We found that edaravone significantly suppressed the X-ray-induced apoptosis. The amount of intracellular ROS production was determined by the chloromethyl-2',7'-dichlorodihydro-fluorescein diacetate system. We found that the intracellular ROS production by X-irradiation was completely suppressed by the addition of edaravone. The accumulation and phosphorylation of p53 and the expression of p21(WAF1), a target protein of p53, which were induced by X-irradiation, were also suppressed by adding edaravone. We conclude that the free radical scavenger edaravone suppresses X-ray-induced apoptosis in MOLT-4 cells by inhibiting p53.

  13. NADPH oxidase-mediated generation of reactive oxygen species: A new mechanism for X-ray-induced HeLa cell death

    SciTech Connect

    Liu Qing; He Xiaoqing; Liu Yongsheng; Du Bingbing; Wang Xiaoyan; Zhang Weisheng; Jia Pengfei; Dong Jingmei; Ma Jianxiu; Wang Xiaohu; Li Sha; Zhang Hong

    2008-12-19

    Oxidative damage is an important mechanism in X-ray-induced cell death. Radiolysis of water molecules is a source of reactive oxygen species (ROS) that contribute to X-ray-induced cell death. In this study, we showed by ROS detection and a cell survival assay that NADPH oxidase has a very important role in X-ray-induced cell death. Under X-ray irradiation, the upregulation of the expression of NADPH oxidase membrane subunit gp91{sup phox} was dose-dependent. Meanwhile, the cytoplasmic subunit p47{sup phox} was translocated to the cell membrane and localized with p22{sup phox} and gp91{sup phox} to form reactive NADPH oxidase. Our data suggest, for the first time, that NADPH oxidase-mediated generation of ROS is an important contributor to X-ray-induced cell death. This suggests a new target for combined gene transfer and radiotherapy.

  14. Sensitivity evaluation and selective plane imaging geometry for x-ray-induced luminescence imaging.

    PubMed

    Quigley, Bryan P; Smith, Corey D; Cheng, Shih-Hsun; Souris, Jeffrey S; Pelizzari, Charles A; Chen, Chin-Tu; Lo, Leu-Wei; Reft, Chester S; Wiersma, Rodney D; La Riviere, Patrick J

    2017-07-13

    X-ray-induced luminescence (XIL) is a hybrid x-ray/optical imaging modality that employs nanophosphors that luminescence in response to x-ray irradiation. X-ray-activated phosphorescent nanoparticles have potential applications in radiation therapy as theranostics, nanodosimeters, or radiosensitizers. Extracting clinically relevant information from the luminescent signal requires the development of a robust imaging model that can determine nanophosphor distributions at depth in an optically scattering environment from surface radiance measurements. The applications of XIL in radiotherapy will be limited by the dose-dependent sensitivity at depth in tissue. We propose a novel geometry called selective plane XIL (SPXIL), and apply it to experimental measurements in optical gel phantoms and sensitivity simulations. An imaging model is presented based on the selective plane geometry which can determine the detected diffuse optical signal for a given x-ray dose and nanophosphor distribution at depth in a semi-infinite, optically homogenous material. The surface radiance in the model is calculated using an analytical solution to the extrapolated boundary condition. Y2 O3 :Eu(3+) nanoparticles are synthesized and inserted into various optical phantom in order to measure the luminescent output per unit dose for a given concentration of nanophosphors and calibrate an imaging model for XIL sensitivity simulations. SPXIL imaging with a dual-source optical gel phantom is performed, and an iterative Richardson-Lucy deconvolution using a shifted Poisson noise model is applied to the measurements in order to reconstruct the nanophosphor distribution. Nanophosphor characterizations showed a peak emission at 611 nm, a linear luminescent response to tube current and nanoparticle concentration, and a quadratic luminescent response to tube voltage. The luminescent efficiency calculation accomplished with calibrated bioluminescence mouse phantoms determines 1.06 photons were emitted

  15. X-ray-induced cell death in the developing hippocampal complex involved neurons and requires protein synthesis

    SciTech Connect

    Ferrer, I.; Serrano, T.; Alcantara, S.; Tortosa, A.; Graus, F.

    1993-07-01

    Sprague-Dawley rats aged 1 or 15 days were irradiated with a single dose of 200 cGy X-rays and killed at different intervals from 3 to 48 hours (h). Dying cells were recognized by their shrunken and often fragmented nuclei and less damaged cytoplasm in the early stages. On the basis of immunocytochemical markers, dying cells probably represented a heterogeneous population which included neurons and immature cells. In rats aged 1 day the number of dying cells rapidly increased in the hippocampal complex with peak values 6 h after irradiation. This was following by a gentle decrease to reach normal values 48 h after irradiation. The most severely affected regions were the subplate and the cellular layer of the subiculum, gyrus dentatus and hilus, and the stratum oriens and pyramidale of the hippocampus (CA1 more affected than CA2, and this more affected than CA3). X-ray-induced cell death was abolished with an injection of cycloheximide (2 [mu]g/g i.p.) given at the time of irradiation. X-ray-induced cell death was not changed after the intraventicular administration of nerve growth factor (NGF; 10 [mu]g in saline) at the time of irradiation. Cell death was not induced by X-irradiation in rats aged 15 days. These results indicate that X-ray-induced cell death in the hippocampal complex of the developing rat is subjected to determinate temporal and regional patterns of vulnerability; it is an active process mediated by protein synthesis but probably not dependent on NGF. 60 refs., 5 figs.

  16. Soft-x-ray-induced spin-state switching of an adsorbed Fe(II) spin-crossover complex

    NASA Astrophysics Data System (ADS)

    Kipgen, Lalminthang; Bernien, Matthias; Nickel, Fabian; Naggert, Holger; Britton, Andrew J.; Arruda, Lucas M.; Schierle, Enrico; Weschke, Eugen; Tuczek, Felix; Kuch, Wolfgang

    2017-10-01

    For probing the nature of spin-state switching in spin-crossover molecules adsorbed on surfaces, x-ray absorption spectroscopy has emerged as a powerful tool due to its high sensitivity and element selectivity in tracing even subtle electronic, magnetic, or chemical changes. However, the x-rays itself can induce a spin transition and might have unwanted influence while investigating the effect of other stimuli such as temperature or light, or of the surface, on the spin switching behaviour. Herein, we present the spin switching of an Fe(II) complex adsorbed on a highly oriented pyrolytic graphite surface with particular emphasis on the x-ray-induced switching. For a submonolayer coverage, the complex undergoes a complete and reversible temperature- and light-induced spin transition. The spin states are switched both ways by x-rays at 5 K, i.e. from the high-spin state to the low-spin state or vice versa, depending on the relative amount of each species. Furthermore, we quantify the fraction of molecules undergoing soft x-ray-induced photochemistry, a process which results in an irreversible low-spin state component, for a particular exposure time. This can be greatly suppressed by reducing the beam intensity.

  17. Soft-x-ray-induced spin-state switching of an adsorbed Fe(II) spin-crossover complex.

    PubMed

    Kipgen, Lalminthang; Bernien, Matthias; Nickel, Fabian; Naggert, Holger; Britton, Andrew J; Arruda, Lucas M; Schierle, Enrico; Weschke, Eugen; Tuczek, Felix; Kuch, Wolfgang

    2017-10-04

    For probing the nature of spin-state switching in spin-crossover molecules adsorbed on surfaces, x-ray absorption spectroscopy has emerged as a powerful tool due to its high sensitivity and element selectivity in tracing even subtle electronic, magnetic, or chemical changes. However, the x-rays itself can induce a spin transition and might have unwanted influence while investigating the effect of other stimuli such as temperature or light, or of the surface, on the spin switching behaviour. Herein, we present the spin switching of an Fe(II) complex adsorbed on a highly oriented pyrolytic graphite surface with particular emphasis on the x-ray-induced switching. For a submonolayer coverage, the complex undergoes a complete and reversible temperature- and light-induced spin transition. The spin states are switched both ways by x-rays at 5 K, i.e. from the high-spin state to the low-spin state or vice versa, depending on the relative amount of each species. Furthermore, we quantify the fraction of molecules undergoing soft x-ray-induced photochemistry, a process which results in an irreversible low-spin state component, for a particular exposure time. This can be greatly suppressed by reducing the beam intensity.

  18. Particle-in-cell simulations of multi-MeV pulsed X-ray induced air plasmas at low pressures

    SciTech Connect

    Ribière, M. D'Almeida, T.; Gaufridy de Dortan, F. de; Maulois, M.; Delbos, C.; Garrigues, A.; Cessenat, O.; Azaïs, B.

    2016-03-15

    A full kinetic modelling of the charge particles dynamics generated upon the irradiation of an air-filled cavity by a multi-MeV pulsed x-ray is performed. From the calculated radiative source generated by the ASTERIX generator, we calculated the electromagnetic fields generated by x-ray induced air plasmas in a metallic cavity at different pressures. Simulations are carried out based on a Particle-In-Cell interpolation method which uses 3D Maxwell-Vlasov calculations of the constitutive charged species densities of air plasmas at different pressures at equilibrium. The resulting electromagnetic fields within the cavity are calculated for different electron densities up to 4 × 10{sup 10 }cm{sup −3}. For each air pressure, we show electronic plasma waves formation followed by Landau damping. As electron density increases, the calculations exhibit space-charged neutralization and return current formation.

  19. Inhibition of X-ray-induced DNA strand break repair in polyamine-depleted HeLa cells.

    PubMed

    Snyder, R D

    1989-05-01

    Treatment of HeLa cells with the polyamine biosynthesis inhibitors, alpha-difluoromethylornithine (DFMO) or methylglyoxal bis(guanylhydrazone) (MGBG), results in, depending on the conditions, partial or complete depletion of the cellular polyamines: putrescine, spermidine and spermine. In this compromised state cells exhibited a distinct deficiency in repair of X-ray-induced DNA strand breaks. The half-time for return of normal DNA sedimentation following 1.6 Gy was 9.5 min for untreated control cells and 22, 32 and 50 min for cells treated with MGBG, DFMO + MGBG and DFMO, respectively. Normal repair kinetics were restored to these cells upon a short incubation in media containing all three polyamines. The rapid early phase of repair following higher X-ray doses (16 Gy) was also delayed in polyamine-depleted cells but later repair occurring 1-4 h post-irradiation, representing chromatin reconstitution, was apparently normal.

  20. Minority additive distributions in a ceramic metal-halide arc lamp using high-energy x-ray induced fluorescence

    NASA Astrophysics Data System (ADS)

    Curry, J. J.; Adler, H. G.; Shastri, S. D.; Lawler, J. E.

    2001-09-01

    X-ray induced fluorescence is used to measure the elemental densities of minority additives in a metal-halide arc contained inside a translucent ceramic envelope. A monochromatic x-ray beam from the Sector 1 Insertion Device beamline at the Advanced Photon Source is used to excite K-shell x-ray fluorescence in the constituents of a ceramic metal-halide arc lamp dosed with DyI3 and CsI. Fluorescence and scattered photons are collected by a cryogenic energy-resolving Ge detector. The high signal-to-noise spectra show strong fluorescence from Dy, Cs, and I, as well as elastic scattering from Hg. Radial distributions of the absolute elemental densities of Dy, Cs, and I are obtained.

  1. Minority additive distributions in a ceramic metal-halide arc lamp using high-energy x-ray induced fluorescence

    SciTech Connect

    Curry, J. J.; Adler, H. G.; Shastri, S. D.; Lawler, J. E.

    2001-09-24

    X-ray induced fluorescence is used to measure the elemental densities of minority additives in a metal-halide arc contained inside a translucent ceramic envelope. A monochromatic x-ray beam from the Sector 1 Insertion Device beamline at the Advanced Photon Source is used to excite K-shell x-ray fluorescence in the constituents of a ceramic metal-halide arc lamp dosed with DyI{sub 3} and CsI. Fluorescence and scattered photons are collected by a cryogenic energy-resolving Ge detector. The high signal-to-noise spectra show strong fluorescence from Dy, Cs, and I, as well as elastic scattering from Hg. Radial distributions of the absolute elemental densities of Dy, Cs, and I are obtained.

  2. Note: Experiments in hard x-ray chemistry: In situ production of molecular hydrogen and x-ray induced combustion

    SciTech Connect

    Pravica, Michael; Bai Ligang; Liu Yu; Galley, Martin; Robinson, John; Park, Changyong; Hatchett, David

    2012-03-15

    We have successfully loaded H{sub 2} into a diamond anvil cell at high pressure using the synchrotron x-ray induced decomposition of NH{sub 3}BH{sub 3}. In a second set of studies, radiation-assisted release of O{sub 2} from KCLO{sub 3}, H{sub 2} release from NH{sub 3}BH{sub 3}, and reaction of these gases in a mixture of the reactants to form liquid water using x-rays at ambient conditions was observed. Similar observations were made using a KCLO{sub 3} and NaBH{sub 4} mixture. Depending on reaction conditions, an explosive or far slower reaction producing water was observed.

  3. X-ray Inducible Luminescence and Singlet Oxygen Sensitization by an Octahedral Molybdenum Cluster Compound: A New Class of Nanoscintillators.

    PubMed

    Kirakci, Kaplan; Kubát, Pavel; Fejfarová, Karla; Martinčík, Jiří; Nikl, Martin; Lang, Kamil

    2016-01-19

    Newly synthesized octahedral molybdenum cluster compound (n-Bu4N)2[Mo6I8(OOC-1-adamantane)6] revealed uncharted features applicable for the development of X-ray inducible luminescent materials and sensitizers of singlet oxygen, O2((1)Δg). The compound exhibits a red-NIR luminescence in the solid state and in solution (e.g., quantum yield of 0.76 in tetrahydrofuran) upon excitation by UV-vis light. The luminescence originating from the excited triplet states is quenched by molecular oxygen to produce O2((1)Δg) with a high quantum yield. Irradiation of the compound by X-rays generated a radioluminescence with the same emission spectrum as that obtained by UV-vis excitation. It proves the formation of the same excited triplet states regardless of the excitation source. By virtue of the described behavior, the compound is suggested as an efficient sensitizer of O2((1)Δg) upon X-ray excitation. The luminescence and radioluminescence properties were maintained upon embedding the compound in polystyrene films. In addition, polystyrene induced an enhancement of the radioluminescence intensity via energy transfer from the scintillating polymeric matrix. Sulfonated polystyrene nanofibers were used for the preparation of nanoparticles which form stable dispersions in water, while keeping intact the luminescence properties of the embedded compound over a long time period. Due to their small size and high oxygen diffusivity, these nanoparticles are suitable carriers of sensitizers of O2((1)Δg). The presented results define a new class of nanoscintillators with promising properties for X-ray inducible photodynamic therapy.

  4. Measurement of the Energy and High-Pressure Dependence of X-ray-Induced Decomposition of Crystalline Strontium Oxalate.

    PubMed

    Goldberger, David; Evlyukhin, Egor; Cifligu, Petrika; Wang, Yonggang; Pravica, Michael

    2017-09-28

    We report measurements of the X-ray-induced decomposition of crystalline strontium oxalate (SrC2O4) as a function of energy and high pressure in two separate experiments. SrC2O4 at ambient conditions was irradiated with monochromatic synchrotron X-rays ranging in energy from 15 to 28 keV. A broad resonance of the decomposition yield was observed with a clear maximum when irradiating with ∼20 keV X-rays and ambient pressure. Little or no decomposition was observed at 15 keV, which is below the Sr K-shell energy of 16.12 keV, suggesting that excitation of core electrons may play an important role in the destabilization of the C2O4(2-) anion. A second experiment was performed to investigate the high-pressure dependence of the X-ray-induced decomposition of strontium oxalate at fixed energy. SrC2O4 was compressed in a diamond anvil cell (DAC) in the pressure range from 0 to 7.6 GPa with 1 GPa increments and irradiated in situ with 20 keV X-rays. A marked pressure dependence of the decomposition yield of SrC2O4 was observed with a decomposition yield maximum at around 1 GPa, suggesting that different crystal structures of the material play an important role in the decomposition process. This may be due in part to a phase transition observed near this pressure.

  5. Search for x-ray induced decay of the 31-yr isomer of {sup 178}Hf using synchrotron radiation

    SciTech Connect

    Ahmad, I.; Gemmell, D.S.; Moore, E.F.; Schiffer, J.P.; Banar, J.C.; Bredeweg, T.A.; Miller, G.G.; Palmer, P.; Pangault, L.N.; Rundberg, R.S.; Wilhelmy, J.B.; Becker, J.A.; Cooper, J.R.; Kraemer, A.; McNabb, D.P.; Wang, T.-F.; Mashayekhi, A.; Shastri, S.D.

    2005-02-01

    Isomeric {sup 178}Hf (t{sub 1/2}=31 yr, E{sub x}=2.446 MeV, J{sup {pi}}=16{sup +}) was bombarded by a white beam of x rays from the Advanced Photon Source at Argonne National Laboratory. A search was made for x-ray induced decay of the isomer by detecting prompt and delayed {gamma} rays associated with the decay. No induced decay was observed. Upper limits for such a process for x-ray energies between 7 and 100 keV were set. The limits between 7 and 30 keV are below {approx_equal}3x10{sup -27} cm{sup 2} keV for induced decay that bypasses the 4-s isomer and {approx_equal}5x10{sup -27} cm{sup 2} keV for induced decay that is delayed through this isomer, which are orders of magnitude below values at which induced decay was reported previously. These limits are consistent with what is known about the properties of atomic nuclei.

  6. Search for x-ray induced decay of the 31-yr isomer of 178Hf using synchrotron radiation

    NASA Astrophysics Data System (ADS)

    Ahmad, I.; Banar, J. C.; Becker, J. A.; Bredeweg, T. A.; Cooper, J. R.; Gemmell, D. S.; Kraemer, A.; Mashayekhi, A.; McNabb, D. P.; Miller, G. G.; Moore, E. F.; Palmer, P.; Pangault, L. N.; Rundberg, R. S.; Schiffer, J. P.; Shastri, S. D.; Wang, T.-F.; Wilhelmy, J. B.

    2005-02-01

    Isomeric 178Hf (t1/2=31 yr, Ex=2.446MeV, Jπ=16+) was bombarded by a white beam of x rays from the Advanced Photon Source at Argonne National Laboratory. A search was made for x-ray induced decay of the isomer by detecting prompt and delayed γ rays associated with the decay. No induced decay was observed. Upper limits for such a process for x-ray energies between 7 and 100 keV were set. The limits between 7 and 30 keV are below ≈3×10-27 cm2keV for induced decay that bypasses the 4-s isomer and ≈5×10-27 cm2keV for induced decay that is delayed through this isomer, which are orders of magnitude below values at which induced decay was reported previously. These limits are consistent with what is known about the properties of atomic nuclei.

  7. Search for X-ray induced decay of the 31-yr isomer of 178Hf using synchrotron radiation

    SciTech Connect

    Ahmad, I; Banar, J C; Becker, J A; Bredeweg, T A; Cooper, J R; Gemmell, D S; Kraemer, A; Mashayekhi, A; McNabb, D P; Miller, G G; Moore, E F; Palmer, P; Pangault, L N; Rundberg, R S; Schiffer, J P; Shastri, S D; Wang, T F; Wilhelmy, J B

    2004-09-13

    Isomeric {sup 178}Hf (t{sub 1/2} = 31 yr, E{sub x} = 2.446 MeV, J{sup {pi}} = 16{sup +}) was bombarded by a white beam of x-rays from the Advanced Photon Source at Argonne National Laboratory. A search was made for x-ray induced decay of the isomer by detecting prompt and delayed {gamma} rays associated with the decay. No induced decay was observed. Upper limits for such a process for x-ray energies between 7-100 keV were set. The limits between 7 and 30 keV are below {approx} 3 x 10{sup -27} cm{sup 2}-keV for induced decay that bypasses the 4-s isomer and {approx} 5 x 10{sup -27} cm{sup 2}-keV for induced decay that is delayed through this isomer, orders of magnitude below values at which induced decay was reported previously. These limits are consistent with what is known about the properties of atomic nuclei.

  8. Ultrafast x-ray-induced nuclear dynamics in diatomic molecules using femtosecond x-ray-pump-x-ray-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Lehmann, C. S.; Picón, A.; Bostedt, C.; Rudenko, A.; Marinelli, A.; Moonshiram, D.; Osipov, T.; Rolles, D.; Berrah, N.; Bomme, C.; Bucher, M.; Doumy, G.; Erk, B.; Ferguson, K. R.; Gorkhover, T.; Ho, P. J.; Kanter, E. P.; Krässig, B.; Krzywinski, J.; Lutman, A. A.; March, A. M.; Ray, D.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-07-01

    The capability of generating two intense, femtosecond x-ray pulses with a controlled time delay opens the possibility of performing time-resolved experiments for x-ray-induced phenomena. We have applied this capability to study the photoinduced dynamics in diatomic molecules. In molecules composed of low-Z elements, K -shell ionization creates a core-hole state in which the main decay mode is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wave packets of the transient two-valence-hole states continue evolving on the femtosecond time scale, leading either to separated atomic ions or long-lived quasibound states. By using an x-ray pump and an x-ray probe pulse tuned above the K -shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K -shell ionization, Auger decay, and the time evolution of the nuclear wave packets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasibound states.

  9. Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study.

    PubMed

    Meents, A; Wagner, A; Schneider, R; Pradervand, C; Pohl, E; Schulze-Briese, C

    2007-03-01

    The cryocooling of protein crystals to temperatures of around 100 K drastically reduces X-ray-induced radiation damage. The majority of macromolecular data collection is therefore performed at 100 K, yielding diffraction data of higher resolution and allowing structure determination from much smaller crystals. However, at third-generation synchrotron sources radiation damage at 100 K still limits the useful data obtainable from a crystal. For data collection at 15 K, realised by the use of an open-flow helium cryostat, a further reduction of radiation damage is expected. However, no systematic studies have been undertaken so far. In this present study, a total of 54 data sets have been collected from holoferritin and insulin crystals at 15 and 90 K in order to identify the effect of the lower data-collection temperature on the radiation damage. It is shown that data collection at 15 K has only a small positive effect for insulin crystals, whereas for holoferritin crystals radiation damage is reduced by 23% compared with data collection at 90 K.

  10. X-ray-induced electron cascades in dielectrics modeled with XCASCADE code: effect of impact ionization cross sections

    NASA Astrophysics Data System (ADS)

    Medvedev, Nikita A.

    2015-05-01

    Characterization of a free-electron laser (FEL) pulse can be done with a pump-probe scheme, using an FEL pump and a visible light probe on an optically transparent solid-state target. With such experimental scheme, pulse duration can be monitored on a shot-to-shot basis. It relies on the changes in optical properties induced by the FEL excitation of electrons. Here we analyze effects of different cross sections used in the modeling of electron kinetics. XCASCADE, a Monte Carlo toolkit for modeling x-ray-induced electron cascades (N. Medvedev, Appl. Phys. B 118 (2015) 417), is used for this purpose. Two different cross sections are compared: atomic BEB model vs complex-dielectric function formalism that accounts for collective effects in solids. It is shown that for photon and electron energies above a few tens of eV, the both models coincide very closely. For lower energies in the VUV regime, the difference in the cross sections become more significant, nevertheless producing qualitatively similar electron kinetics and increase in the density of excited electrons.

  11. Dopant concentration dependent optical and X-Ray induced photoluminescence in Eu3+ doped La2Zr2O7

    NASA Astrophysics Data System (ADS)

    Pokhrel, Madhab; Brik, Mikhail; Mao, Yuanbing

    2015-03-01

    Herein, we will be presenting the dopant (Eu) concentration dependent high density La2Zr2O7 nanoparticles for optical and X-ray scintillation applications by use of X - ray diffraction, Raman, FTIR, scanning electron microscope (SEM), transmission electron microscopy (TEM), optically and X-ray excited photoluminescence (PL). Several theoretical methods have been used in order to investigate the structural, electronic, optical, elastic, dynamic properties of Eu doped La2Zr2O7. It is observed that Eu: La2Zr2O7 shows an intense red luminescence under 258, 322, 394 and 465 nm excitation. The optical intensity of Eu: La2Zr2O7 depends on the dopant concentration of Eu3+. Following high energy excitation with X-rays, Eu: La2Zr2O7 shows an atypical Eu PL response (scintillation) with a red emission. The intense color emission of Eu obtained under 258 nm excitation, the X-ray induced luminescence property along with reportedly high density of La2Zr2O7, makes these nanomaterials attractive for optical and X-ray applications. The authors thank the support from the Defense Threat Reduction Agency (DTRA) of the U.S. Department of Defense (Award #HDTRA1-10-1-0114).

  12. Exogenous Nitric Oxide Suppresses in Vivo X-ray-Induced Targeted and Non-Targeted Effects in Zebrafish Embryos

    PubMed Central

    Kong, E.Y.; Yeung, W.K.; Chan, T.K.Y.; Cheng, S.H.; Yu, K.N.

    2016-01-01

    The present paper studied the X-ray-induced targeted effect in irradiated zebrafish embryos (Danio rerio), as well as a non-targeted effect in bystander naïve embryos partnered with irradiated embryos, and examined the influence of exogenous nitric oxide (NO) on these targeted and non-targeted effects. The exogenous NO was generated using an NO donor, S-nitroso-N-acetylpenicillamine (SNAP). The targeted and non-targeted effects, as well as the toxicity of the SNAP, were assessed using the number of apoptotic events in the zebrafish embryos at 24 h post fertilization (hpf) revealed through acridine orange (AO) staining. SNAP with concentrations of 20 and 100 µM were first confirmed to have no significant toxicity on zebrafish embryos. The targeted effect was mitigated in zebrafish embryos if they were pretreated with 100 µM SNAP prior to irradiation with an X-ray dose of 75 mGy but was not alleviated in zebrafish embryos if they were pretreated with 20 µM SNAP. On the other hand, the non-targeted effect was eliminated in the bystander naïve zebrafish embryos if they were pretreated with 20 or 100 µM SNAP prior to partnering with zebrafish embryos having been subjected to irradiation with an X-ray dose of 75 mGy. These findings revealed the importance of NO in the protection against damages induced by ionizing radiations or by radiation-induced bystander signals, and could have important impacts on development of advanced cancer treatment strategies. PMID:27529238

  13. Role of x-ray-induced transcripts in adaptive responses following x-rays. Progress report, year 1

    SciTech Connect

    Boothman, D.A.

    1992-09-01

    Potentially lethal damage repair (PLDR) and sublethal damage repair, may be the same manifestations of a series of common enzymatic steps. PLDR, has two distinct phases based upon DNA lesion repair and survival recovery studies. The first phase of PLDR occurs very quickly (t{sub {1/2}}:2--20 mins) to increase the survival of X-irradiated cells by mending the vast array of DNA lesions created by ionizing radiation. The second slower phase of PLDR proceeds much later (i.e., >1--2 hrs) following X-irradiation, during which the remaining double-stranded DNA breaks are completely repaired. This second phase of repair closely corresponds to the restructuring of gross chromosomal damage, and can be partially blocked in some human cells by inhibiting protein synthesis. This slower phase of PLDR correlated with a rapid decline in X-ray-induced transformation of normal cells. The fast component of PLDR may be due to constitutively synthesized DNA ligases, topoisomerases, or polymerases, which act immediately to repair damaged, DNA. In contrast, the slow phase of PLDR in human cells may require the induction of specific genes and gene product`s involved in the repair of potentially lethal or carcinogenic DNA lesions. Induced gene products (i.e., proteins) specifically synthesized in response to physiological doses of ionizing radiation in radioresistant human melanoma (U1-Mel) cells, and in a variety of other human normal and cancer-prone cells, were identified using two-dimensional gel electrophoresis. We identified and partially characterized ten proteins synthesized by U1-Mel cells. The synthesis of eight of these proteins were specifically induced by ionizing radiation and two proteins were repressed Neither heat shock, UV-irradiation, nor bifunctional alkylating agent treatments resulted in the induction of these proteins. The expression of one protein, XIP269, correlated very well with PLDR capacity.

  14. Differential mechanisms of x-ray-induced cell death in human endothelial progenitor cells isolated from cord blood and adults.

    PubMed

    Mendonca, Marc S; Chin-Sinex, Helen; Dhaemers, Ryan; Mead, Laura E; Yoder, Merv C; Ingram, David A

    2011-08-01

    Endothelial colony-forming cells (ECFCs) are endothelial progenitor cells that circulate at low concentration in human umbilical cord and adult peripheral blood and are largely resident in blood vessels. ECFCs not only appear to be critical for normal vascular homeostasis and repair but may also contribute to tumor angiogenesis and response to therapy. To begin to characterize the potential role of ECFCs during the treatment of tumors in children and adults with radiation, we characterized the X-ray sensitivity of cord and adult blood-derived ECFCs. We found both cord blood and adult ECFCs to be highly radiation sensitive (3 Gy resulted in >90% killing without induction of apoptosis). The X-ray survival curves suggested reduced potential for repair capacity, but X-ray fractionation studies demonstrated that all the ECFCs exhibited repair when the radiation was fractionated. Finally, the mechanisms of X-ray-induced cell death for cord blood and adult ECFCs were different at low and high dose. At low dose, all ECFCs appear to die by mitotic death/catastrophe. However, at high radiation doses (≥ 10 Gy) cord blood ECFCs underwent p53 stabilization and Bax-dependent apoptosis as well as p21-dependent G₁ and G₂/M cell cycle checkpoints. By contrast, after 10 Gy adult ECFCs undergo only large-scale radiation-induced senescence, which is a cellular phenotype linked to premature development of atherosclerosis and vasculopathies. These data demonstrate that the ECFC response to radiation is dose-dependent and developmentally regulated and may provide potential mechanistic insight into their role in tumor and normal tissue response after ionizing radiation treatment.

  15. Novel applications of diagnostic x-rays in activating photo-agents through x-ray induced visible luminescence from rare-earth particles: an in vitro study

    NASA Astrophysics Data System (ADS)

    Abliz, Erkinay; Collins, Joshua E.; Friedberg, Joseph S.; Kumar, Ajith; Bell, Howard; Waynant, Ronald W.; Tata, Darrell B.

    2010-02-01

    Photodynamic agents such as Photofrin II (Photo II) utilized in photodynamic therapy (PDT) possess a remarkable property to become preferentially retained within the tumor's micro-environment. Upon the photo-agent's activation through visible light photon absorption, the agents exert their cellular cytotoxicity through type II and type I mechanistic pathways through extensive generation of reactive oxygen species (ROS): singlet oxygen 1O2, superoxide anion O2 -, and hydrogen peroxide H2O2, within the intratumoral environment. Unfortunately, due to shallow visible light penetration depth (~2mm to 5mm) in tissues, the PDT strategy currently has largely been restricted to the treatments of surface tumors, such as the melanomas. Additional invasive strategies through optical fibers are currently utilized in getting the visible light into the intended deep seated targets within the body for PDT. In this communication, we report on a novel strategy in utilizing "soft" energy diagnostic X-rays to indirectly activate Photo II through X-ray induced luminescence from Gadolinium oxysulfide (20 micron dimension) particles doped with Terbium: Gd2O2S:Tb. X-ray induced visible luminescence from Gd2O2S:Tb particles was spectroscopically characterized and the ROS production levels from clinically relevant concentration (10 μg/ml) of Photo II was quantified through changes in the Vitamin C absorbance. ROS kinetics through X-ray induced luminescence was found to be similar to the ROS kinetics from red He-Ne laser exposures used in the clinics. Taken together, in-vitro findings herein provide the basis for future studies in determining the safety and efficacy of this non-invasive X-ray induced luminescence strategy in activating photo-agent in deep seated tumors.

  16. Cellular proliferation in the skin of X-rayed newt limbs (with a note on x-ray-induced limb regression)

    SciTech Connect

    Wertz, R.L.

    1982-07-01

    Left hind limbs, including the pelvis, of adult newts (Notophthalmus viridescens) were locally irradiated with a dose of x-rays that inhibited regeneration (2,000 R). This x-ray dose and other doses (700-2,000 R) capable of inhibiting limb regeneration also cause limb regression prior to amputation. Before limb regression occurred, there was a latent period of 3 to 6 weeks. Limb regression was characterized by necrotic wasting and resorption of distal elements. The degree of loss was variable and dependent upon dosage. After this further degenerative changes were not noted. Proliferation of epidermal cells was examined 4 days after irradiation prior to limb regression or after x-ray-induced degeneration of the limbs had ended. Proliferative activity in x-rayed limbs was also compared at various stages of contralateral control limb regeneration. Limbs examined after x-ray-induced limb regression had ended showed levels of (/sup 3/H)-thymidine incorporation into DNA comparable to normal epidermis. In contrast, limbs examined 4 days after irradiation had lower levels of DNA synthesis (P much less than 0.01). Amputation of limbs in both groups caused an increase in DNA synthesis (P much less than 0.01). Histological examination showed that cellular proliferation was associated primarily with the epidermis. These results indicate that epidermal cell proliferation was not resistant to x-rays. However, levels of normal cell division were observed after amputation of after cessation of x-ray-induced limb regression.

  17. Wortmannin-enhanced X-ray-induced apoptosis of human T-cell leukemia MOLT-4 cells possibly through the JNK/SAPK pathway.

    PubMed

    Tomita, Masanori; Suzuki, Norio; Matsumoto, Yoshihisa; Enomoto, Atsushi; Yin, Hong Lan; Hosoi, Yoshio; Hirano, Kazuya; Sakai, Kazuo

    2003-10-01

    We demonstrated that enhancement of X-ray-induced apoptosis/rapid cell death by wortmannin accompanied by increased activation of JNK/SAPK in human leukemia MOLT-4 cells. Rapid cell death/apoptosis was determined either by the dye exclusion test or by the appearance of Annexin V-positive cells and cleaved PARP fragments. Enhancement was observed only at higher concentrations of wortmannin, i.e. 1 microM or more. At these high concentrations, both DNA-PK and ATM were inhibited. X-ray-induced phosphorylation of Ser 15 of p53/TP53, accumulation of both p53/TP53 and p21/WAF1/CDKN1A, and phosphorylation of XRCC4 were all suppressed. The enhancement of apoptosis/rapid cell death by wortmannin was prevented by addition of caspase inhibitors, Z-VAD-FMK or Ac-DEVD-CHO, or by transfection and overexpression of mouse Bcl2, which is known as an anti-apoptosis protein. The requirement for a high concentration of wortmannin, i.e. 1 microM or more, indicates that inhibition of both DNA-PK and ATM was necessary for the enhanced apoptosis/rapid cell death. Phosphorylation of AKT/PKB was completely suppressed at a much lower concentration, i.e. 0.1 microM wortmannin, where no enhancement of X-ray-induced apoptosis/rapid cell death was observed. On the other hand, X-ray-induced phosphorylation of JNK and its kinase activity as well as apoptosis/rapid cell death were all significantly enhanced only at high concentrations of wortmannin, i.e. 1 microM or more. Furthermore, the extent of enhancement of both JNK phosphorylation and of apoptosis/rapid cell death by wortmannin was less in Rh1a cells, which are ceramide- and radiation-resistant variant cells compared to the parental MOLT-4 cells. Therefore, activation of the JNK pathway was considered important for the enhancement of X-ray-induced apoptosis/rapid cell death of MOLT-4 cells by wortmannin, because of the requirement for a higher concentration of wortmannin than that required for inhibition of AKT phosphorylation. The

  18. X-Ray Induced Formation of γ-H2AX Foci after Full-Field Digital Mammography and Digital Breast-Tomosynthesis

    PubMed Central

    Schwab, Siegfried A.; Brand, Michael; Schlude, Ina-Kristin; Wuest, Wolfgang; Meier-Meitinger, Martina; Distel, Luitpold; Schulz-Wendtland, Ruediger; Uder, Michael; Kuefner, Michael A.

    2013-01-01

    Purpose To determine in-vivo formation of x-ray induced γ-H2AX foci in systemic blood lymphocytes of patients undergoing full-field digital mammography (FFDM) and to estimate foci after FFDM and digital breast-tomosynthesis (DBT) using a biological phantom model. Materials and Methods The study complies with the Declaration of Helsinki and was performed following approval by the ethic committee of the University of Erlangen-Nuremberg. Written informed consent was obtained from every patient. For in-vivo tests, systemic blood lymphocytes were obtained from 20 patients before and after FFDM. In order to compare in-vivo post-exposure with pre-exposure foci levels, the Wilcoxon matched pairs test was used. For in-vitro experiments, isolated blood lymphocytes from healthy volunteers were irradiated at skin and glandular level of a porcine breast using FFDM and DBT. Cells were stained against the phosphorylated histone variant γ-H2AX, and foci representing distinct DNA damages were quantified. Results Median in-vivo foci level/cell was 0.086 (range 0.067–0.116) before and 0.094 (0.076–0.126) after FFDM (p = 0.0004). In the in-vitro model, the median x-ray induced foci level/cell after FFDM was 0.120 (range 0.086–0.140) at skin level and 0.035 (range 0.030–0.050) at glandular level. After DBT, the median x-ray induced foci level/cell was 0.061 (range 0.040–0.081) at skin level and 0.015 (range 0.006–0.020) at glandular level. Conclusion In patients, mammography induces a slight but significant increase of γ-H2AX foci in systemic blood lymphocytes. The introduced biological phantom model is suitable for the estimation of x-ray induced DNA damages in breast tissue in different breast imaging techniques. PMID:23936236

  19. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

    SciTech Connect

    Sutton, Kristin A.; Black, Paul J.; Mercer, Kermit R.; Garman, Elspeth F.; Owen, Robin L.; Snell, Edward H.; Bernhard, William A.

    2013-12-01

    Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process. Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

  20. Investigating the electron density of multi-MeV X-ray-induced air plasmas at low pressures based on electromagnetic resonant cavity analysis

    NASA Astrophysics Data System (ADS)

    Ribière, M.; d'Almeida, T.; Cessenat, O.; Maulois, M.; Pouzalgues, R.; Crabos, B.; Delbos, C.; Garrigues, A.; Azaïs, B.

    2016-12-01

    We investigate air plasmas generated by multi-MeV pulsed X-rays at pressures ranging from 10-5 to 10-1 mbar. The experimental approach used for these studies is based on measurements of resonant frequencies damping and shift for different electromagnetic modes within a cylindrical cavity. Time-integrated electron densities in X-ray-induced air plasmas are inferred from the damping rate of the measured magnetic fields and their corresponding frequency shifts. In the present study, electron densities ranging from 108 to 109 cm-3 at pressures ranging from 10-3 to 10-1 mbar have been measured. Experimental results were confronted to 3D Maxwell-Vlasov Particle-In-Cell simulations incorporating a radiation-induced electric conductivity model. The method used in this work enables determining microscopic and macroscopic physical quantities within low pressure air plasmas generated by pulsed X-ray.

  1. Effects of inhibitors of DNA, RNA and protein synthesis on frequencies and types of premature chromosome condensation from X-ray induced micronuclei.

    PubMed

    Madle, S; Nowak, J; Obe, G

    1976-10-28

    Cells containing X-ray induced micronuclei were treated for a few hours before fixation with inhibitors of DNA synthesis (cytosine arabinoside; azathioprine; thymidine; trenimon), of RNA synthesis (actinomycin D; ethidium bromide), and of protein synthesis (puromycin). Only the inhibitors of DNA synthesis lead to a significant suppression of the frequencies of mitoses with micronucleus derived premature chromosome condensation (PCC). We tend to interprete the result as follows: Micronuclei that are in the G1 phase of their cell cycles are accumulated at the G1/S border or in the early S phase of their cell cycles under the influence of the inhibitors of the DNA synthesis. Micronuclei blocked in this way cannot be induced to undergo PCC and seem to disappear from the cells.

  2. Poly(ADP-ribose) polymerase activation mediates synchrotron radiation X-ray-induced damage of rodent testes by exacerbating DNA damage and apoptotic changes.

    PubMed

    Sheng, Caibin; Chen, Heyu; Wang, Ban; Wang, Caixia; Lin, Li; Li, Yexin; Ying, Weihai

    2014-07-01

    Synchrotron radiation (SR) X-ray has great potential for cancer treatment and medical imaging. It is of significance to investigate the mechanisms underlying the effects of SR X-ray irradiation on biological tissues, and search for the strategies for preventing the damaging effects of SR X-ray irradiation on normal tissues. The major aim of our current study is to test our hypothesis that poly(ADP-ribose) polymerase (PARP) plays a significant role in SR X-ray-induced tissue damage. The testes of rodents were pre-treated with PARP inhibitor 3-aminobenzamide (3-AB) or antioxidant N-acetyl-acetylcysteine (NAC), followed by SR X-ray irradiation. PARP activation, double-strand DNA breaks (DSB), Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) signals, caspase-3 activity and weight of the testes were determined. SR X-ray irradiation produced dose-dependent increases in poly(ADP-ribose) (PAR) formation - an index of PARP activation, which can be prevented by NAC administration. Administration of 10 or 20 mg/kg 3-AB attenuated a variety of tissue injury induced by SR X-ray, including caspase-3 activation, increases in TUNEL signals and loss of testical weight. The PARP inhibitor also significantly decreased SR X-ray-induced γ-H2AX signal - a marker of DSB. Our study has provided the first evidence suggesting that SR X-ray can induce PARP activation by generating oxidative stress, which leads to various tissue injuries at least partially by exacerbating DNA damage and apoptotic changes.

  3. Novel applications of diagnostic X-rays in activating a clinical photodynamic drug: Photofrin II through X-ray induced visible luminescence from "rare-earth" formulated particles.

    PubMed

    Abliz, Erkinay; Collins, Joshua E; Bell, Howard; Tata, Darrell B

    2011-01-01

    In this communication we report on a novel non-invasive methodology in utilizing "soft" energy diagnostic X-rays to indirectly activate a photo-agent utilized in photodynamic therapy (PDT): Photofrin II (Photo II) through X-ray induced luminescence from Gadolinium Oxysulfide (20 micron dimension) particles doped with Terbium: Gd_{2}O_{2}S:Tb. Photodynamic agents such as Photo II utilized in PDT possess a remarkable property to become preferentially retained within the tumor's micro-environment. Upon the photo-agent's activation through (visible light) photon absorption, the agents exert their cellular cytotoxicity through type I and type II pathways through extensive generation of reactive oxygen species (ROS); namely, singlet oxygen ^{1}O_{2}, superoxide anion O_{2}^{-}, and hydrogen peroxide H_{2}O_{2}, within the intra-tumoral environment. Unfortunately, due to shallow visible light penetration depth (∼ 2 mm to 5 mm) in tissues, the current PDT strategy has largely been restricted to the treatment of surface tumors, such as the melanomas. Additional invasive strategies through optical fibers are currently utilized in getting the visible light into the intended deep seated targets within the body for PDT. X-ray induced visible luminescence from Gd_{2}O_{2}S:Tb particles were spectroscopically characterized, and the potential in-vitro cellular cytotoxicity of Gd_{2}O_{2}S:Tb particles on human glioblastoma cells (due to 48 Hrs Gd_{2}O_{2}S:Tb particle exposure) was screened through the MTS cellular metabolic assay. In-vitro human glioblastoma cellular exposures in presence of Photo II with Gd_{2}O_{2}S:Tb particles were performed in the dark in sterile 96 well tissue culture plates

  4. Evidence of internucleosomal DNA fragmentation and identification of dying cells in X-ray-induced cell death in the developing brain.

    PubMed

    Ferrer, I; Macaya, A; Blanco, R; Olivé, M; Cinós, C; Munell, F; Planas, A M

    1995-02-01

    Newborn Sprague-Dawley rats received a single dose of 2 Gy X-rays and were killed 6 hr later. Dying cells were characterized by extreme chromatin condensation and nuclear fragmentation. Dying cells were distributed in the primary and secondary germinal zones and in other brain regions. Among these latter, dying cells occurred in the cortical layers of the olfactory bulb, layers II-III and VIb of the neocortex, piriform and entorhinal cortex, stratum oriens and pyramidale of the hippocampus, striatum, thalamus, amygdala, brainstem, internal granular layer of the cerebellum, and cerebral and cerebellar white matter. Dying cells were immature cells, neurons and glial cells (including radial glia). In-situ labeling of nuclear DNA fragmentation identified individual cells bearing fragmented DNA. Since the number of cells stained with this method was larger than the number of dying cells, as revealed with current histological techniques, it is suggested that nuclear DNA fragmentation precedes chromatin condensation and nuclear fragmentation in X-ray-induced apoptosis. Furthermore, agarose gel electrophoresis of extracted DNA from irradiated brains showed a "ladder" pattern which is typical of internucleosomal DNA fragmentation and endonuclease activation.

  5. Mechanisms for dominance: Adh heterodimer formation in heterozygotes between ENU or x-ray induced null alleles and normal alleles in drosophila melanogaster

    SciTech Connect

    Jiang, J.C.; Lee, W.R.; Chang, S.H.; Silverman, H. )

    1992-01-01

    To study mechanisms for dominance of phenotype, eight ENU- and four x-ray-induced mutations at the alcohol dehydrogenase (Adh) locus were analyzed for partial dominance in their interaction with normal alleles. All ENU and one of the x-ray mutations were single base substitutions; the other three x-ray mutations were 9-21 base deletions. All but one of the 12 mutant alleles were selected for this study because they produced detectable mutant polypeptides, but seven of the 11 producing a peptide could not form dimers with the normal peptide and the enzyme activity of heterozygotes was about half that of normal homozygotes. Four mutations formed dimers with a decreased catalytic efficiency and two of these were near the limit of detectability; these two also inhibited the formation of normal homodimers. The mutant alleles therefore show multiple mechanisms leading to partial enzyme expression in heterozygotes and a wide range of dominance ranging from almost complete recessive to nearly dominant. All amino acid changes in mutant peptides that form dimers are located between amino acids 182 and 194, so this region is not critical for dimerization. It may, however, be an important surface domain for catalyzation. 34 refs., 8 figs., 2 tabs.

  6. First glimpse of the soft x-ray induced excited spin-state trapping effect dynamics on spin cross-over molecules

    SciTech Connect

    Davesne, V.; Gruber, M.; Miyamachi, T.; Da Costa, V.; Boukari, S.; Scheurer, F.; Joly, L.; Bowen, M.; Beaurepaire, E.; Ohresser, P.; Otero, E.; Choueikani, F.; Gaspar, A. B.; Real, J. A.; Wulfhekel, W.

    2013-08-21

    The dynamics of the soft x-ray induced excited spin state trapping (SOXIESST) effect of Fe(phen){sub 2}(NCS){sub 2} (Fe-phen) powder have been investigated by x-ray absorption spectroscopy (XAS) using the total electron yield method, in a wide temperature range. The low-spin (LS) state is excited into the metastable high-spin (HS) state at a rate that depends on the intensity of the x-ray illumination it receives, and both the temperature and the intensity of the x-ray illumination will affect the maximum HS proportion that is reached. We find that the SOXIESST HS spin state transforms back to the LS state at a rate that is similar to that found for the light induced excited spin state trapping (LIESST) effect. We show that it is possible to use the SOXIESST effect in combination with the LIESST effect to investigate the influence of cooperative behavior on the dynamics of both effects. To investigate the impact of molecular cooperativity, we compare our results on Fe-phen with those obtained for Fe([Me{sub 2}Pyrz]{sub 3}BH){sub 2} (Fe-pyrz) powder, which exhibits a similar thermal transition temperature but with a hysteresis. We find that, while the time constant of the dynamic is identical for both molecules, the SOXIESST effect is less efficient at exciting the HS state in Fe-pyrz than in Fe-phen.

  7. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies.

    PubMed

    Sutton, Kristin A; Black, Paul J; Mercer, Kermit R; Garman, Elspeth F; Owen, Robin L; Snell, Edward H; Bernhard, William A

    2013-12-01

    Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV-visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5-0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

  8. X-ray-induced DNA double-strand breaks in mouse l1210 cells: a new computational method for analyzing neutral filter elution data.

    PubMed

    Cedervall, Björn; Edgren, Margareta R; Lewensohn, Rolf

    2003-04-01

    The aim of this article is to present a method for studying the shape of the dose and repair responses for X-ray-induced double-strand breaks (DSBs) as measured by neutral filter elution (NFE). The approach is closely related to a method we developed for the use of specific molecular size markers and used for determination of the absolute number of randomly distributed radiation-induced DSBs by pulsed-field gel electrophoresis (PFGE). Mouse leukemia L1210 cells were X-irradiated with 0-50 Gy. Samples were then evaluated both with PFGE and with NFE. Assuming that with both migration (PFGE) and elution (NFE), a heterogeneous population of double-stranded DNA fragments will start with the smallest fragments and proceed with increasingly larger fragments, it is possible to match the migration behavior of fractions of fragments smaller than a certain size to the fraction eluted at a specific time. This assumption does not exclude the possibility of DNA being sheared in the NFE filter. The yield, as determined by the size markers in PFGE, was used to find the corresponding elution times in the NFE experiment. These experimentally used elution times could then reversely be interpreted as size markers which finally were used to calculate DSBs/Mbp as a function of X-ray dose. The resulting lines were almost straight. The data were also plotted as relative elution and showed that, as expected, the dose response then appears with a more pronounced sigmoid shape.

  9. Ultrafast x-ray-induced nuclear dynamics in diatomic molecules using femtosecond x-ray / x-ray pump-probe spectroscopy

    SciTech Connect

    Lehmann, C. S.; Picon, A.; Bostedy, C.; Rudenko, A; Marinelli, A.; Moonshiram, D.; Osipov, T; Rolles, D; Berrah, N; Bomme, C; Bucher, M.; Doumy, G.; Ho, P. J.; Kanter, E.P.; Krassig, B.; March, A. M.; Young, L.; Pratt, S. T.; Southworth, S.H.

    2016-07-26

    The availability at x-ray free electron lasers of generating two intense, femtosecond x-ray pulses with controlled time delay opens the possibility of performing time-resolved experiments for x-ray induced phenomena. We have applied this capability to molecular dynamics. In diatomic molecules composed of low-Z elements, K-shell ionization creates a core-hole state in which the main decay is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wavepackets of the transient two-valence-hole states continue evolving on the femtosecond timescale, leading either to separated atomic ions or long-lived quasi-bound states. By using an x-ray pump and an x-ray probe pulse tuned above the K-shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K-shell ionization, Auger decay, and time evolution of the nuclear wavepackets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasi-bound states.

  10. Multistep nature of X-ray-induced neoplastic transformation in golden hamster embryo cells: expression of transformed phenotypes and stepwise changes in karyotypes

    SciTech Connect

    Suzuki, K.; Suzuki, F.; Watanabe, M.; Nikaido, O.

    1989-04-15

    We have examined the expression of transformed phenotypes and genetic changes associated with the expression of each transformed phenotype after X-ray irradiation. Unirradiated cells grown at a constant growth rate until 8 passages (population doubling number, 15) exhibited little morphological change and ceased to divide thereafter. X-irradiated cells escaped from senescence and showed morphological alteration and anchorage independence after a population doubling number of 20. The acquisition of tumorigenicity in nude mice was observed much later (35 population doublings after irradiation). From cytogenetic analysis, all anchorage-independent clones were consistently found to have trisomy of chromosome 7. Furthermore, cells derived from tumors contained three copies of chromosome 9q in addition to the trisomy of chromosome 7. We have not detected any augmented expression of v-Ha-ras- and v-myc-related oncogenes with RNA dot-blot analysis and could not find activation of any type of oncogenes by NIH3T3 transfection experiments. Our studies demonstrated that X-ray-induced neoplastic transformation is a multistep phenomenon and that the numerical change of specific chromosomes may play an important role in the expression of each transformed phenotype. The results suggest that different endogenous oncogenes, other than the ras gene family and myc oncogene, could be responsible for the progressive nature of neoplastic transformation.

  11. Study on X-ray-induced apoptosis and chromosomal damage in G2 human lymphocytes in the presence of pifithrin-α, an inhibitor of p53.

    PubMed

    Ortenzi, Vincenza; Meschini, Roberta; Berni, Andrea; Mancinelli, Pierluigi; Palitti, Fabrizio

    2011-11-27

    The aim of this study is to investigate the role of the cell-cycle phase in cells exposed to radiation and chemicals in relation to the cellular response. The analysis was focused on the G2 cell-cycle phase, exploring the impact of p53 inhibition in human lymphocytes irradiated with X-rays in the presence or absence of pifithrin-α (PFT-α), a p53-specific inhibitor. Lymphocytes, 44h after stimulation to proliferate, were X-irradiated with 0.5Gy both in the presence or the absence of PFT-α and post-treated with a pulse of 5-bromodeoxyuridine (BrdUrd) to distinguish cells in the S- or G2-phase at the moment of irradiation. At early sampling times after X-ray exposure the following parameters were analysed: cellular proliferation, apoptosis, chromosomal aberrations and p53 expression. The results show an enhancement of apoptotic cells in G2 at early sampling times after irradiation and no differences in terms of chromosomal aberration induction both in cells treated with X-rays alone and in cells treated with X-rays plus PFT-α. Expression of p53 was not detectable at all recovery times. The results suggest a p53-independent apoptotic pathway acting at early times after X-ray exposure in G2 lymphocytes. Furthermore, the same yield of X-ray-induced chromatid breaks was observed both in the presence or absence of PFT-α implying that in G2 X-irradiated lymphocytes this inhibitor of the p53 protein does not affect DNA repair.

  12. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states

    PubMed Central

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-01-01

    During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an F o − F c map for Glu451a O∊2 indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth-MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth-MCO-C1–8) with different X-ray-absorbed doses allowed the observation of different O2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure. PMID:26627648

  13. Differential sensitivity of a mouse myeloid leukemia cell line and normal mouse bone marrow cells to X-ray-induced chromosome aberrations

    SciTech Connect

    Aardema, M.J.; Au, W.W.; Hand, R.E. Jr.; Preston, R.J.

    1985-11-01

    Cell line ML-1 was established from a myelogenous leukemia of an RFM mouse. The ML-1 cells and in vitro normal mouse bone marrow cells were analyzed to determine if there was a differential sensitivity to X-ray-induced chromosome aberrations in G1 cells and/or differences in postirradiation cell cycle progression. Cells identified as being in G1 at the time of irradiation by their staining pattern after replication in 5-bromodeoxyuridine were analyzed for all types of chromosomal aberrations following X-ray doses of 0.5, 1.0, 1.5, and 2.0 Gy. ML-1 cells showed a greater sensitivity to the induction of both chromosome-type aberrations and chromatid-type aberrations compared to normal mouse bone marrow cells, which only contained chromosome-type aberrations. The presence of chromatid-type aberrations in the ML-1 cells and not normal bone marrow cells suggested a differential progression through the cell cycle for the two cell types after irradiation. Mitotic index and flow cytometric analyses were performed and showed that both cell types have a delay in progression from G2 into mitosis, but only the normal mouse bone marrow cells have a delay in progression from G1 into S, as well as delayed progression through the S phase following X-irradiation. These results indicate that the ML-1 leukemia cells have an increased radiosensitivity. These same characteristics have been observed in ataxia telangiectasia cells and may well represent a general feature of cells with increased radiosensitivity.

  14. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

    PubMed

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-12-01

    During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an Fo - Fc map for Glu451a O(ℇ2) indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth-MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth-MCO-C1-8) with different X-ray-absorbed doses allowed the observation of different O2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.

  15. Electronic structure studies of Ni-X (X: B, S, P) alloys using x-ray photoelectron spectroscopy, x-ray induced Auger electron spectroscopy and density functional theory calculations.

    PubMed

    Diplas, S; Løvvik, O M

    2009-06-17

    The electronic structure of Ni-X (X = B, S, P) alloys was studied using x-ray photoelectron spectroscopy, x-ray induced Auger electron spectroscopy and density functional theory. The spectroscopic data in the form of the Ni 2p shake-up satellite and the Ni 2p LMM, P 2p KLL and S 2p KLL Auger parameters combined with density of states (DOS) and charge difference plots suggest an overall charge transfer from the Ni sites towards the alloying addition sites. However, this is masked, with intra-atomic charge redistribution leading to an increased occupancy of the Ni 3d states in the alloys. The Ni 3d DOS shows strong similarity to that of Pt which is the best catalyst for hydrogen evolution.

  16. Electronic structure and soft-X-ray-induced photoreduction studies of iron-based magnetic polyoxometalates of type {(M)M5}12Fe(III)30 (M = Mo(VI), W(VI)).

    PubMed

    Kuepper, Karsten; Derks, Christine; Taubitz, Christian; Prinz, Manuel; Joly, Loïc; Kappler, Jean-Paul; Postnikov, Andrei; Yang, Wanli; Kuznetsova, Tatyana V; Wiedwald, Ulf; Ziemann, Paul; Neumann, Manfred

    2013-06-14

    Giant Keplerate-type molecules with a {Mo72Fe30} core show a number of very interesting properties, making them particularly promising for various applications. So far, only limited data on the electronic structure of these molecules from X-ray spectra and electronic structure calculations have been available. Here we present a combined electronic and magnetic structure study of three Keplerate-type nanospheres--two with a {Mo72Fe30} core and one with a {W72Fe30} core by means of X-ray absorption spectroscopy, X-ray magnetic circular dichroism (XMCD), SQUID magnetometry, and complementary theoretical approaches. Furthermore, we present detailed studies of the Fe(3+)-to-Fe(2+) photoreduction process, which is induced under soft X-ray radiation in these molecules. We observe that the photoreduction rate greatly depends on the ligand structure surrounding the Fe ions, with negatively charged ligands leading to a dramatically reduced photoreduction rate. This opens the possibility of tailoring such polyoxometalates by X-ray spectroscopic studies and also for potential applications in the field of X-ray induced photochemistry.

  17. Continuous-time photon-stimulated desorption spectroscopy studies on soft x-ray-induced reactions of CF{sub 3}Br adsorbed on Si(111)-7x7

    SciTech Connect

    Tsai, W.-C.; Wang, S.-K.; He, T.-M.; Chou, L.-C.; Hsieh, Y.-C.; Liao, K.-Y.; Chen, H.-C.; Wen, C.-R.

    2011-10-28

    Continuous-time core-level photon-stimulated desorption (PSD) spectroscopy was used to study the soft x-ray-induced reactions of CF{sub 3}Br molecules adsorbed on Si(111)-7x7 near the Si(2p) edge (98-110 eV). The monochromatic synchrotron radiation was employed as a soft x-ray light source in the photon-induced reactions and also as a probe for investigating the produced fluorination states of the bonding surface Si atom in the positive-ion PSD spectroscopy. Several different surface coverages were investigated. The PSD spectra from the low-CF{sub 3}Br-covered surfaces show the production of surface SiF species, while those from the high-CF{sub 3}Br-covered surfaces depict the formation of surface SiF, SiF{sub 2}, and SiF{sub 3} species. The photolysis cross section of the submonolayer CF{sub 3}Br-covered surface is determined as {approx}4.3x10{sup -18} cm{sup 2}. A comparison with the results on CF{sub 3}Cl/Si(111)-7x7 surface is discussed.

  18. Application of PIXE, RBS and high energy proton microbeams to the elemental analysis of coal and coal waste. [Proton and x-ray induced x-ray emission and Rutherford backscattering

    SciTech Connect

    Kraner, H.W.; Hanson, A.L.; Jones, K.W.; Oakley, S.A.; Duedall, I.W.; Woodhead, P.M.J.

    1980-01-01

    Proton and x-ray induced x-ray emission have proved to be sensitive and convenient methods to measure major trace element concentrations in bulk quantities of coal and coal waste materials. These techniques are complementary in their sensitivities as a function of atomic number, and both require little sample preparation. The PIXE measurements were made with the proton beam in air in a microprobe configuration. Collimated proton beam scans were made on several thin sections of fly ash/sludge block materials and good trace sensitivities were observed for small specific volumes; SEM scans showed a high degree of material homogeneity which precluded significant elemental variations at the approx. 100 ..mu..m spatial resolution used. Rutherford backscattering was used to directly observe major and minor elemental concentrations in coal waste materials and in several representative ranks of coals. RBS is useful for only trace concentrations of heavy elements, but it does provide a method independent of fluoresced x rays for detection of possible middle Z interferences. Arsenic, present in trace amounts in coal, is an element of concern and is enriched in fly ash. The form of As in fly ash is unknown. However, because of its volatility most of the As probably becomes attached to the surfaces of the fly ash particles during and subsequent to combustion processes. This view is supported by the fact that As is rapidly mobilized in aqueous solutions whose pH > 9.

  19. X-ray induced Sm{sup 3+} to Sm{sup 2+} conversion in fluorophosphate and fluoroaluminate glasses for the monitoring of high-doses in microbeam radiation therapy

    SciTech Connect

    Vahedi, Shahrzad; Okada, Go; Morrell, Brian; Muzar, Edward; Koughia, Cyril; Kasap, Safa; Edgar, Andy; Varoy, Chris; Belev, George; Wysokinski, Tomasz; Chapman, Dean

    2012-10-01

    Fluorophosphate and fluoroaluminate glasses doped with trivalent samarium were evaluated as sensors of x-ray radiation for microbeam radiation therapy at the Canadian Light Source using the conversion of trivalent Sm{sup 3+} to the divalent form Sm{sup 2+}. Both types of glasses show similar conversion rates and may be used as a linear sensor up to {approx}150 Gy and as a nonlinear sensor up to {approx}2400 Gy, where saturation is reached. Experiments with a multi-slit collimator show high spatial resolution of the conversion pattern; the pattern was acquired by a confocal fluorescence microscopy technique. The effects of previous x-ray exposure may be erased by annealing at temperatures exceeding the glass transition temperature T{sub g} while annealing at T{sub A} < T{sub g} enhances the Sm conversion. This enhancement is explained by a thermally stimulated relaxation of host glass ionic matrix surrounding x-ray induced Sm{sup 2+} ions. In addition, some of the Sm{sup 3+}-doped glasses were codoped with Eu{sup 2+}-ions but the results show that there is no marked improvement in the conversion efficiency by the introduction of Eu{sup 2+}.

  20. X-ray induced optical reflectivity

    NASA Astrophysics Data System (ADS)

    Durbin, Stephen M.

    2012-12-01

    The change in optical reflectivity induced by intense x-ray pulses can now be used to study ultrafast many body responses in solids in the femtosecond time domain. X-ray absorption creates photoelectrons and core level holes subsequently filled by Auger or fluorescence processes, and these excitations ultimately add conduction and valence band carriers that perturb optical reflectivity. Optical absorption associated with band filling and band gap narrowing is shown to explain the basic features found in recent measurements on an insulator (silicon nitride, Si3N4), a semiconductor (gallium arsenide, GaAs), and a metal (gold, Au), obtained with ˜100 fs x-ray pulses at 500-2000 eV and probed with 800 nm laser pulses. In particular GaAs exhibits an abrupt drop in reflectivity, persisting only for a time comparable to the x-ray excitation pulse duration, consistent with prompt band gap narrowing.

  1. Initial experimental demonstration of the principles of a xenon gas shield designed to protect optical components from soft x-ray induced opacity (blanking) in high energy density experiments

    DOE PAGES

    Swadling, G. F.; Ross, J. S.; Manha, D.; ...

    2017-03-16

    The design principles of a xenon gas shield device that is intended to protect optical components from x-ray induced opacity (“x-ray blanking”) have been experimentally demonstrated at the OMEGA-60 Laser Facility at the Laboratory for Laser Energetics, University of Rochester. A volume of xenon gas placed in front of an optical component absorbs the incoming soft x-ray radiation but transmits optical and ultra-violet radiation. The time-resolved optical (532 nm) transmission of samples was recorded as they were exposed to soft x-rays produced by a gold sphere source (1.5 kJ sr$-$1, 250–300 eV). Blanking of fused silica (SiO2) was measured tomore » occur over a range of time-integrated soft x-ray (<3 keV) fluence from ~0.2–2.5 J cm$-$2. A shield test device consisting of a 30 nm silicon nitride (Si3N4) and a 10 cm long volume of 0.04 bar xenon gas succeeded in delaying loss of transmission through a magnesium fluoride sample; optical transmission was observed over a longer period than for the unprotected sample. It is hoped that the design of this x-ray shield can be scaled in order to produce a shield device for the National Ignition Facility optical Thomson scattering collection telescope, in order to allow measurements of hohlraum plasma conditions produced in inertial confinement fusion experiments. Finally, if successful, it will also have applications in many other high energy density experiments where optical and ultra-violet measurements are desirable.« less

  2. Initial experimental demonstration of the principles of a xenon gas shield designed to protect optical components from soft x-ray induced opacity (blanking) in high energy density experiments

    NASA Astrophysics Data System (ADS)

    Swadling, G. F.; Ross, J. S.; Manha, D.; Galbraith, J.; Datte, P.; Sorce, C.; Katz, J.; Froula, D. H.; Widmann, K.; Jones, O. S.; Divol, L.; Landen, O. L.; Kilkenny, J. D.; Moody, J. D.

    2017-03-01

    The design principles of a xenon gas shield device that is intended to protect optical components from x-ray induced opacity ("x-ray blanking") have been experimentally demonstrated at the OMEGA-60 Laser Facility at the Laboratory for Laser Energetics, University of Rochester. A volume of xenon gas placed in front of an optical component absorbs the incoming soft x-ray radiation but transmits optical and ultra-violet radiation. The time-resolved optical (532 nm) transmission of samples was recorded as they were exposed to soft x-rays produced by a gold sphere source (1.5 kJ sr-1, 250-300 eV). Blanking of fused silica (SiO2) was measured to occur over a range of time-integrated soft x-ray (<3 keV) fluence from ˜0.2-2.5 J cm-2. A shield test device consisting of a 30 nm silicon nitride (Si3N4) and a 10 cm long volume of 0.04 bar xenon gas succeeded in delaying loss of transmission through a magnesium fluoride sample; optical transmission was observed over a longer period than for the unprotected sample. It is hoped that the design of this x-ray shield can be scaled in order to produce a shield device for the National Ignition Facility optical Thomson scattering collection telescope, in order to allow measurements of hohlraum plasma conditions produced in inertial confinement fusion experiments. If successful, it will also have applications in many other high energy density experiments where optical and ultra-violet measurements are desirable.

  3. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2 -reduction states

    SciTech Connect

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-11-26

    During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth -MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (~7 Å from the TNC) and Glu451b (~4.5 Å from the TNC). A positive peak of electron density above 3.5σ in anFo-Fc map for Glu451a Oε2 indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth -MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth -MCO-C1–8) with different X-ray-absorbed doses allowed the observation of different O2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.

  4. Reduction of X-ray induced DNA double-strand breaks in blood lymphocytes during coronary CT angiography using high-pitch spiral data acquisition with prospective ECG-triggering.

    PubMed

    Kuefner, Michael A; Hinkmann, Fabian M; Alibek, Sedat; Azoulay, Sascha; Anders, Katharina; Kalender, Willi A; Achenbach, Stephan; Grudzenski, Saskia; Löbrich, Markus; Uder, Michael

    2010-04-01

    Purpose of this study was to compare the effect of high-pitch spiral data acquisition with prospective electrocardiography (ECG)-triggering on the x-ray induced DNA damages to blood lymphocytes with commonly used low-pitch spiral scans. Thirty four patients underwent coronary computed tomography angiography either using high-pitch spiral data acquisition (n = 15; dual-source computed tomography (CT) scanner, 38.4 mm collimation, 100-120 kV, 320-456 mAs/rotation, pitch value 3.2-3.4) or using a low-pitch protocol (n = 19; dual-source CT scanner, 19.2 mm collimation, 120 kV, 330-438 mAs/rotation, pitch 0.2-0.39, ECG-based tube current modulation). Blood samples were obtained before and 30 minutes after CT. Lymphocytes were isolated, stained against the phosphorylated histone variant gammaH2AX, and DNA double-strand breaks (DSBs) were visualized using fluorescence microscopy. Radiation dose to the blood was estimated by relating in vivo DSB levels to values of in vitro irradiated blood samples (50 mGy). Dose length product was registered as provided by the patient protocol. Total dose length product ranged from 101 to 237 (median 112) mGy cm in high-pitch and from 524 to 1283 (median 1025) mGy cm in low-pitch scans (P < 0.0001). The median CT induced DSB level 30 minutes after exposure was significantly lower after high-pitch (0.04 DSBs/cell, range 0.02-0.10 DSBs/cell) compared with low-pitch scans (0.39 DSBs/cell, 0.22-0.71 DSBs/cell, P < 0.0001). Both DSB levels and radiation dose to the blood showed a significant correlation to the dose length product (r = 0.82, P < 0.0001). The radiation dose to the blood was significantly reduced in the high-pitch (median 3.1, range 2.0-8.1 mGy) compared with the low-pitch group (median 26.9; range 14.2-44.9 mGy, P < 0.0001). Prospectively ECG-triggered high-pitch spiral data acquisition can considerably reduce the radiation dose to the blood in coronary CT angiography as compared with low pitch protocols.

  5. Species-specific polyamines from diatoms control silica morphology

    PubMed Central

    Kröger, Nils; Deutzmann, Rainer; Bergsdorf, Christian; Sumper, Manfred

    2000-01-01

    Biomineralizing organisms use organic molecules to generate species-specific mineral patterns. Here, we describe the chemical structure of long-chain polyamines (up to 20 repeated units), which represent the main organic constituent of diatom biosilica. These substances are the longest polyamine chains found in nature and induce rapid silica precipitation from a silicic acid solution. Each diatom is equipped with a species-specific set of polyamines and silica-precipitating proteins, which are termed silaffins. Different morphologies of precipitating silica can be generated by polyamines of different chain lengths as well as by a synergistic action of long-chain polyamines and silaffins. PMID:11106386

  6. Developmental Origins of Species-Specific Muscle Pattern

    PubMed Central

    Tokita, Masayoshi; Schneider, Richard A.

    2009-01-01

    Vertebrate jaw muscle anatomy is conspicuously diverse but developmental processes that generate such variation remain relatively obscure. To identify mechanisms that produce species-specific jaw muscle pattern we conducted transplant experiments using Japanese quail and White Pekin duck, which exhibit considerably different jaw morphologies in association with their particular modes of feeding. Previous work indicates that cranial muscle formation requires interactions with adjacent skeletal and muscular connective tissues, which arise from neural crest mesenchyme. We transplanted neural crest mesenchyme from quail to duck embryos, to test if quail donor-derived skeletal and muscular connective tissues could confer species-specific identity to duck host jaw muscles. Our results show that duck host jaw muscles acquire quail-like shape and attachment sites due to the presence of quail donor neural crest-derived skeletal and muscular connective tissues. Further, we find that these species-specific transformations are preceded by spatiotemporal changes in expression of genes within skeletal and muscular connective tissues including Sox9, Runx2, Scx, and Tcf4, but not by alterations to histogenic or molecular programs underlying muscle differentiation or specification. Thus, neural crest mesenchyme plays an essential role in generating species-specific jaw muscle pattern and in promoting structural and functional integration of the musculoskeletal system during evolution. PMID:19450573

  7. Species-specific toxicity of ceria nanoparticles to Lactuca plants.

    PubMed

    Zhang, Peng; Ma, Yuhui; Zhang, Zhiyong; He, Xiao; Li, Yuanyuan; Zhang, Jing; Zheng, Lirong; Zhao, Yuliang

    2015-02-01

    Species-specific differences in the toxicity of manufactured nanoparticles (MNPs) have been reported, but the underlying mechanisms are unknown. We previously found that CeO2 NPs inhibited root elongation of head lettuce, whereas no toxic effect was observed on other plants (such as wheat, cucumber and radish). In this study, interactions between Lactuca plants and three types of CeO2 NPs (lab-synthesized 7 and 25 nm CeO2 NPs, and a commercial CeO2 NPs) were investigated. It was found that CeO2 NPs were toxic to three kinds of Lactuca genus plants and different CeO2 NPs showed different degrees of toxicity. The results of X-ray absorption near edge fine structure indicate that small parts of CeO2 NPs were transformed from Ce(IV) to Ce(III) in roots of the plants that were treated with CeO2 NPs during the seed germination stage. But the high sensitivity of Lactuca plants to the released Ce(3+) ions caused the species-specific phytotoxicity of CeO2 NPs. Differences in sizes and zeta potentials among three types of CeO2 NPs resulted in their different degrees of biotransformation which accounted for the discrepancy in the toxicity to Lactuca plants. This study is among the few, and may indeed the first, that addresses the relation between the physicochemical properties of nanoparticles and its species-specific phytotoxicity.

  8. Species-Specific Cuticular Hydrocarbon Stability within European Myrmica Ants.

    PubMed

    Guillem, Rhian M; Drijfhout, Falko P; Martin, Stephen J

    2016-10-01

    Recognition is a fundamental process on which all subsequent behaviors are based at every organizational level, from the gene up to the super-organism. At the whole organism level, visual recognition is the best understood. However, chemical communication is far more widespread than visual communication, but despite its importance is much less understood. Ants provide an excellent model system for chemical ecology studies as it is well established that compounds known as cuticular hydrocarbons (CHCs) are used as recognition cues in ants. Therefore, stable species-specific odors should exist, irrespective of geographic locality. We tested this hypothesis by comparing the CHC profiles of workers of twelve species of Myrmica ants from four countries across Europe, from Iberia to the Balkans and from the Mediterranean to Fennoscandia. CHCs remained qualitatively stable within each species, right down to the isomer level. Despite the morphological similarity that occurs within the genus Myrmica, their CHCs were highly diverse but remarkably species-specific and stable across wide geographical areas. This indicates a genetic mechanism under strong selection that produces these species-specific chemical profiles, despite each species encountering different environmental conditions across its range.

  9. Species specificity of symbiosis and secondary metabolism in ascidians

    PubMed Central

    Tianero, Ma Diarey B; Kwan, Jason C; Wyche, Thomas P; Presson, Angela P; Koch, Michael; Barrows, Louis R; Bugni, Tim S; Schmidt, Eric W

    2015-01-01

    Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these ‘chemical symbioses'. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R=−0.037, P-value=0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and

  10. Species-specific protein sequence and fold optimizations

    PubMed Central

    Dumontier, Michel; Michalickova, Katerina; Hogue, Christopher WV

    2002-01-01

    Background An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to identify and exploit the amino-acid signatures that make species-specific protein adaptation possible across 100 complete genomes. Results Environmental niche was determined to be a significant factor in variability from correspondence analysis using the amino acid composition of over 360,000 predicted open reading frames (ORFs) from 17 archae, 76 bacteria and 7 eukaryote complete genomes. Additionally, we found clusters of phylogenetically unrelated archae and bacteria that share similar environments by amino acid composition clustering. Composition analyses of conservative, domain-based homology modeling suggested an enrichment of small hydrophobic residues Ala, Gly, Val and charged residues Asp, Glu, His and Arg across all genomes. However, larger aromatic residues Phe, Trp and Tyr are reduced in folds, and these results were not affected by low complexity biases. We derived two simple log-odds scoring functions from ORFs (CG) and folds (CF) for each of the complete genomes. CF achieved an average cross-validation success rate of 85 ± 8% whereas the CG detected 73 ± 9% species-specific sequences when competing against all other non-redundant CG. Continuously updated results are available at . Conclusion Our analysis of amino acid compositions from the complete genomes provides stronger evidence for species-specific and environmental residue preferences in genomic sequences as well as in folds. Scoring functions derived from this work will be useful in future protein engineering experiments and possibly in identifying horizontal transfer events. PMID:12487631

  11. Species specificity of symbiosis and secondary metabolism in ascidians.

    PubMed

    Tianero, Ma Diarey B; Kwan, Jason C; Wyche, Thomas P; Presson, Angela P; Koch, Michael; Barrows, Louis R; Bugni, Tim S; Schmidt, Eric W

    2015-03-01

    Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these 'chemical symbioses'. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R=-0.037, P-value=0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and

  12. Can Hyperspectral Remote Sensing Detect Species Specific Biochemicals ?

    NASA Astrophysics Data System (ADS)

    Vanderbilt, V. C.; Daughtry, C. S.

    2011-12-01

    Discrimination of a few plants scattered among many plants is a goal common to detection of agricultural weeds, invasive plant species and illegal Cannabis clandestinely grown outdoors, the subject of this research. Remote sensing technology provides an automated, computer based, land cover classification capability that holds promise for improving upon the existing approaches to Cannabis detection. In this research, we investigated whether hyperspectral reflectance of recently harvested, fully turgid Cannabis leaves and buds depends upon the concentration of the psychoactive ingredient Tetrahydrocannabinol (THC) that, if present at sufficient concentration, presumably would allow species-specific identification of Cannabis.

  13. OXA-258 from Achromobacter ruhlandii: a species-specific marker.

    PubMed

    Papalia, Mariana; Almuzara, Marisa; Cejas, Daniela; Traglia, German; Ramírez, Maria Soledad; Galanternik, Laura; Vay, Carlos; Gutkind, Gabriel; Radice, Marcela

    2013-05-01

    A new blaOXA-258 gene is described as a species-specific taxonomic marker for Achromobacter ruhlandii isolates (all recovered from cystic fibrosis patients). Even though OXA-258 differs from OXA-114 variants, isolates could be misidentified as A. xiloxosidans by the amplification of an inner fragment from the OXA-coding gene. A robust identification of A. ruhlandii can be achieved by sequencing this single OXA gene, as well as by a more laborious recently proposed multilocus sequence-typing (MLST) scheme.

  14. OXA-258 from Achromobacter ruhlandii: a Species-Specific Marker

    PubMed Central

    Papalia, Mariana; Almuzara, Marisa; Cejas, Daniela; Traglia, German; Ramírez, Maria Soledad; Galanternik, Laura; Vay, Carlos; Radice, Marcela

    2013-01-01

    A new blaOXA-258 gene is described as a species-specific taxonomic marker for Achromobacter ruhlandii isolates (all recovered from cystic fibrosis patients). Even though OXA-258 differs from OXA-114 variants, isolates could be misidentified as A. xiloxosidans by the amplification of an inner fragment from the OXA-coding gene. A robust identification of A. ruhlandii can be achieved by sequencing this single OXA gene, as well as by a more laborious recently proposed multilocus sequence-typing (MLST) scheme. PMID:23467601

  15. Site- and species-specific hydrolysis rates of heroin.

    PubMed

    Szöcs, Levente; Orgován, Gábor; Tóth, Gergő; Kraszni, Márta; Gergó, Lajos; Hosztafi, Sándor; Noszál, Béla

    2016-06-30

    The hydroxide-catalyzed non-enzymatic, simultaneous and consecutive hydrolyses of diacetylmorphine (DAM, heroin) are quantified in terms of 10 site- and species-specific rate constants in connection with also 10 site- and species-specific acid-base equilibrium constants, comprising all the 12 coexisting species in solution. This characterization involves the major and minor decomposition pathways via 6-acetylmorphine and 3-acetylmorphine, respectively, and morphine, the final product. Hydrolysis has been found to be 18-120 times faster at site 3 than at site 6, depending on the status of the amino group and the rest of the molecule. Nitrogen protonation accelerates the hydrolysis 5-6 times at site 3 and slightly less at site 6. Hydrolysis rate constants are interpreted in terms of intramolecular inductive effects and the concomitant local electron densities. Hydrolysis fraction, a new physico-chemical parameter is introduced and determined to quantify the contribution of the individual microspecies to the overall hydrolysis. Hydrolysis fractions are depicted as a function of pH.

  16. Are temperate canopy spiders tree-species specific?

    PubMed

    Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

    2014-01-01

    Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.

  17. Are Temperate Canopy Spiders Tree-Species Specific?

    PubMed Central

    Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

    2014-01-01

    Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood. PMID:24586251

  18. A small molecule species specifically inhibits Fusarium myosin I.

    PubMed

    Zhang, Chengqi; Chen, Yun; Yin, Yanni; Ji, Huan-Hong; Shim, Won-Bo; Hou, Yiping; Zhou, Mingguo; Li, Xiang-Dong; Ma, Zhonghua

    2015-08-01

    Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease of cereal crops worldwide. Recently, a novel fungicide JS399-19 has been launched into the marketplace to manage FHB. It is compelling that JS399-19 shows highly inhibitory activity towards some Fusarium species, but not to other fungi, indicating that it is an environmentally compatible fungicide. To explore the mode of action of this species-specific compound, we conducted a whole-genome transcript profiling together with genetic and biochemical assays, and discovered that JS399-19 targets the myosin I of F. graminearum (FgMyo1). FgMyo1 is essential for F. graminearum growth. A point mutation S217L or E420K in FgMyo1 is responsible for F. graminearum resistance to JS399-19. In addition, transformation of F. graminearum with the myosin I gene of Magnaporthe grisea, the causal agent of rice blast, also led to JS399-19 resistance. JS399-19 strongly inhibits the ATPase activity of the wild-type FgMyo1, but not the mutated FgMyo1(S217L/E420K) . These results provide us a new insight into the design of species-specific antifungal compounds. Furthermore, our strategy can be applied to identify novel drug targets in various pathogenic organisms. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Halal authenticity of gelatin using species-specific PCR.

    PubMed

    Shabani, Hessam; Mehdizadeh, Mehrangiz; Mousavi, Seyed Mohammad; Dezfouli, Ehsan Ansari; Solgi, Tara; Khodaverdi, Mahdi; Rabiei, Maryam; Rastegar, Hossein; Alebouyeh, Mahmoud

    2015-10-01

    Consumption of food products derived from porcine sources is strictly prohibited in Islam. Gelatin, mostly derived from bovine and porcine sources, has many applications in the food and pharmaceutical industries. To ensure that food products comply with halal regulations, development of valid and reliable analytical methods is very much required. In this study, a species-specific polymerase chain reaction (PCR) assay using conserved regions of mitochondrial DNA (cytochrome b gene) was performed to evaluate the halal authenticity of gelatin. After isolation of DNA from gelatin powders with known origin, conventional PCR using species-specific primers was carried out on the extracted DNA. The amplified expected PCR products of 212 and 271 bp were observed for porcine and bovine gelatin, respectively. The sensitivity of the method was tested on binary gelatin mixtures containing 0.1%, 1%, 10%, and 100% (w/w) of porcine gelatin within bovine gelatin and vice versa. Although most of the DNA is degraded due to the severe processing steps of gelatin production, the minimum level of 0.1% w/w of both porcine and bovine gelatin was detected. Moreover, eight food products labeled as containing bovine gelatin and eight capsule shells were subjected to PCR examination. The results showed that all samples contained bovine gelatin, and the absence of porcine gelatin was verified. This method of species authenticity is very useful to verify whether gelatin and gelatin-containing food products are derived from halal ingredients. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Species-Specific Associations Between Bacterioplankton and Photosynthetic Picoeukaryotes

    NASA Astrophysics Data System (ADS)

    Farnelid, H.; Turk-Kubo, K.; Zehr, J. P.

    2016-02-01

    Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Interactions between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. Currently, partly due to methodological difficulties for studying microbial associations in situ, these ecological interactions are poorly characterized. Here we use flow cytometry sorting to identify novel bacterial phylotypes found in physical association with photosynthetic picoeukaryotes. Samples were collected on eight occasions at the Santa Cruz wharf on Monterey Bay during summer and fall, 2014. The phylogeny of associated microbes was assessed through clone libraries and Illumina MiSeq sequencing of amplicons of the 16S rRNA gene. In addition, 16 bacterial isolates comprised of 14 taxa were obtained from sorted photosynthetic picoeukaryote cells. The most frequently detected bacterioplankton phyla were Alphaproteobacteria, Bacteriodetes, and Gammaproteobacteria. The sequences from the sorted populations were a community distinct from the unsorted seawater samples suggesting species-specific functional associations. These species-specific patterns were further supported by re-occurring patterns between replicates and sampling dates. The finding of sequences from the free-living genera Synechococcus and Pelagibacter also suggest that photosynthetic picoeukaryotes can be bacterivores, possibly feeding on some of the most numerically abundant bacteria. The results show that specific bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing the interactions, their metabolic pathways and ecological functions.

  1. Alternative strategies for toxicity testing of species-specific biopharmaceuticals.

    PubMed

    Bussiere, Jeanine L; Martin, Pauline; Horner, Michelle; Couch, Jessica; Flaherty, Meghan; Andrews, Laura; Beyer, Joseph; Horvath, Christopher

    2009-01-01

    Although toxicology studies should always be conducted in pharmacologically relevant species, the specificity of many biopharmaceuticals can present challenges in identification of a relevant species. In certain cases, that is, when the clinical product is active only in humans or chimpanzees, or if the clinical candidate is active in other species but immunogenicity limits the ability to conduct a thorough safety assessment, alternative approaches to evaluating the safety of a biopharmaceutical must be considered. Alternative approaches, including animal models of disease, genetically modified mice, or use of surrogate molecules, may improve the predictive value of preclinical safety assessments of species-specific biopharmaceuticals, although many caveats associated with these models must be considered. Because of the many caveats that are discussed in this article, alternative approaches should only be used to evaluate safety when the clinical candidate cannot be readily tested in at least one relevant species to identify potential hazards.

  2. Species-specific bioluminescence facilitates speciation in the deep sea.

    PubMed

    Davis, Matthew P; Holcroft, Nancy I; Wiley, Edward O; Sparks, John S; Leo Smith, W

    2014-01-01

    The vast darkness of the deep sea is an environment with few obvious genetic isolating barriers, and little is known regarding the macroevolutionary processes that have shaped present-day biodiversity in this habitat. Bioluminescence, the production and emission of light from a living organism through a chemical reaction, is thought to occur in approximately 80 % of the eukaryotic life that inhabits the deep sea (water depth greater than 200 m). In this study, we show, for the first time, that deep-sea fishes that possess species-specific bioluminescent structures (e.g., lanternfishes, dragonfishes) are diversifying into new species at a more rapid rate than deep-sea fishes that utilize bioluminescence in ways that would not promote isolation of populations (e.g., camouflage, predation). This work adds to our understanding of how life thrives and evolution shaped present-day biodiversity in the deep sea, the largest and arguably least explored habitat on earth.

  3. Requirements for species-specific papovavirus DNA replication.

    PubMed Central

    Bennett, E R; Naujokas, M; Hassell, J A

    1989-01-01

    Replication of papovavirus DNA requires a functional replication origin, a virus-encoded protein, large T antigen, and species-specific permissive factors. How these components interact to initiate and sustain viral DNA replication is not known. Toward that end, we have attempted to identify the viral target(s) of permissive factors. The functionally defined replication origins of polyomavirus and simian virus 40, two papovaviruses that replicate in different species (mice and monkeys, respectively), are composed of two functionally distinct domains: a core domain and an auxiliary domain. The origin cores of the two viruses are remarkably similar in primary structure and have common binding sites for large T antigen. By contrast, their auxiliary domains share few sequences and serve as binding sites for cellular proteins. It seemed plausible, therefore, that if cellular permissive factors interacted with the replication origin, their targets were likely to be in the auxiliary domain. To test this hypothesis we constructed hybrid origins for DNA replication that were composed of the auxiliary domain of one virus and the origin core of the other and assessed their capacity to replicate in a number of mouse and monkey cell lines, which express the large T antigen of one or the other virus. The results of this analysis showed that the auxiliary domains of the viral replication origins could substitute for one another in DNA replication, provided that the viral origin core and its cognate large T antigen were present in a permissive cellular milieu. Surprisingly, the large T antigens of the viruses could not substitute for one another, regardless of the species of origin of the host cell, even though the two large T antigens bind to the same sequence motif in vitro. These results suggest that species-specific permissive factors do not interact with the origin-auxiliary domains but, rather, with either the origin core or the large T antigen or with both components to

  4. Dating human bone: is racemization dating species-specific?

    PubMed

    Moini, Mehdi; Rollman, Christopher M; France, Christine A M

    2013-12-03

    Our recently developed dating technique based on the racemization rate of aspartic acid was applied to dating human bone, as well as that of other mammals, utilizing capillary electrophoresis mass spectrometry. First, several well-dated (mostly (14)C-dated and with strong archeological evidence) human bones ranging in age from 150 to ~10,000 years were used to develop a calibration curve for human bone. The D/L ratio of aspartic acid for these specimens ranged from 2.4% to ~10%, with a correlation coefficient of better than 0.99, indicating a strong linear relationship between the d/l ratio of aspartic acid and the age of the specimens. This calibration curve can now be used to date human archeological specimens of unknown age, up to ~10,000 years. However, when the technique was applied to well-dated mixed species of larger mammal bones such as bison, whale, llama, etc., the calibration curve showed a slower rate of racemization with a lower correlation (0.88). As additional large mammal bones with less certain age (i.e., using archeological evidence alone with no (14)C-dating) were dated the correlation coefficient decreased to 0.70. The correlation coefficient decreased further to 0.58 when the racemization data from all mammals (including human) were added to the calibration curve, indicating the importance of using well-dated, species-specific specimens for forming a calibration curve. This conclusion is consistent with our previously published calibration curve for a single species of silk (Bombyx mori), which followed the expected reversible first-order kinetics. These results support species specificity of amino acid racemization dating.

  5. Forest Transpiration: Resolving Species-Specific Root Water Uptake Patterns

    NASA Astrophysics Data System (ADS)

    Blume, T.; Heidbuechel, I.; Simard, S.; Guntner, A.; Weiler, M.; Stewart, R. D.

    2016-12-01

    Transpiration and its spatio-temporal variability are still not fully understood, despite their importance for the global water cycle. This is in part due to our inability to measure transpiration comprehensively. Transpiration is usually either estimated with empirical equations based on climatic variables and crop factors, by measuring sap velocities, estimating sap wood area and scaling up to the forest stand based on a number of assumptions or by measuring the integral signal across a footprint with eddy flux towers. All these methods are focused on the cumulated loss of water to the atmosphere and do not provide information on where this water is coming from. In this study, spatio-temporal variability of root water uptake was investigated in a forest in the northeastern German lowlands. The soils are sandy and the depth of the unsaturated zone ranges from 1 to 30 m. We estimated root water uptake from different soil depths, from 0.1 m down to 2 m, based on diurnal fluctuations in soil moisture content during rain-free days. The 15 field sites cover different topographic positions and forest stands: 4 pure stands of both mature and young beech and pine and 9 mixed stands. The resulting daily data set of root water uptake shows that the forest stands differ in total amounts as well as in uptake depth distributions. Temporal dynamics of signal strength within the profile suggest a locally shifting spatial distribution of uptake that changes with water availability. The relationship of these depth-resolved uptake rates to overall soil water availability varies considerably between tree species. Using the physically-based soil hydrological model HYDRUS we investigated to what extent the observed patterns in uptake can be related to soil physical relationships alone and where tree species-specific aspects come into play. We furthermore used the model to test assumptions and estimate uncertainties of this soil moisture based estimation of plant water uptake. The

  6. Species-Specific Transmission of Novel Picornaviruses in Lemurs

    PubMed Central

    Lim, Efrem S.; Deem, Sharon L.; Porton, Ingrid J.; Cao, Song

    2015-01-01

    ABSTRACT The roles of host genetics versus exposure and contact frequency in driving cross-species transmission remain the subject of debate. Here, we used a multitaxon lemur collection at the Saint Louis Zoo in the United States as a model to gain insight into viral transmission in a setting of high interspecies contact. Lemurs are a diverse and understudied group of primates that are highly endangered. The speciation of lemurs, which are endemic to the island of Madagascar, occurred in geographic isolation apart from that of continental African primates. Although evidence of endogenized viruses in lemur genomes exists, no exogenous viruses of lemurs have been described to date. Here we identified two novel picornaviruses in fecal specimens of ring-tailed lemurs (Lemur catta) and black-and-white ruffed lemurs (Varecia variegata). We found that the viruses were transmitted in a species-specific manner (lesavirus 1 was detected only in ring-tailed lemurs, while lesavirus 2 was detected only in black-and-white ruffed lemurs). Longitudinal sampling over a 1-year interval demonstrated ongoing infection in the collection. This was supported by evidence of viral clearance in some animals and new infections in previously uninfected animals, including a set of newly born triplets that acquired the infection. While the two virus strains were found to be cocirculating in a mixed-species exhibit of ring-tailed lemurs, black-and-white ruffed lemurs, and black lemurs, there was no evidence of cross-species transmission. This suggests that despite high-intensity contact, host species barriers can prevent cross-species transmissions of these viruses. IMPORTANCE Up to 75% of emerging infectious diseases in humans today are the result of zoonotic transmission. However, a challenge in understanding transmission dynamics has been the limited models of cross-species transmission. Zoos provide a unique opportunity to explore parameters defining viral transmission. We demonstrated that

  7. Species-specific identification of penicillium linked to patulin contamination.

    PubMed

    Dombrink-Kurtzman, Mary Ann; McGovern, Amy E

    2007-11-01

    Certain species of Penicillium have been reported to produce the mycotoxin patulin, and research was undertaken to identify these with the use of oligonucleotide primer pairs. Species examined were found in food, plants, and soil and were reported to produce patulin. Penicillium expansum is the most commonly detected species linked to the presence of patulin in apple juice. At least 10 different enzymes are involved in the patulin biosynthetic pathway, including the isoepoxydon dehydrogenase (idh) gene. Based on nucleotide sequences previously determined for the idh gene in Penicillium species, PCR primers were designed for the species-specific detection of patulin-producing species. The 5' primers were based on differences in the second intron of the idh gene. To ensure that the primer pairs produced a PCR product restricted to the species for which it was designed, and not to unrelated species, all of the primer pairs were tested against all of the Penicillium species. With one exception, it was possible to detect a reaction only with the organism of interest. The primer pair for Penicillium griseofulvum also amplified DNA from Penicillium dipodomyicola, a closely related species; however, it was possible to distinguish between these two species by doing a second amplification, with a different primer pair specific only for P. dipodomyicola. Consequently, with different primer sets, it was possible to identify individual patulin-producing species of Penicillium.

  8. Influenza virus and endothelial cells: a species specific relationship

    PubMed Central

    Short, Kirsty R.; Veldhuis Kroeze, Edwin J. B.; Reperant, Leslie A.; Richard, Mathilde; Kuiken, Thijs

    2014-01-01

    Influenza A virus (IAV) infection is an important cause of respiratory disease in humans. The original reservoirs of IAV are wild waterfowl and shorebirds, where virus infection causes limited, if any, disease. Both in humans and in wild waterbirds, epithelial cells are the main target of infection. However, influenza virus can spread from wild bird species to terrestrial poultry. Here, the virus can evolve into highly pathogenic avian influenza (HPAI). Part of this evolution involves increased viral tropism for endothelial cells. HPAI virus infections not only cause severe disease in chickens and other terrestrial poultry species but can also spread to humans and back to wild bird populations. Here, we review the role of the endothelium in the pathogenesis of influenza virus infection in wild birds, terrestrial poultry and humans with a particular focus on HPAI viruses. We demonstrate that whilst the endothelium is an important target of virus infection in terrestrial poultry and some wild bird species, in humans the endothelium is more important in controlling the local inflammatory milieu. Thus, the endothelium plays an important, but species-specific, role in the pathogenesis of influenza virus infection. PMID:25520707

  9. Species-specific patterns of hyperostosis in marine teleost fishes

    USGS Publications Warehouse

    Smith-Vaniz, William F.; Kaufman, L.S.; Glowacki, J.

    1995-01-01

    The occurrence of swollen or hyperostotic bones in skeletal preparations, preserved museum material or whole fresh specimens of marine teleost fishes was identified in 92 species belonging to 22 families. Patterns of hyperostotic skeletal growth were typically consistent and often species-specific in all individuals larger than a certain size. The taxonomic distribution of hyperostosis in diverse phylogenetic groups suggests that it has arisen independently many times. Selected bones from two species of the family Carangidae, horse-eye jack Caranx latus Agassiz and crevalle jackCaranx hippos (Linnaeus), were examined in detail by light and electron microscopy. Nonhyperostotic bone contained osteoid-producing osteoblasts, resorbing osteoclasts, occasional osteocytes, and a rich vascular network, all characteristics of cellular bone. Thus, these fishes have a spatial juxtaposition of cellular and acellular bone tissues in adjacent and often serially homologous bone sites. The functional significance of hyperostosis is unknown, but it is a predictable manifestation of bone growth and development for the many taxa in which it occurs.

  10. Defining species specific genome differences in malaria parasites.

    PubMed

    Liew, Kingsley J L; Hu, Guangan; Bozdech, Zbynek; Peter, Preiser R

    2010-02-23

    In recent years a number of genome sequences for different plasmodium species have become available. This has allowed the identification of numerous conserved genes across the different species and has significantly enhanced our understanding of parasite biology. In contrast little is known about species specific differences between the different genomes partly due to the lower sequence coverage and therefore relatively poor annotation of some of the draft genomes particularly the rodent malarias parasite species. To improve the current annotation and gene identification status of the draft genomes of P. berghei, P. chabaudi and P. yoelii, we performed genome-wide comparisons between these three species. Through analyses via comparative genome hybridizations using a newly designed pan-rodent array as well as in depth bioinformatics analysis, we were able to improve on the coverage of the draft rodent parasite genomes by detecting orthologous genes between these related rodent parasite species. More than 1,000 orthologs for P. yoelii were now newly associated with a P. falciparum gene. In addition to extending the current core gene set for all plasmodium species this analysis also for the first time identifies a relatively small number of genes that are unique to the primate malaria parasites while a larger gene set is uniquely conserved amongst the rodent malaria parasites. These findings allow a more thorough investigation of the genes that are important for host specificity in malaria.

  11. Structural basis for the species-specific activity of TFIIS.

    PubMed

    Shimasaki, N B; Kane, C M

    2000-11-24

    Many proteins involved in eukaryotic transcription are similar in function and in sequence between organisms. Despite the sequence similarities, there are many factors that do not function across species. For example, transcript elongation factor TFIIS is highly conserved among eukaryotes, and yet the TFIIS protein from Saccharomyces cerevisiae cannot function with mammalian RNA polymerase II and vice versa. To determine the reason for this species specificity, chimeras were constructed linking three structurally independent regions of the TFIIS proteins from yeast and human cells. Two independently folding domains, II and III, have been examined previously using NMR (). Yeast domain II alone is able to bind yeast RNA polymerase II with the same affinity as the full-length TFIIS protein, and this domain was expected to confer the species selectivity. Domain III has previously been shown to be readily exchanged between mammalian and yeast factors. However, the results presented here indicate that domain II is insufficient to confer species selectivity, and a primary determinant lies in a 30-amino acid highly conserved linker region connecting domain II with domain III. These 30 amino acids may physically orient domains II and III to support functional interactions between TFIIS and RNA polymerase II.

  12. Species specificity in avian sperm:perivitelline interaction.

    PubMed

    Stewart, Sarah G; Bausek, Nina; Wohlrab, Franz; Schneider, Wolfgang J; Janet Horrocks, A; Wishart, Graham J

    2004-04-01

    The interaction of chicken spermatozoa with the inner perivitelline layer from different avian species in vitro during a 5 min co-incubation was measured as the number of points of hydrolysis produced per unit area of inner perivitelline layer. The average degree of interaction, as a proportion of that between chicken spermatozoa and their homologous inner perivitelline layer, was: equal to or greater than 100% within Galliformes (chicken, turkey, quail, pheasant, peafowl and guineafowl); 44% within Anseriformes (goose, duck); and less than 30% in Passeriformes (Zebra Finch) and Columbiformes (collared-dove). The homologue of the putative chicken sperm-binding proteins, chicken ZP1 and ZP3, were identified by Western blotting with anti-chicken ZP1/ZP3 antibody in the perivitelline layers of all species. The functional cross-reactivity between chicken spermatozoa and heterologous inner perivitelline layer appeared to be linked to known phylogenetic distance between the species, although it was not related to the relative affinity of the different ZP3 homologues for anti-chicken ZP3. This work demonstrates that sperm interaction with the egg investment does not represent such a stringent species-specific barrier in birds as it does in mammals and marine invertebrates. This may be a factor in the frequency of hybrid production in birds.

  13. Species-specific differences in X chromosome inactivation in mammals.

    PubMed

    Sado, Takashi; Sakaguchi, Takehisa

    2013-10-01

    In female mammals, the dosage difference in X-linked genes between XX females and XY males is compensated for by inactivating one of the two X chromosomes during early development. Since the discovery of the X inactive-specific transcript (XIST) gene in humans and its subsequent isolation of the mouse homolog, Xist, in the early 1990s, the molecular basis of X chromosome inactivation (X-inactivation) has been more fully elucidated using genetically manipulated mouse embryos and embryonic stem cells. Studies on X-inactivation in other mammals, although limited when compared with those in the mice, have revealed that, while their inactive X chromosome shares many features with those in the mice, there are marked differences in not only some epigenetic modifications of the inactive X chromosome but also when and how X-inactivation is initiated during early embryonic development. Such differences raise the issue about what extent of the molecular basis of X-inactivation in the mice is commonly shared among others. Recognizing similarities and differences in X-inactivation among mammals may provide further insight into our understanding of not only the evolutionary but also the molecular aspects for the mechanism of X-inactivation. Here, we reviewed species-specific differences in X-inactivation and discussed what these differences may reveal.

  14. Greek PDO saffron authentication studies using species specific molecular markers.

    PubMed

    Bosmali, I; Ordoudi, S A; Tsimidou, M Z; Madesis, P

    2017-10-01

    Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C. sativus L. from the cultivation area of "Krokos Kozanis" as well as the potential differences with the band pattern produced by other Crocus species. Then, species-specific markers were developed taking advantage of an advanced molecular technique such as the HRM analysis coupled with universal DNA barcoding regions (trnL) (Bar-HRM) and applied to saffron admixtures with some of the most common plant adulterants (Calendula officinalis, Carthamus tinctorius, Gardenia jasminoides, Zea mays and Curcuma longa). The sensitivity of the procedure was tested for turmeric as a case study whereas HPLC-fluorescence determination of secondary metabolites was also employed for comparison. The overall results indicated that the Bar-HRM approach is quite effective in terms of specificity and sensitivity. Its effectiveness regarding the detection of turmeric was comparable to that of a conventional HPLC method (0.5% vs 1.0%, w/w). Yet, the proposed DNA-based method is much faster, cost-effective and can be used even by non-geneticists, in any laboratory having access to an HRM-capable real-time PCR instrumentation. It can be, thus, regarded as a strong analytical tool in saffron authentication studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance.

    PubMed

    Yildirim, Suleyman; Yeoman, Carl J; Janga, Sarath Chandra; Thomas, Susan M; Ho, Mengfei; Leigh, Steven R; White, Bryan A; Wilson, Brenda A; Stumpf, Rebecca M

    2014-12-01

    Bacterial communities colonizing the reproductive tracts of primates (including humans) impact the health, survival and fitness of the host, and thereby the evolution of the host species. Despite their importance, we currently have a poor understanding of primate microbiomes. The composition and structure of microbial communities vary considerably depending on the host and environmental factors. We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. The nine primate species included: humans (Homo sapiens), yellow baboons (Papio cynocephalus), olive baboons (Papio anubis), lemurs (Propithecus diadema), howler monkeys (Alouatta pigra), red colobus (Piliocolobus rufomitratus), vervets (Chlorocebus aethiops), mangabeys (Cercocebus atys) and chimpanzees (Pan troglodytes). Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and diversity. In contrast to the gut microbiome, the vaginal microbiome showed limited congruence with host phylogeny, and neither captivity nor diet elicited substantial effects on the vaginal microbiomes of primates. Permutational multivariate analysis of variance and Wilcoxon tests revealed correlations among vaginal microbiota and host species-specific socioecological factors, particularly related to sexuality, including: female promiscuity, baculum length, gestation time, mating group size and neonatal birth weight. The proportion of unclassified taxa observed in nonhuman primate samples increased with phylogenetic distance from humans, indicative of the existence of previously unrecognized microbial taxa. These findings contribute to our understanding of host-microbe variation and coevolution, microbial biogeography, and disease risk, and have important

  16. Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

    PubMed Central

    Yildirim, Suleyman; Yeoman, Carl J; Janga, Sarath Chandra; Thomas, Susan M; Ho, Mengfei; Leigh, Steven R; Consortium, Primate Microbiome; White, Bryan A; Wilson, Brenda A; Stumpf, Rebecca M

    2014-01-01

    Bacterial communities colonizing the reproductive tracts of primates (including humans) impact the health, survival and fitness of the host, and thereby the evolution of the host species. Despite their importance, we currently have a poor understanding of primate microbiomes. The composition and structure of microbial communities vary considerably depending on the host and environmental factors. We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. The nine primate species included: humans (Homo sapiens), yellow baboons (Papio cynocephalus), olive baboons (Papio anubis), lemurs (Propithecus diadema), howler monkeys (Alouatta pigra), red colobus (Piliocolobus rufomitratus), vervets (Chlorocebus aethiops), mangabeys (Cercocebus atys) and chimpanzees (Pan troglodytes). Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and diversity. In contrast to the gut microbiome, the vaginal microbiome showed limited congruence with host phylogeny, and neither captivity nor diet elicited substantial effects on the vaginal microbiomes of primates. Permutational multivariate analysis of variance and Wilcoxon tests revealed correlations among vaginal microbiota and host species-specific socioecological factors, particularly related to sexuality, including: female promiscuity, baculum length, gestation time, mating group size and neonatal birth weight. The proportion of unclassified taxa observed in nonhuman primate samples increased with phylogenetic distance from humans, indicative of the existence of previously unrecognized microbial taxa. These findings contribute to our understanding of host–microbe variation and coevolution, microbial biogeography, and disease risk, and have important

  17. Species-specific effects of aortic valve decellularization.

    PubMed

    VeDepo, Mitchell C; Buse, Eric E; Quinn, Rachael W; Williams, Todd D; Detamore, Michael S; Hopkins, Richard A; Converse, Gabriel L

    2017-03-01

    Decellularized heart valves have great potential as a stand-alone valve replacement or as a scaffold for tissue engineering heart valves. Before decellularized valves can be widely used clinically, regulatory standards require pre-clinical testing in an animal model, often sheep. Numerous decellularization protocols have been applied to both human and ovine valves; however, the ways in which a specific process may affect valves of these species differently have not been reported. In the current study, the comparative effects of decellularization were evaluated for human and ovine aortic valves by measuring mechanical and biochemical properties. Cell removal was equally effective for both species. The initial cell density of the ovine valve leaflets (2036±673cells/mm(2)) was almost triple the cell density of human leaflets (760±386cells/mm(2); p<0.001). Interestingly, post-decellularization ovine leaflets exhibited significant increases in biaxial areal strain (p<0.001) and circumferential peak stretch (p<0.001); however, this effect was not observed in the human counterparts (p>0.10). This species-dependent difference in the effect of decellularization was likely due to the higher initial cellularity in ovine valves, as well as a significant decrease in collagen crosslinking following the decellularization of ovine leaflets that was not observed in the human leaflet. Decellularization also caused a significant decrease in the circumferential relaxation of ovine leaflets (p<0.05), but not human leaflets (p>0.30), which was credited to a greater reduction of glycosaminoglycans in the ovine tissue post-decellularization. These results indicate that an identical decellularization process can have differing species-specific effects on heart valves.

  18. Seasonal dynamics of tree species specific soil moisture patterns

    NASA Astrophysics Data System (ADS)

    Heidbuechel, I.; Blume, T.; Guntner, A.; Dreibrodt, J.; Simard, S.

    2015-12-01

    Soil moisture patterns in the landscape are largely controlled by soil types (pore size distributions), landscape position and precipitation events. But how strong is the influence of vegetation on patterns within a single soil type? While we would envision a clear difference in soil moisture patterns and responses between for example bare soil, a pasture and a forest, our conceptual images start to become less clear when we compare different forest stands. Do different tree species cause species specific moisture patterns to emerge? Do these patterns change with the seasons? To investigate this question we analyzed data from 15 sensor clusters in the lowlands of north-eastern Germany (within the TERENO observatory) which were instrumented with soil moisture sensors (5 profiles per site), tensiometers, sap flow sensors, throughfall and stemflow gauges. Data has been collected at these sites since May 2014. While the soils under beech trees were more often relatively wet and more often relatively dry, the soils under pine trees showed less variability and more often average soil moisture. These differences could be explained by differences in the complex interactions between throughfall and stemflow on the one hand as well as root water uptake and sap flow patterns on the other hand. Further analysis will explore hydraulic redistribution between soil layers and hydraulic lift of groundwater (using root zone water balance methods and stable water isotope samples that were taken at different depths in the soil, in the groundwater and from the sapwood). The manifestation of tree species differences in soil moisture patterns and dynamics is likely to have implications for groundwater recharge, transit times and hydrologic partitioning within the critical zone.

  19. [Thyroid hormones and their precursors. II. Species-specific properties].

    PubMed

    Tóth, Gergo; Noszál, Béla

    2014-01-01

    This paper surveys the species-specific physico-chemical parameters (basicity and lipophilicity) and related biological functions of thyroid hormones (thyroxine, liothyronine and reverse liothyronine) and their biological precursors (tyrosine, monoiodotyrosine and diiodotyrosine). The protonation macroconstants were determined by 1H NMR-pH titrations while the microconstants were determined by a multimodal spectroscopic-deductive methodology using auxiliary derivatives of reduced complexity. Our results show that the different number and/or position of iodine are the key factors to influence the phenolate basicity. The ionization state of the phenolate site is crucial in the biosynthesis and protein binding of thyroid hormones. The role of the protonation state in the receptor binding was investigated by an in silico docking method. Microspecies of thyroid hormones were docked to the thyroid hormone receptor isoforms. Our results quantitate at the molecular level how the ionization stage and the charge distribution influence the protein binding. The anionic form of the carboxyl group is essential for the protein binding, whereas the protonated form of the amino group loosens it. The protonation state of the phenolate plays a role of secondary importance in the receptor binding. The combined results of docking and microspeciation studies show that microspecies of the highest concentration at the pH of blood are not the strongest binding ones. The site-specific lipophilicity of our investigated molecules was determined with the measurement of distribution coefficients at different pH using carboxymethyl- and O-methyl-derivatives to mimic the partition of some of the individual microspecies. Correction factors were determined and introduced. Our data show that the iodinated aromatic ring system is the definitive structural element that fundamentally determines the lipophilicity of thyroid hormones, whereas the protonation state of the aliphatic part is essential in

  20. Comparison of the pathogen species-specific immune response in udder derived cell types and their models.

    PubMed

    Günther, Juliane; Koy, Mirja; Berthold, Anne; Schuberth, Hans-Joachim; Seyfert, Hans-Martin

    2016-02-01

    The outcome of an udder infection (mastitis) largely depends on the species of the invading pathogen. Gram-negative pathogens, such as Escherichia coli often elicit acute clinical mastitis while Gram-positive pathogens, such as Staphylococcus aureus tend to cause milder subclinical inflammations. It is unclear which type of the immune competent cells residing in the udder governs the pathogen species-specific physiology of mastitis and which established cell lines might provide suitable models. We therefore profiled the pathogen species-specific immune response of different cell types derived from udder and blood. Primary cultures of bovine mammary epithelial cells (pbMEC), mammary derived fibroblasts (pbMFC), and bovine monocyte-derived macrophages (boMdM) were challenged with heat-killed E. coli, S. aureus and S. uberis mastitis pathogens and their immune response was scaled against the response of established models for MEC (bovine MAC-T) and macrophages (murine RAW 264.7). Only E. coli provoked a full scale immune reaction in pbMEC, fibroblasts and MAC-T cells, as indicated by induced cytokine and chemokine expression and NF-κB activation. Weak reactions were induced by S. aureus and none by S. uberis challenges. In contrast, both models for macrophages (boMdM and RAW 264.7) reacted strongly against all the three pathogens accompanied by strong activation of NF-κB factors. Hence, the established cell models MAC-T and RAW 264.7 properly reflected key aspects of the pathogen species-specific immune response of the respective parental cell type. Our data imply that the pathogen species-specific physiology of mastitis likely relates to the respective response of MEC rather to that of professional immune cells.

  1. Synchrotron X-Ray Induced Gold Nanoparticle Formation

    SciTech Connect

    Yang, Y. C.; Wang, C. H.; Yang, T. Y.; Hwu, Y.; Chen, C. H.; Je, J. H.; Margaritondo, G.

    2007-01-19

    We reported a simple approach to generate gold nanoparticles from HAuCl4 containing aqueous solution by synchrotron x-ray irradiation at room temperature. The gold colloidal were investigated by a variety of characterization methods including Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Fourier transformation infrared (FTIR), Ultraviolet and Visible (UV-VIS) spectrometer and the effects of variables including pH value, radiation time were examined.

  2. X-ray induced modification of metal/fluoropolymer interfaces

    NASA Astrophysics Data System (ADS)

    Shi, Ming-Kun; Lamontagne, Boris; Martinu, Ludvik; Selmani, Amine

    1993-08-01

    Metal adhesion to polymers depends on the chemical structure at the interface. In the present work, we study the evaporation of Cr, Ti, and Au onto Teflon PFA (perfluoromethyl-vinyl-ether) substrates, and we modify the interface by post-deposition x-ray irradiation. In situ x-ray photoelectron spectroscopy shows that deposition of reactive metals such as Cr and Ti leads immediately to crosslinking and to the formation of carbide and fluoride species. Less reactive metals, such as Au, cause only small loss of fluorine without formation of any new species. The metal/PFA interface is strongly affected by x-ray irradiation in the case of Cr and Ti: remarkably enhanced crosslinking has been observed, which further increases with the metal coverage, while the carbides and fluorides remain basically unaffected. On the other hand, crosslinking increases only very slightly for pure PFA and for the Au/PFA interface, regardless of the Au thickness. These results suggest that radical recombination reactions are responsible for crosslinking at the interface between PFA and reactive metals.

  3. X-ray induced demagnetization of single-molecule magnets

    SciTech Connect

    Dreiser, Jan; Westerström, Rasmus; Piamonteze, Cinthia; Nolting, Frithjof; Rusponi, Stefano; Brune, Harald; Yang, Shangfeng; Popov, Alexey; Dunsch, Lothar; Greber, Thomas

    2014-07-21

    Low-temperature x-ray magnetic circular dichroism measurements on the endohedral single-molecule magnet DySc{sub 2}N@C{sub 80} at the Dy M{sub 4,5} edges reveal a shrinking of the opening of the observed hysteresis with increasing x-ray flux. Time-dependent measurements show that the exposure of the molecules to x-rays resonant with the Dy M{sub 5} edge accelerates the relaxation of magnetization more than off-resonant x-rays. The results cannot be explained by a homogeneous temperature rise due to x-ray absorption. Moreover, the observed large demagnetization cross sections indicate that the resonant absorption of one x-ray photon induces the demagnetization of many molecules.

  4. Species-specific PCR for the identification of goat cashmere and sheep wool.

    PubMed

    Geng, Rong-Qing

    2015-02-01

    In order to establish rapid and species-specific method of goat cashmere and sheep wool identification, a polymerase chain reaction using specific primer pairs targeting mitochondrial D-loop was developed. The goat specific primers yielded a 294 bp PCR fragment and the sheep specific primers yielded three PCR fragments of which only the 404 bp fragment was found highly diagnostic. The specificity and reliability of the developed species-specific PCR assay was validated by considering as many as 500 cashmere and wool samples. The developed species-specific PCR was found effective in detecting mixed samples of cashmere and wool precisely with the relative content over 9.09%. The species-specific PCR method proved to be low cost, fast, easy and reliable alternative to determine the addition of sheep wool in goat cashmere.

  5. Assessing Species-specific Contributions To Craniofacial Development Using Quail-duck Chimeras

    PubMed Central

    Fish, Jennifer L.; Schneider, Richard A.

    2014-01-01

    The generation of chimeric embryos is a widespread and powerful approach to study cell fates, tissue interactions, and species-specific contributions to the histological and morphological development of vertebrate embryos. In particular, the use of chimeric embryos has established the importance of neural crest in directing the species-specific morphology of the craniofacial complex. The method described herein utilizes two avian species, duck and quail, with remarkably different craniofacial morphology. This method greatly facilitates the investigation of molecular and cellular regulation of species-specific pattern in the craniofacial complex. Experiments in quail and duck chimeric embryos have already revealed neural crest-mediated tissue interactions and cell-autonomous behaviors that regulate species-specific pattern in the craniofacial skeleton, musculature, and integument. The great diversity of neural crest derivatives suggests significant potential for future applications of the quail-duck chimeric system to understanding vertebrate development, disease, and evolution. PMID:24962088

  6. Development and Evaluation of Species-Specific PCR for Detection of Nine Acinetobacter Species.

    PubMed

    Li, Xue Min; Choi, Ji Ae; Choi, In Sun; Kook, Joong Ki; Chang, Young-Hyo; Park, Geon; Jang, Sook Jin; Kang, Seong Ho; Moon, Dae Soo

    2016-05-01

    Molecular methods have the potential to improve the speed and accuracy of Acinetobacter species identification in clinical settings. The goal of this study is to develop species-specific PCR assays based on differences in the RNA polymerase beta-subunit gene (rpoB) to detect nine commonly isolated Acinetobacter species including Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter lwoffii, Acinetobacter ursingii, Acinetobacter bereziniae, Acinetobacter haemolyticus, and Acinetobacter schindleri. The sensitivity and specificity of these nine assays were measured using genomic DNA templates from 55 reference strains and from 474 Acinetobacter clinical isolates. The sensitivity of A. baumannii-specific PCR assay was 98.9%, and the sensitivity of species-specific PCR assays for all other species was 100%. The specificities of A. lwoffii- and A. schindleri-specific PCR were 97.8 and 98.9%, respectively. The specificity of species-specific PCR for all other tested Acinetobacter species was 100%. The lower limit of detection for the nine species-specific PCR assays developed in this study was 20 or 200 pg of genomic DNA from type strains of each species. The Acinetobacter species-specific PCR assay would be useful to determine the correct species among suggested candidate Acinetobacter species when conventional methods including MALDI-TOF MS identify Acinetobacter only to the genus level. The species-specific assay can be used to screen large numbers of clinical and environmental samples obtained for epidemiologic study of Acinetobacter for the presence of target species.

  7. Zonadhesin is essential for species specificity of sperm adhesion to the egg zona pellucida.

    PubMed

    Tardif, Steve; Wilson, Michael D; Wagner, Rebecca; Hunt, Peter; Gertsenstein, Marina; Nagy, Andras; Lobe, Corrinne; Koop, Ben F; Hardy, Daniel M

    2010-08-06

    Interaction of rapidly evolving molecules imparts species specificity to sperm-egg recognition in marine invertebrates, but it is unclear whether comparable interactions occur during fertilization in any vertebrate species. In mammals, the sperm acrosomal protein zonadhesin is a rapidly evolving molecule with species-specific binding activity for the egg zona pellucida (ZP). Here we show using null mice produced by targeted disruption of Zan that zonadhesin confers species specificity to sperm-ZP adhesion. Sperm capacitation selectively exposed a partial von Willebrand D domain of mouse zonadhesin on the surface of living, motile cells. Antibodies to the exposed domain inhibited adhesion of wild-type spermatozoa to the mouse ZP but did not inhibit adhesion of spermatozoa lacking zonadhesin. Zan(-/-) males were fertile, and their spermatozoa readily fertilized mouse eggs in vitro. Remarkably, however, loss of zonadhesin increased adhesion of mouse spermatozoa to pig, cow, and rabbit ZP but not mouse ZP. We conclude that zonadhesin mediates species-specific ZP adhesion, and Zan(-/-) males are fertile because their spermatozoa retain adhesion capability that is not species-specific. Mammalian sperm-ZP adhesion is therefore molecularly robust, and species-specific egg recognition by a protein in the sperm acrosome is conserved between invertebrates and vertebrates, even though the adhesion molecules themselves are unrelated.

  8. Use of species-specific PCR for the identification of 10 sea cucumber species

    NASA Astrophysics Data System (ADS)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  9. Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes.

    PubMed

    Mehes-Smith, Melanie; Michael, Paul; Nkongolo, Kabwe

    2010-10-01

    Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana, Picea rubens, Pinus strobus, or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

  10. Being Nature: Interspecies Articulation as a Species-Specific Practice of Relating to Environment

    ERIC Educational Resources Information Center

    Rautio, Pauliina

    2013-01-01

    Rather than categorically teaching us ways to be less anthropocentric, environmental education could be about educating us of the ways in which we already are nature as human animals. In this paper, one species-specific practice of human relating to environment--interspecies articulation--is argued as one way of being nature. Interspecies…

  11. Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner▿

    PubMed Central

    Suckow, Gaia; Seitz, Patrick; Blokesch, Melanie

    2011-01-01

    Although it is a human pathogen, Vibrio cholerae is a regular member of aquatic habitats, such as coastal regions and estuaries. Within these environments, V. cholerae often takes advantage of the abundance of zooplankton and their chitinous molts as a nutritious surface on which the bacteria can form biofilms. Chitin also induces the developmental program of natural competence for transformation in several species of the genus Vibrio. In this study, we show that V. cholerae does not distinguish between species-specific and non-species-specific DNA at the level of DNA uptake. This is in contrast to what has been shown for other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae. However, species specificity with respect to natural transformation still occurs in V. cholerae. This is based on a positive correlation between quorum sensing and natural transformation. Using mutant-strain analysis, cross-feeding experiments, and synthetic cholera autoinducer-1 (CAI-1), we provide strong evidence that the species-specific signaling molecule CAI-1 plays a major role in natural competence for transformation. We suggest that CAI-1 can be considered a competence pheromone. PMID:21784943

  12. Development of a species-specific gene probe for Hyphomicrobium facilis with the inverse PCR.

    PubMed Central

    Fesefeldt, A; Poetsch, M; Gliesche, C G

    1997-01-01

    A species-specific gene probe for Hyphomicrobium facilis was generated from a transposon Tn5-132 insertion mutant defective in methanol oxidation by the inverse PCR. With this probe, the abundance of H. facilis in a garden soil was determined as a subfraction of the total cultivable hyphomicrobia. PMID:8979362

  13. Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner.

    PubMed

    Suckow, Gaia; Seitz, Patrick; Blokesch, Melanie

    2011-09-01

    Although it is a human pathogen, Vibrio cholerae is a regular member of aquatic habitats, such as coastal regions and estuaries. Within these environments, V. cholerae often takes advantage of the abundance of zooplankton and their chitinous molts as a nutritious surface on which the bacteria can form biofilms. Chitin also induces the developmental program of natural competence for transformation in several species of the genus Vibrio. In this study, we show that V. cholerae does not distinguish between species-specific and non-species-specific DNA at the level of DNA uptake. This is in contrast to what has been shown for other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae. However, species specificity with respect to natural transformation still occurs in V. cholerae. This is based on a positive correlation between quorum sensing and natural transformation. Using mutant-strain analysis, cross-feeding experiments, and synthetic cholera autoinducer-1 (CAI-1), we provide strong evidence that the species-specific signaling molecule CAI-1 plays a major role in natural competence for transformation. We suggest that CAI-1 can be considered a competence pheromone.

  14. Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling

    NASA Astrophysics Data System (ADS)

    Sohmen, Daniel; Chiba, Shinobu; Shimokawa-Chiba, Naomi; Innis, C. Axel; Berninghausen, Otto; Beckmann, Roland; Ito, Koreaki; Wilson, Daniel N.

    2015-04-01

    Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5-3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.

  15. Being Nature: Interspecies Articulation as a Species-Specific Practice of Relating to Environment

    ERIC Educational Resources Information Center

    Rautio, Pauliina

    2013-01-01

    Rather than categorically teaching us ways to be less anthropocentric, environmental education could be about educating us of the ways in which we already are nature as human animals. In this paper, one species-specific practice of human relating to environment--interspecies articulation--is argued as one way of being nature. Interspecies…

  16. Nonstructural Protein L* Species Specificity Supports a Mouse Origin for Vilyuisk Human Encephalitis Virus.

    PubMed

    Drappier, Melissa; Opperdoes, Fred R; Michiels, Thomas

    2017-07-15

    Vilyuisk human encephalitis virus (VHEV) is a picornavirus related to Theiler's murine encephalomyelitis virus (TMEV). VHEV was isolated from human material passaged in mice. Whether this VHEV is of human or mouse origin is therefore unclear. We took advantage of the species-specific activity of the nonstructural L* protein of theiloviruses to track the origin of TMEV isolates. TMEV L* inhibits RNase L, the effector enzyme of the interferon pathway. By using coimmunoprecipitation and functional RNase L assays, the species specificity of RNase L antagonism was tested for L* from mouse (DA) and rat (RTV-1) TMEV strains as well as for VHEV. Coimmunoprecipitation and functional assay data confirmed the species specificity of L* activity and showed that L* from rat strain RTV-1 inhibited rat but not mouse or human RNase L. Next, we showed that the VHEV L* protein was phylogenetically related to L* of mouse viruses and that it failed to inhibit human RNase L but readily antagonized mouse RNase L, unambiguously showing the mouse origin of VHEV.IMPORTANCE Defining the natural host of a virus can be a thorny issue, especially when the virus was isolated only once or when the isolation story is complex. The species Theilovirus includes Theiler's murine encephalomyelitis virus (TMEV), infecting mice and rats, and Saffold virus (SAFV), infecting humans. One TMEV strain, Vilyuisk human encephalitis virus (VHEV), however, was isolated from mice that were inoculated with cerebrospinal fluid of a patient presenting with chronic encephalitis. It is therefore unclear whether VHEV was derived from the human sample or from the inoculated mouse. The L* protein encoded by TMEV inhibits RNase L, a cellular enzyme involved in innate immunity, in a species-specific manner. Using binding and functional assays, we show that this species specificity even allows discrimination between TMEV strains of mouse and of rat origins. The VHEV L* protein clearly inhibited mouse but not human RNase L

  17. A rapidly diverging EGF protein regulates species-specific signal transduction in early sea urchin development.

    PubMed

    Kamei, N; Swanson, W J; Glabe, C G

    2000-09-15

    The macromolecules mediating species-specific events during fertilization and early development and their molecular evolution are only beginning to be understood. We screened sea urchin ovary mRNA for species-specific gene products using representational differential analysis to identify unique transcripts in Strongylocentrotus franciscanus that are absent or divergent from a closely related species, S. purpuratus. One of the transcripts identified by this screening process is SfEGF-II, which contains four EGF repeats. SfEGF-II is orthologous to the previously reported genes S. purpuratus SpEGF-II and Anthocidaris crassispina AcEGF-II, encoding exogastrulation-inducing peptides (EGIP). EGF peptides derived from EGIP induce exogastrulation, a classical developmental defect, when added to embryos prior to gastrulation. The first three EGF repeats (EGF1-3) share 50 to 60% identity among the three species, but the fourth repeat (EGF4) is more divergent, displaying only 30% identity. Analysis of the sequence divergence indicates that the EGF-II genes display a relatively high nonsynonymous-to-synonymous ratio, a significant excess of radical compared to conservative amino acid substitutions, and a lack of polymorphism within SfEGF-II, indicating that these genes have been subjected to positive Darwinian selection. Recombinant EGF3 from S. franciscanus induces exogastrulation in both S. franciscanus and S. purpuratus. In contrast, recombinant EGF4 from both S. franciscanus and S. purpuratus induces exogastrula in a species-specific manner. In hybrid embryos, both species of EGF4 induce exogastrulation, suggesting that the receptor for this EGF molecule is expressed from both parental genomes during development. Both EGF3 and EGF4 induce the phosphorylation of membrane proteins of the blastula stage embryos, but EGF4 stimulates phosphorylation of proteins only in membranes prepared from homologous embryos, suggesting that it utilizes a unique pathway involving a species-specific

  18. Species-specific heavy metal accumulation patterns of earthworms on a floodplain in Japan.

    PubMed

    Kamitani, Takafumi; Kaneko, Nobuhiro

    2007-01-01

    We identified all earthworm species found on a floodplain contaminated by heavy metals (Cu, Zn, Cd, and Pb) from an old mine in central Japan and compared their abundance, biomass, and heavy metal concentrations in tissue. There were six species belonging to three families: Megascolecidae, Moniligastridae, and Lumbricidae. Earthworm community structure seemed to be influenced mostly by soil properties, especially pH and clay fraction. Despite the same endogeic characteristics, species-specific patterns of heavy metal accumulation were observed: species in Megascolecidae and Lumbricidae had relatively lower concentrations compared to those in Moniligastridae. Within Moniligastridae, Drawida sp. accumulated Cu and Pb markedly higher than Drawida japonica. Based on heavy metal concentrations in extracts of CaCl(2) and diethylenetriaminepentaacetic acid, the aging caused remarkably low concentrations in pore water, indicating low availability by dermal uptake. Therefore the different patterns of heavy metal accumulation among species would partly result from species-specific gut process.

  19. Bacterial communities and species-specific associations with the mucus of Brazilian coral species

    PubMed Central

    Carlos, Camila; Torres, Tatiana T.; Ottoboni, Laura M. M.

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  20. Retroperitoneal inflammation

    MedlinePlus

    ... page: //medlineplus.gov/ency/article/001255.htm Retroperitoneal inflammation To use the sharing features on this page, please enable JavaScript. Retroperitoneal inflammation is swelling that occurs in the retroperitoneal space. ...

  1. Programmed death in a unicellular organism has species-specific fitness effects.

    PubMed

    Durand, Pierre M; Choudhury, Rajdeep; Rashidi, Armin; Michod, Richard E

    2014-02-01

    Programmed cell death (PCD) is an ancient phenomenon and its origin and maintenance in unicellular life is unclear. We report that programmed death provides differential fitness effects that are species specific in the model organism Chlamydomonas reinhardtii. Remarkably, PCD in this organism not only benefits others of the same species, but also has an inhibitory effect on the growth of other species. These data reveal that the fitness effects of PCD can depend upon genetic relatedness.

  2. Species-specific toxicity of troglitazone on rats and human by gel entrapped hepatocytes

    SciTech Connect

    Shen, Chong; Meng, Qin; Zhang, Guoliang

    2012-01-01

    Troglitazone, despite passing preclinical trials on animals, was shortly withdrawn from market due to its severe hepatotoxicity in clinic. As rat hepatocyte monolayer consistently showed sensitive troglitazone toxicity as human hepatocyte monolayer in contrast to the species-specific toxicity in vivo, this paper utilized both hepatocytes in three-dimensional culture of gel entrapment to reflect the species difference on hepatotoxicity. Rat hepatocytes in gel entrapment did not show obvious cellular damage even under a long-term exposure for 21 days while gel entrapped human hepatocytes significantly displayed oxidative stress, steatosis, mitochondrial damage and cell death at a short exposure for 4 days. As a result, the detected species-specific toxicity of troglitazone between gel entrapped rat and human hepatocytes consisted well with the situation in vivo but was in a sharp contrast to the performance of two hepatocytes by monolayer culture. Such contradictory toxicity of rat hepatocytes between monolayer and gel entrapment culture could be explained by the fact that troglitazone was cleared more rapidly in gel entrapment than in monolayer culture. Similarly, the differential clearance of troglitazone in rat and human might also explain its species-specific toxicity. Therefore, gel entrapment of hepatocytes might serve as a platform for evaluation of drug toxicity at early stage of drug development by reducing costs, increasing the likelihood of clinical success and limiting human exposure to unsafe drugs. -- Highlights: ► Species-specific toxicity of troglitazone reflected by rat/human hepatocytes ► 3D hepatocytes in 21 days’ long-term culture used for drug hepatotoxicity ► Oversensitive toxicity in hepatocyte monolayer by slow troglitazone clearance.

  3. Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response.

    PubMed

    Webb, Andrew E; Gerek, Z Nevin; Morgan, Claire C; Walsh, Thomas A; Loscher, Christine E; Edwards, Scott V; O'Connell, Mary J

    2015-07-01

    It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Distinct antimicrobial peptide expression determines host species-specific bacterial associations

    PubMed Central

    Franzenburg, Sören; Walter, Jonas; Künzel, Sven; Wang, Jun; Baines, John F.; Bosch, Thomas C. G.; Fraune, Sebastian

    2013-01-01

    Animals are colonized by coevolved bacterial communities, which contribute to the host’s health. This commensal microbiota is often highly specific to its host-species, inferring strong selective pressures on the associated microbes. Several factors, including diet, mucus composition, and the immune system have been proposed as putative determinants of host-associated bacterial communities. Here we report that species-specific antimicrobial peptides account for different bacterial communities associated with closely related species of the cnidarian Hydra. Gene family extensions for potent antimicrobial peptides, the arminins, were detected in four Hydra species, with each species possessing a unique composition and expression profile of arminins. For functional analysis, we inoculated arminin-deficient and control polyps with bacterial consortia characteristic for different Hydra species and compared their selective preferences by 454 pyrosequencing of the bacterial microbiota. In contrast to control polyps, arminin-deficient polyps displayed decreased potential to select for bacterial communities resembling their native microbiota. This finding indicates that species-specific antimicrobial peptides shape species-specific bacterial associations. PMID:24003149

  5. Species-specific PCR for the identification of Cooperia curticei (Nematoda: Trichostrongylidae) in sheep.

    PubMed

    Amarante, M R V; Bassetto, C C; Neves, J H; Amarante, A F T

    2014-12-01

    Agricultural ruminants usually harbour mixed infections of gastrointestinal nematodes. A specific diagnosis is important because distinct species can differ significantly in their fecundity and pathogenicity. Haemonchus spp. and Cooperia spp. are the most important gastrointestinal nematodes infecting ruminants in subtropical/tropical environments. In Brazil, C. punctata is more adapted to cattle than sheep. Additionally, C. spatulata appears to be more adapted to cattle, whereas C. curticei is more adapted to sheep. However, infection of sheep with C. punctata is common when cattle and sheep share the same pasture. Although morphological analyses have been widely used to identify nematodes, molecular methods can overcome technical limitations and help improve species-specific diagnoses. Genetic markers in the first and second internal transcribed spacers (ITS-1 and ITS-2, respectively) of nuclear ribosomal DNA (rDNA) have been used successfully to detect helminths. In the present study, the ITS-1 region was analysed and used to design a species-specific oligonucleotide primer pair to identify C. curticei. The polymerase chain reaction (PCR) product was sequenced and showed 97% similarity to C. oncophora partial ITS-1 clones and 99% similarity to the C. curticei sequence JF680982. The specificity of this primer pair was corroborated by the analysis of 17 species of helminths, including C. curticei, C. punctata and C. spatulata. Species-specific diagnosis, which has implications for rapid and reliable identification, can support studies on the biology, ecology and epidemiology of trichostrongylid nematodes in a particular geographical location.

  6. Measuring and modeling the variation in species-specific transpiration in temperate deciduous hardwoods.

    PubMed

    Bowden, Joseph D; Bauerle, William L

    2008-11-01

    We investigated which parameters required by the MAESTRA model were most important in predicting leaf-area-based transpiration in 5-year-old trees of five deciduous hardwood species-yoshino cherry (Prunus x yedoensis Matsum.), red maple (Acer rubrum L. 'Autumn Flame'), trident maple (Acer buergeranum Miq.), Japanese flowering cherry (Prunus serrulata Lindl. 'Kwanzan') and London plane-tree (Platanus x acerifolia (Ait.) Willd.). Transpiration estimated from sap flow measured by the heat balance method in branches and trunks was compared with estimates predicted by the three-dimensional transpiration, photosynthesis and absorbed radiation model, MAESTRA. MAESTRA predicted species-specific transpiration from the interactions of leaf-level physiology and spatially explicit micro-scale weather patterns in a mixed deciduous hardwood plantation on a 15-min time step. The monthly differences between modeled mean daily transpiration estimates and measured mean daily sap flow ranged from a 35% underestimation for Acer buergeranum in June to a 25% overestimation for A. rubrum in July. The sensitivity of the modeled transpiration estimates was examined across a 30% error range for seven physiological input parameters. The minimum value of stomatal conductance as incident solar radiation tends to zero was determined to be eight times more influential than all other physiological model input parameters. This work quantified the major factors that influence modeled species-specific transpiration and confirmed the ability to scale leaf-level physiological attributes to whole-crown transpiration on a species-specific basis.

  7. Development of a species-specific coproantigen ELISA for human Taenia solium taeniasis.

    PubMed

    Guezala, Maria-Claudia; Rodriguez, Silvia; Zamora, Humberto; Garcia, Hector H; Gonzalez, Armando E; Tembo, Alice; Allan, James C; Craig, Philip S

    2009-09-01

    Taenia solium causes human neurocysticercosis and is endemic in underdeveloped countries where backyard pig keeping is common. Microscopic fecal diagnostic methods for human T. solium taeniasis are not very sensitive, and Taenia saginata and Taenia solium eggs are indistinguishable under the light microscope. Coproantigen (CoAg) ELISA methods are very sensitive, but currently only genus (Taenia) specific. This paper describes the development of a highly species-specific coproantigen ELISA test to detect T. solium intestinal taeniasis. Sensitivity was maintained using a capture antibody of rabbit IgG against T. solium adult whole worm somatic extract, whereas species specificity was achieved by utilization of an enzyme-conjugated rabbit IgG against T. solium adult excretory-secretory (ES) antigen. A known panel of positive and negative human fecal samples was tested with this hybrid sandwich ELISA. The ELISA test gave 100% specificity and 96.4% sensitivity for T. solium tapeworm carriers (N = 28), with a J index of 0.96. This simple ELISA incorporating anti-adult somatic and anti-adult ES antibodies provides the first potentially species-specific coproantigen test for human T. solium taeniasis.

  8. To open or to close: species-specific stomatal responses to simultaneously applied opposing environmental factors.

    PubMed

    Merilo, Ebe; Jõesaar, Indrek; Brosché, Mikael; Kollist, Hannes

    2014-04-01

    Plant stomatal responses to single environmental factors are well studied; however, responses to a change in two (or more) factors - a common situation in nature - have been less frequently addressed. We studied the stomatal responses to a simultaneous application of opposing environmental factors in six evolutionarily distant mono- and dicotyledonous herbs representing different life strategies (ruderals, competitors and stress-tolerators) to clarify whether the crosstalk between opening- and closure-inducing pathways leading to stomatal response is universal or species-specific. Custom-made gas exchange devices were used to study the stomatal responses to a simultaneous application of two opposing factors: decreased/increased CO2 concentration and light availability or reduced air humidity. The studied species responded similarly to changes in single environmental factors, but showed species-specific and nonadditive responses to two simultaneously applied opposing factors. The stomata of the ruderals Arabidopsis thaliana and Thellungiella salsuginea (previously Thellungiella halophila) always opened, whereas those of competitor-ruderals either closed in all two-factor combinations (Triticum aestivum), remained relatively unchanged (Nicotiana tabacum) or showed a response dominated by reduced air humidity (Hordeum vulgare). Our results, indicating that in changing environmental conditions species-specific stomatal responses are evident that cannot be predicted from studying one factor at a time, might be interesting for stomatal modellers, too.

  9. Species-specific transpiration responses to intermediate disturbance in a northern hardwood forest

    NASA Astrophysics Data System (ADS)

    Matheny, Ashley M.; Bohrer, Gil; Vogel, Christoph S.; Morin, Timothy H.; He, Lingli; Frasson, Renato Prata de Moraes; Mirfenderesgi, Golnazalsadat; Schäfer, Karina V. R.; Gough, Christopher M.; Ivanov, Valeriy Y.; Curtis, Peter S.

    2014-12-01

    Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large-scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem girdling all canopy-dominant early successional trees to simulate an accelerated age-related senescence associated with natural succession. Using 3 years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance-induced changes to plot level and species-specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species-specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during postdisturbance (62.5 and 132.2%, respectively), red maple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porous anisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, and paper birch, all diffuse porous species, had the lowest relative hysteresis. We employed the Penman-Monteith model for LE to demonstrate that these species-specific responses to disturbance are not well captured using current modeling strategies and that accounting for changes to leaf area index and plot microclimate are insufficient to fully describe the effects of disturbance on transpiration.

  10. Screening of species-specific lactic acid bacteria for veal calves multi-strain probiotic adjuncts.

    PubMed

    Ripamonti, Barbara; Agazzi, Alessandro; Bersani, Carla; De Dea, Paola; Pecorini, Chiara; Pirani, Silvia; Rebucci, Raffaella; Savoini, Giovanni; Stella, Simone; Stenico, Alberta; Tirloni, Erica; Domeneghini, Cinzia

    2011-06-01

    The selection of promising specific species of lactic acid bacteria with potential probiotic characteristics is of particular interest in producing multi species-specific probiotic adjuncts in veal calves rearing. The aim of the present work was to select and evaluate in vitro the functional activity of lactic acid bacteria, Bifidobacterium longum and Bacillus coagulans strains isolated from veal calves in order to assess their potential use as multi species-specific probiotics for veal calves. For this purpose, bacterial strains isolated from faeces collected from 40 healthy 50-day-calves, were identified by RiboPrinter and 16s rRNA gene sequence. The most frequent strains belonged to the species B. longum, Streptococcus bovis, Lactobacillus animalis and Streptococcus macedonicus. Among these, 7 strains were chosen for testing their probiotic characteristics in vitro. Three strains, namely L. animalis SB310, Lactobacillus paracasei subsp. paracasei SB137 and B. coagulans SB117 showed varying individual but promising capabilities to survive in the gastrointestinal tract, to adhere, to produce antimicrobial compounds. These three selected species-specific bacteria demonstrated in vitro, both singularly and mixed, the functional properties needed for their use as potential probiotics in veal calves.

  11. SPECIES SPECIFIC DIETARY ARSENIC EXPOSURE ASSESSMENT: THE NEED TO ESTIMATE BIOACCESSIBILITY AND ASSESSING THE IMPLIED PRESYSTEMIC METABOLISM IMPLICATIONS

    EPA Science Inventory

    The chemical form specific toxicity of arsenic dictates the need for species specific quantification in order to accurately assess the risk from an exposure. The literature has begun to produce preliminary species specific databases for certain dietary sources, but a quantitativ...

  12. SPECIES SPECIFIC DIETARY ARSENIC EXPOSURE ASSESSMENT: THE NEED TO ESTIMATE BIOACCESSIBILITY AND ASSESSING THE IMPLIED PRESYSTEMIC METABOLISM IMPLICATIONS

    EPA Science Inventory

    The chemical form specific toxicity of arsenic dictates the need for species specific quantification in order to accurately assess the risk from an exposure. The literature has begun to produce preliminary species specific databases for certain dietary sources, but a quantitativ...

  13. Defining species-specific immunodominant B cell epitopes for molecular serology of Chlamydia species.

    PubMed

    Rahman, K Shamsur; Chowdhury, Erfan U; Poudel, Anil; Ruettger, Anke; Sachse, Konrad; Kaltenboeck, Bernhard

    2015-05-01

    Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Defining Species-Specific Immunodominant B Cell Epitopes for Molecular Serology of Chlamydia Species

    PubMed Central

    Rahman, K. Shamsur; Chowdhury, Erfan U.; Poudel, Anil; Ruettger, Anke; Sachse, Konrad

    2015-01-01

    Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. PMID:25761461

  15. Species-specific separation of lake plankton reveals divergent food assimilation patterns in rotifers

    PubMed Central

    Burian, Alfred; Kainz, Martin J; Schagerl, Michael; Yasindi, Andrew

    2014-01-01

    1. The analysis of functional groups with a resolution to the individual species level is a basic requirement to better understand complex interactions in aquatic food webs. Species-specific stable isotope analyses are currently applied to analyse the trophic role of large zooplankton or fish species, but technical constraints complicate their application to smaller-sized plankton. 2. We investigated rotifer food assimilation during a short-term microzooplankton bloom in the East African soda lake Nakuru by developing a method for species-specific sampling of rotifers. 3. The two dominant rotifers, Brachionus plicatilis and Brachionus dimidiatus, were separated to single-species samples (purity >95%) and significantly differed in their isotopic values (4.1‰ in δ13C and 1.5‰ in δ15N). Bayesian mixing models indicated that isotopic differences were caused by different assimilation of filamentous cyanobacteria and particles <2 μm and underlined the importance of species-specific sampling of smaller plankton compartments. 4. A main difference was that the filamentous cyanobacterium Arthrospira fusiformis, which frequently forms blooms in African soda lakes, was an important food source for the larger-sized B. plicatilis (48%), whereas it was hardly ingested by B. dimidiatus. Overall, A. fusiformis was, relative to its biomass, assimilated to small extents, demonstrating a high grazing resistance of this species. 5. In combination with high population densities, these results demonstrate a strong potential of rotifer blooms to shape phytoplankton communities and are the first in situ demonstration of a quantitatively important direct trophic link between rotifers and filamentous cyanobacteria. PMID:25866422

  16. Species-specific regulation of fibrinogen synthesis with implications for porcine hepatocyte xenotransplantation.

    PubMed

    Ramackers, Wolf; Klose, Johannes; Vondran, Florian W R; Schrem, Harald; Kaltenborn, Alexander; Klempnauer, Jürgen; Kleine, Moritz

    2014-01-01

    Patients with liver failure could potentially be bridged with porcine xenogeneic liver cell transplantation. We examined species-specific differences between primary human and porcine hepatocytes in the regulation of coagulation protein expression and function. Isolated primary human and porcine hepatocytes were stimulated with either porcine or human interleukin (IL)-6 (10 ng/ml), IL-1β (10 ng/ml), and tumor necrosis factor-alpha (TNF-α, 30 ng/ml). mRNA expression of coagulation factors were measured by RT-PCR and real-time PCR. Cell culture supernatants were used for the measurement of fibrinogen by ELISA and determination of fibrin clot generation. Fibrinogen expression in human hepatocytes increased after IL-6 treatment (P = 0.010) and decreased after TNF-α treatment (P = 0.005). Porcine hepatocytes displayed a lower increase in fibrinogen expression after IL-6 treatment as compared to hepatocytes of human origin (P = 0.021). Porcine hepatocytes responded contrarily following TNF-α treatment with an increased expression of fibrinogen resulting in a significant species-specific difference between human and porcine hepatocytes (P = 0.029). Fibrin polymer generation by human hepatocytes was stable and widely branched after IL-6 treatment, while stimulation with TNF-α displayed no fibrin generation at all. In contrast, treatment of porcine hepatocytes with TNF-α resulted in generation of a stable and widely branched fibrin polymer, and stimulation with IL-6 only leads to generation of partial fibrin aggregates. We identified species-specific differences in the regulation of fibrinogen mRNA expression and fibrin generation under inflammatory stimuli. In hepatic xenotransplantation of porcine origin, these interspecies differences might lead to a loss of physiological coagulation function and a loss of transplanted cells. © 2014 John Wiley & Sons A/S Published by John Wiley & Sons Ltd.

  17. The development of species-specific immunodiagnostics for Stachybotrys chartarum: the role of cross-reactivity.

    PubMed

    Schmechel, Detlef; Simpson, Janet P; Beezhold, Donald; Lewis, Daniel M

    2006-02-20

    Mold contamination and exposure to fungi in indoor environments has been associated with various adverse health effects but little is known about the significance of individual fungal species in the initiation or exacerbation of such effects. Using Stachybotrys chartarum as a model fungus we sought to demonstrate that monoclonal antibodies (mAbs) can provide species-specific diagnostic reagents and also be used to investigate immunological cross-reactivity patterns among fungi. Mice were immunized with S. chartarum spore walls and monoclonal antibodies were screened against 60 fungal species and 24 different isolates of S. chartarum using an indirect ELISA. One species-specific mAb (IgG(1)) reacted only with spore preparations but not mycelium of S. chartarum or propagules of any other fungus. Five cross-reactive mAbs (IgM) documented extensive cross-reactivity among nine related Stachybotrys species and several non-related genera including several species of Cladosporium, Memnoniella, Myrothecium and Trichoderma. We also found that the ELISA reactivity for cross-reactive antigens and different isolates of S. chartarum differed considerably for normalized total amounts of mycelial antigen. We demonstrate that mAbs and immunoassays have the potential to detect S. chartarum species-specifically. The observed reactivity patterns with cross-reactive mAbs suggest that several fungi may share common antigens and that the majority of antigens are expressed by spores and mycelia. The observed cross-reactivity patterns need to be considered for accurate interpretations of environmental and serological analyses.

  18. Species-specific bird functions in a forest-canopy food web.

    PubMed Central

    Murakami, M; Nakano, S

    2000-01-01

    Bird functions in a forest-canopy food web were evaluated by a large-scale field experiment using 'canopy' enclosures. By controlling the presence of two bird species, great tits (Parus major; foliage gleaner) and nuthatches (Sitta europaea; trunk gleaner), in the enclosures, their effect on predatory insects (ants), herbivorous insects (Lepidoptera larvae) and producers (oak trees) was quantified. Great tits reduced the density of Lepidoptera larvae and, indirectly, leaf damage, but had no impact on ants. Nuthatches decreased the density of ants but did not influence either Lepidoptera larvae or leaf damage. These results highlight species-specific functions of birds in the maintenance of forest ecosystems. PMID:11467421

  19. Species-specific impact of the autophagy machinery on Chikungunya virus infection.

    PubMed

    Judith, Delphine; Mostowy, Serge; Bourai, Mehdi; Gangneux, Nicolas; Lelek, Mickaël; Lucas-Hourani, Marianne; Cayet, Nadège; Jacob, Yves; Prévost, Marie-Christine; Pierre, Philippe; Tangy, Frédéric; Zimmer, Christophe; Vidalain, Pierre-Olivier; Couderc, Thérèse; Lecuit, Marc

    2013-06-01

    Chikungunya virus (CHIKV) is a recently re-emerged arbovirus that triggers autophagy. Here, we show that CHIKV interacts with components of the autophagy machinery during its replication cycle, inducing a cytoprotective effect. The autophagy receptor p62 protects cells from death by binding ubiquitinated capsid and targeting it to autophagolysosomes. By contrast, the human autophagy receptor NDP52--but not its mouse orthologue--interacts with the non-structural protein nsP2, thereby promoting viral replication. These results highlight the distinct roles of p62 and NDP52 in viral infection, and identify NDP52 as a cellular factor that accounts for CHIKV species specificity.

  20. Chlamydospore formation on Staib agar as a species-specific characteristic of Candida dubliniensis.

    PubMed

    Staib, P; Morschhäuser, J

    1999-01-01

    Staib agar (Syn. Guizotia abyssinica creatinine agar) was evaluated for differentiation between the highly related yeast species Candida albicans and Candida dubliniensis. On these agar plates C. dubliniensis formed rough colonies due to mycelial growth and produced abundant chlamydospores whereas C. albicans grew only in smooth colonies and without chlamydospore formation. The rough colonies of C. dubliniensis could be readily distinguished from the smooth C. albicans colonies. These results demonstrate that, under certain growth conditions, mycelial growth with chlamydospore formation is a species-specific marker that can be used for the identification of C. dubliniensis.

  1. Identification of Lactobacillus brevis using a species-specific AFLP-derived marker.

    PubMed

    Fusco, Vincenzina; Quero, Grazia Marina; Chieffi, Daniele; Franz, Charles M A P

    2016-09-02

    A simple and specific method for the rapid detection and identification of Lactobacillus brevis was developed. A fAFLP (Fluorescent Amplified Fragment Length Polymorphisms) marker for L. brevis was used to design oligonucleotide primers for a species-specific PCR assay, targeting a 125bp fragment of the gene encoding the aldo/keto reductase of the diketogulonate-reductase family of L. brevis. This assay resulted in 100% inclusivity and exclusivity of assignment of strains to the species L. brevis. The analytical specificity of this assay was successfully tested to identify L. brevis isolates from sourdoughs.

  2. In vivo model for evaluation of species-specific virus vaccines.

    PubMed

    Skinner, G R; Davies, J; Billstrom, M A; Buchan, A

    1992-01-01

    It is difficult to evaluate the protective efficacy of species-specific viruses of humans and expensive companion animals where there is no non-human animal model. This study describes an in vivo model system which allows simultaneous operation of humoral, cell-mediated, interferon-like or other unidentified immunological defence mechanisms. There was evidence of in vivo inactivation of both enveloped and unenveloped DNA and RNA viruses including retrovirus mouse sarcoma virus/mouse leukaemia virus as evaluated by assay of the enzyme reverse transcriptase. This model will allow examination of vaccine efficacy in immunocompetent host animals while avoiding morbidity and/or mortality from virus infection in these animals.

  3. LINE-1 repetitive DNA probes for species-specific cloning from Mus spretus and Mus domesticus genomes.

    PubMed

    Rikke, B A; Hardies, S C

    1991-12-01

    Mus domesticus and Mus spretus mice are closely related subspecies. For genetic investigations involving hybrid mice, we have developed a set of species-specific oligonucleotide probes based on the detection of LINE-1 sequence differences. LINE-1 is a repetitive DNA family whose many members are interspersed among the genes. In this study, library screening experiments were used to fully characterize the species specificity of four M. domesticus LINE-1 probes and three M. spretus LINE-1 probes. It was found that the nucleotide differences detected by the probes define large, species-specific subfamilies. We show that collaborative use of such probes can be employed to selectively detect thousands of species-specific library clones. Consequently, these probes could be exploited to monitor and access almost any given species-specific region of interest within hybrid genomes.

  4. Species-specific size expansion and molecular evolution of the oleosins in angiosperms.

    PubMed

    Liu, Qi; Sun, Yepeng; Su, Wujie; Yang, Jing; Liu, Xiuming; Wang, Yanfang; Wang, Fawei; Li, Haiyan; Li, Xiaokun

    2012-11-10

    Oleosins are hydrophobic plant proteins thought to be important for the formation of oil bodies, which supply energy for seed germination and subsequent seedling growth. To better understand the evolutionary history and diversity of the oleosin gene family in plants, especially angiosperms, we systematically investigated the molecular evolution of this family using eight representative angiosperm species. A total of 73 oleosin members were identified, with six members in each of four monocot species and a greater but variable number in the four eudicots. A phylogenetic analysis revealed that the angiosperm oleosin genes belonged to three monophyletic lineages. Species-specific gene duplications, caused mainly by segmental duplication, led to the great expansion of oleosin genes and occurred frequently in eudicots after the monocot-eudicot divergence. Functional divergence analyses indicate that significant amino acid site-specific selective constraints acted on the different clades of oleosins. Adaptive evolution analyses demonstrate that oleosin genes were subject to strong purifying selection after their species-specific duplications and that rapid evolution occurred with a high degree of evolutionary dynamics in the pollen-specific oleosin genes. In conclusion, this study serves as a foundation for genome-wide analyses of the oleosins. These findings provide insight into the function and evolution of this gene family in angiosperms and pave the way for studies in other plants.

  5. Species-Specific Responses of Carnivores to Human-Induced Landscape Changes in Central Argentina.

    PubMed

    Caruso, Nicolás; Lucherini, Mauro; Fortin, Daniel; Casanave, Emma B

    2016-01-01

    The role that mammalian carnivores play in ecosystems can be deeply altered by human-driven habitat disturbance. While most carnivore species are negatively affected, the impact of habitat changes is expected to depend on their ecological flexibility. We aimed to identify key factors affecting the habitat use by four sympatric carnivore species in landscapes of central Argentina. Camera trapping surveys were carried out at 49 sites from 2011 to 2013. Each site was characterized by 12 habitat attributes, including human disturbance and fragmentation. Four landscape gradients were created from Principal Component Analysis and their influence on species-specific habitat use was studied using Generalized Linear Models. We recorded 74 events of Conepatus chinga, 546 of Pseudalopex gymnocercus, 193 of Leopardus geoffroyi and 45 of Puma concolor. We found that the gradient describing sites away from urban settlements and with low levels of disturbance had the strongest influence. L. geoffroyi was the only species responding significantly to the four gradients and showing a positive response to modified habitats, which could be favored by the low level of persecution by humans. P. concolor made stronger use of most preserved sites with low proportion of cropland, even though the species also used sites with an intermediate level of fragmentation. A more flexible use of space was found for C. chinga and P. gymnocercus. Our results demonstrate that the impact of human activities spans across this guild of carnivores and that species-specific responses appear to be mediated by ecological and behavioral attributes.

  6. Species-Specific Responses of Carnivores to Human-Induced Landscape Changes in Central Argentina

    PubMed Central

    Caruso, Nicolás; Lucherini, Mauro; Fortin, Daniel; Casanave, Emma B.

    2016-01-01

    The role that mammalian carnivores play in ecosystems can be deeply altered by human-driven habitat disturbance. While most carnivore species are negatively affected, the impact of habitat changes is expected to depend on their ecological flexibility. We aimed to identify key factors affecting the habitat use by four sympatric carnivore species in landscapes of central Argentina. Camera trapping surveys were carried out at 49 sites from 2011 to 2013. Each site was characterized by 12 habitat attributes, including human disturbance and fragmentation. Four landscape gradients were created from Principal Component Analysis and their influence on species-specific habitat use was studied using Generalized Linear Models. We recorded 74 events of Conepatus chinga, 546 of Pseudalopex gymnocercus, 193 of Leopardus geoffroyi and 45 of Puma concolor. We found that the gradient describing sites away from urban settlements and with low levels of disturbance had the strongest influence. L. geoffroyi was the only species responding significantly to the four gradients and showing a positive response to modified habitats, which could be favored by the low level of persecution by humans. P. concolor made stronger use of most preserved sites with low proportion of cropland, even though the species also used sites with an intermediate level of fragmentation. A more flexible use of space was found for C. chinga and P. gymnocercus. Our results demonstrate that the impact of human activities spans across this guild of carnivores and that species-specific responses appear to be mediated by ecological and behavioral attributes. PMID:26950300

  7. [Species-specific detection of Proteus vulgaris and Proteus mirabilis by the polymerase chain reaction].

    PubMed

    Limanskiĭ, A; Minukhin, V; Limanskaia, O; Pavlenko, N; Mishina, M; Tsygenenko, A

    2005-01-01

    Sets of primers for the species-specific detection of P. mirabilis and P. vulgaris by the polymerase chain reaction (PCR) were developed. As targets for these primers beta-lactamase and 16S rRNA gene fragments were chosen on the basis of the multiple leveling of the sequences of the DNA of all known P. mirabilis and P. vulgaris isolates. For differential detection oligonucleotides were selected in such a way that primers, specific for P. vulgaris, contained the non-paired nucleotide for P. mirabilis isolate at the 3'-end, and all other nucleotides were complementary to the beta-lactamase gene fragment. Primers, specific for gene 16S rRNA of P. mirabilis, contained the non-paired nucleotide for P. vulgaris isolates at the 3'-end. Standard PCR was carried out for 6 P. mirabilis and P. vulgaris strains. The use of PCR species-specific primers to P. vulgaris DNA made it possible to amplify the DNA fragment of the expected length only for P. vulgaris isolates, while the result of PCR for P. mirabilis was negative. PCR with primers specific to P. mirabilis permitted the detection of amplicon sized 101 nucleotides pairs only for P. mirabilis strains. These primers were optimized so as to use them in the specific differentiation of closely related P. mirabilis and P. vulgaris species by multiplex PCR. Genus-specific primers permitted the detection of bacterial gyrB gene of the genus Proteus were developed also.

  8. Species-specific PCR primers for the rapid identification of yeasts of the genus Zygosaccharomyces.

    PubMed

    Harrison, Elizabeth; Muir, Alastair; Stratford, Malcolm; Wheals, Alan

    2011-06-01

    Species-specific primer pairs that produce a single band of known product size have been developed for members of the Zygosaccharomyces clade including Zygosaccharomyces bailii, Zygosaccharomyces bisporus, Zygosaccharomyces kombuchaensis, Zygosaccharomyces lentus, Zygosaccharomyces machadoi, Zygosaccharomyces mellis and Zygosaccharomyces rouxii. An existing primer pair for the provisional new species Zygosaccharomyces pseudorouxii has been confirmed as specific. The HIS3 gene, encoding imidazole-glycerolphosphate dehydratase, was used as the target gene. This housekeeping gene evolves slowly and is thus well conserved among different isolates, but shows a significant number of base pair changes between even closely related species, sufficient for species-specific primer design. The primers were tested on type and wild strains of the genus Zygosaccharomyces and on members of the Saccharomycetaceae. Sequencing of the D1/D2 region of rDNA was used to confirm the identification of all nonculture collection isolates. This approach used extracted genomic DNA, but in practice, it can be used efficiently with a rapid colony PCR protocol. The method also successfully detected known and new hybrid strains of Z. rouxii and Z. pseudorouxii. The method is rapid, robust and inexpensive. It requires little expertise by the user and is thus useful for preliminary, large-scale screens.

  9. Species-Specific Seed Dispersal in an Obligate Ant-Plant Mutualism

    PubMed Central

    Youngsteadt, Elsa; Baca, Jeniffer Alvarez; Osborne, Jason; Schal, Coby

    2009-01-01

    Throughout lowland Amazonia, arboreal ants collect seeds of specific plants and cultivate them in nutrient-rich nests, forming diverse yet obligate and species-specific symbioses called Neotropical ant-gardens (AGs). The ants depend on their symbiotic plants for nest stability, and the plants depend on AGs for substrate and nutrients. Although the AGs are limited to specific participants, it is unknown at what stage specificity arises, and seed fate pathways in AG epiphytes are undocumented. Here we examine the specificity of the ant-seed interaction by comparing the ant community observed at general food baits to ants attracted to and removing seeds of the AG plant Peperomia macrostachya. We also compare seed removal rates under treatments that excluded vertebrates, arthropods, or both. In the bait study, only three of 70 ant species collected P. macrostachya seeds, and 84% of observed seed removal by ants was attributed to the AG ant Camponotus femoratus. In the exclusion experiment, arthropod exclusion significantly reduced seed removal rates, but vertebrate exclusion did not. We provide the most extensive empirical evidence of species specificity in the AG mutualism and begin to quantify factors that affect seed fate in order to understand conditions that favor its departure from the typical diffuse model of plant-animal mutualism. PMID:19194502

  10. Species-specificity of amphibia carbohydrate chains: the Bufo viridis case study.

    PubMed

    Coppin, Alexandra; Maes, Emmanuel; Strecker, Gérard

    2002-02-05

    The jelly coat surrounding the eggs of amphibia is composed of oviducal mucins and plays an important role in the fertilization process. From a structural and chemical point of view, these jellies are very different from one species to another. Bufo viridis is the 13th amphibia species studied in term of carbohydrate structural analysis. The oligosaccharides have been released from the oviducal mucins by reductive beta elimination, purified by various chromatography procedures and analyzed by (1)H and (13)C 1D-2D NMR spectroscopy. Among the 15 compounds, ten have novel structures, although they possess some well-known structural patterns as blood group epitopes (Le(x), Le(y)) or other sequences already observed in other amphibia species. These results reinforce our hypothesis about the strict species-specificity of these carbohydrate chains. It must be noted that such species-specificity does not depend on one particular monosaccharide but it is rather due to a set of particular tri- or tetrasaccharide sequences. Hence, B. viridis species could be characterized by the simultaneous presence of a 2,3,6-trisubstituted galactosyl residue, the GlcNAc(beta 1-3)[Fuc(alpha 1-4)]GlcNAc beta sequence and the Le(x), Le(y) or Cad determinants. The anionic charge of the oligosaccharides is carried only by sialic acid alpha-(2-->6)-linked to GalNAc-ol residue as in Bufo bufo or in Bufo arenarum.

  11. Species-specific responses to landscape fragmentation: implications for management strategies

    PubMed Central

    Blanchet, Simon; Rey, Olivier; Etienne, Roselyne; Lek, Sovan; Loot, Géraldine

    2010-01-01

    Habitat fragmentation affects the integrity of many species, but little is known about species-specific sensitivity to fragmentation. Here, we compared the genetic structure of four freshwater fish species differing in their body size (Leuciscus cephalus; Leuciscus leuciscus; Gobio gobio and Phoxinus phoxinus) between a fragmented and a continuous landscape. We tested if, overall, fragmentation affected the genetic structure of these fish species, and if these species differed in their sensitivity to fragmentation. Fragmentation negatively affected the genetic structure of these species. Indeed, irrespective of the species identity, allelic richness and heterozygosity were lower, and population divergence was higher in the fragmented than in the continuous landscape. This response to fragmentation was highly species-specific, with the smallest fish species (P. phoxinus) being slightly affected by fragmentation. On the contrary, fish species of intermediate body size (L. leuciscus and G. gobio) were highly affected, whereas the largest fish species (L. cephalus) was intermediately affected by fragmentation. We discuss the relative role of dispersal ability and effective population size on the responses to fragmentation we report here. The weirs studied here are of considerable historical importance. We therefore conclude that restoration programmes will need to consider both this societal context and the biological characteristics of the species sharing this ecosystem. PMID:25567925

  12. Endogenous retroviruses function as species-specific enhancer elements in the placenta

    PubMed Central

    Chuong, Edward B.; Rumi, M. A. Karim; Soares, Michael J.; Baker, Julie C.

    2013-01-01

    The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification1. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers between mouse and rat trophoblast stem cells (TSCs) and find that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific H3K4me1/H3K27ac-defined enhancers that functionally bind Cdx2, Eomes, and Elf5 - core factors that define the TSC regulatory network. Furthermore, we demonstrate that RLTR13D5 is capable of driving gene expression in rat placental cells. Comparison with other tissues revealed that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive to ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer cooption as a mechanism underlying the striking evolutionary diversification of placental development. PMID:23396136

  13. Species-specific response-topography of chickens' and pigeons' water-induced autoshaped responding.

    PubMed

    Ploog, Bertram O

    2014-07-01

    Four pigeons and eight chickens received autoshaping training where a keylight (conditioned stimulus) signaled response-independent deliveries of water (unconditioned stimulus). Pigeons drink while keeping their beaks submerged in water and moving their beaks to create suction ("mumbling"), whereas chickens drink by trapping a small amount of water in their mouths and then lifting their heads so the water trickles down. This experiment tested whether these and other species-specific differences in drinking and related behaviors of pigeons and chickens would be reflected in the form of conditioned (autoshaped) responding. Touchscreens and videotapes were used for data recording. Results showed that chickens moved their heads more than pigeons when drinking (unconditioned response). The birds also differed in conditioned responding in the presence of the keylight: Pigeons produced more keyswitch closures and mumbled at the keylight more than chickens whereas chickens scratched more than pigeons. In conclusion, with this unique comparative method that employed identical contingencies and comparable deprivation levels, species-specific differences in unconditioned responses and, more importantly, differences in their corresponding conditioned responses were observed. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Comparative phylogeography of two sympatric beeches in subtropical China: Species-specific geographic mosaic of lineages

    PubMed Central

    Zhang, Zhi-Yong; Wu, Rong; Wang, Qun; Zhang, Zhi-Rong; López-Pujol, Jordi; Fan, Deng-Mei; Li, De-Zhu

    2013-01-01

    In subtropical China, large-scale phylogeographic comparisons among multiple sympatric plants with similar ecological preferences are scarce, making generalizations about common response to historical events necessarily tentative. A phylogeographic comparison of two sympatric Chinese beeches (Fagus lucida and F. longipetiolata, 21 and 28 populations, respectively) was conducted to test whether they have responded to historical events in a concerted fashion and to determine whether their phylogeographic structure is exclusively due to Quaternary events or it is also associated with pre-Quaternary events. Twenty-three haplotypes were recovered for F. lucida and F. longipetiolata (14 each one and five shared). Both species exhibited a species-specific mosaic distribution of haplotypes, with many of them being range-restricted and even private to populations. The two beeches had comparable total haplotype diversity but F. lucida had much higher within-population diversity than F. longipetiolata. Molecular dating showed that the time to most recent common ancestor of all haplotypes was 6.36 Ma, with most haplotypes differentiating during the Quaternary. [Correction added on 14 October 2013, after first online publication: the timeunit has been corrected to ‘6.36’.] Our results support a late Miocene origin and southwards colonization of Chinese beeches when the aridity in Central Asia intensified and the monsoon climate began to dominate the East Asia. During the Quaternary, long-term isolation in subtropical mountains of China coupled with limited gene flow would have lead to the current species-specific mosaic distribution of lineages. PMID:24340187

  15. Species-specific trajectories of nitrogen isotopes in Indiana hardwood forests, USA

    NASA Astrophysics Data System (ADS)

    McLauchlan, K. K.; Craine, J. M.

    2011-06-01

    Humans have drastically altered the global nitrogen (N) cycle, and these alterations have begun to affect a variety of ecosystems. In North America, N deposition rates are highest in the Central US, yet there are few studies that examine whether N availability has been increasing to different tree species in the forests of the region. To determine the species-specific trajectories of N availability in secondary temperate forests experiencing high N deposition, we measured the N concentrations and composition of stable N isotopes in wood of four tree species from six hardwood forest remnants in Northern Indiana, USA. Annual nitrogen deposition rates averaged 5.8 kg ha-1 from 2000 to 2008 in this region. On average, wood δ15N values in Quercus alba have been increasing steadily over the past 100 yr. In contrast, wood δ15N values have been declining in three other hardwood species - Acer saccharum, Carya ovata, and Fagus grandifolia - over the same time period. The species-specific trends suggest a change in the partitioning of ammonium and nitrate among species, a change in nitrification rates, and/or offsetting changes in the dependence of species on mycorrhizal fungi. With no apparent net change in wood δ15N over the past century at the stand level, on average there appears to have been little change in N availability for these forests despite high levels of N deposition in the region.

  16. Species-specific trajectories of nitrogen isotopes in Indiana hardwood forests, USA

    NASA Astrophysics Data System (ADS)

    McLauchlan, K. K.; Craine, J. M.

    2012-02-01

    Humans have drastically altered the global nitrogen (N) cycle, and these alterations have begun to affect a variety of ecosystems. In North America, N deposition rates are highest in the central US, yet there are few studies that examine whether N availability has been increasing to different tree species in the forests of the region. To determine the species-specific trajectories of N availability in secondary temperate forests experiencing high N deposition, we measured the N concentrations and composition of stable N isotopes in wood of four tree species from six hardwood forest remnants in northern Indiana, USA. Annual nitrogen deposition rates averaged 5.8 kg ha-1 from 2000 to 2008 in this region. On average, wood δ15N values in Quercus alba have been increasing steadily over the past 100 years. In contrast, wood δ15N values have been declining in three other hardwood species - Acer saccharum, Carya ovata, and Fagus grandifolia - over the same time period. The species-specific trends suggest a change in the partitioning of ammonium and nitrate among species, due to an increase in nitrification rates over time. With no apparent net change in wood δ15N over the past century at the stand level, there is currently little evidence for consistent trends in stand-level N availability over time in the Indiana forests.

  17. Species-specific footdrumming in kangaroo rats: Dipodomys ingens, D. deserti, D. spectabilis

    PubMed

    Randall

    1997-11-01

    Footdrumming was compared in three allopatric species of kangaroo rat, Dipodomysfrom three habitats. Analysis of footdrumming recordings revealed species-specific patterns of drumming ranging from single thumps to individual footdrumming signatures. The desert kangaroo rat, D. desertidrums single thumps spaced 0.25-0.30 s apart that are sometimes introduced with a short footroll. The giant kangaroo rat, D. ingensdrums long footrolls that can average over 100 drums at 18 drums/s. The banner-tailed kangaroo rat, D. spectabilisdrums three to 38 footdrums in a footroll combined into sequences of two to 12 footrolls at a rate of 17 drums/s. In playback tests, all three species stood in alert postures and entered the burrow in response to footdrumming of their own and the other species. The rats also responded in species-specific ways. Dipodomys spectabilisdrummed to its own species' footdrumming, but not to playbacks of the single drums of D. desertiInstead of footdrumming to playbacks of its own species, D. deserti approached the speaker more frequently than did either of the other two species. Dipodomys ingens footdrummed equally to all footdrumming playbacks. The species' differences reflect differences in social tolerance and spacing. Dipodomys deserti rarely engages in footdrumming exchanges and chases visitors from the burrow. Dipodomys spectabilis engages in frequent footdrumming exchanges and some chases, and D. ingens seems to tolerate close neighbours and footdrums periodically.Copyright 1997 The Association for the Study of Animal Behaviour1997The Association for the Study of Animal Behaviour

  18. Species specificities among primates probed with commercially available fluorescence-based multiplex PCR typing kits.

    PubMed

    Hiroshige, Yuuji; Ohtaki, Hiroyuki; Yoshimoto, Takashi; Ogawa, Hisae; Ishii, Akira; Yamamoto, Toshimichi

    2015-09-01

    To assess species specificities among primates of signals from short tandem repeat (STR) loci included in two commercially available kits, mainly the AmpFlSTR Identifiler kit and additionally the GenePrint PowerPlex 16 system, we analyzed 69 DNA samples from 22 nonhuman primate species representing apes, Old World Monkeys (OWMs), New World Monkeys (NWMs), and prosimians. Each prosimian species and the NWM cotton-top tamarin apparently lacked all STR loci probed. Only one peak, the amelogenin-X peak, was evident in samples from all other NWMs, except the owl monkey. In contrast, several loci, including the amelogenin-X peak, was evident in samples from each OWM species. Notably, for each ape sample, the amelogenin peaks were concordant with morphological gender of the individual. Among the primates, especially in apes, the numbers of alleles for STR loci were increasing according to their phylogenetic order: prosimiansspecies specificities among primates for a few commercially released multiplex STR kits examined in this study would contribute to forensic examinations.

  19. Boechera Species Exhibit Species-Specific Responses to Combined Heat and High Light Stress

    PubMed Central

    Gallas, Genna; Waters, Elizabeth R.

    2015-01-01

    As sessile organisms, plants must be able to complete their life cycle in place and therefore tolerance to abiotic stress has had a major role in shaping biogeographical patterns. However, much of what we know about plant tolerance to abiotic stresses is based on studies of just a few plant species, most notably the model species Arabidopsis thaliana. In this study we examine natural variation in the stress responses of five diverse Boechera (Brassicaceae) species. Boechera plants were exposed to basal and acquired combined heat and high light stress. Plant response to these stresses was evaluated based on chlorophyll fluorescence measurements, induction of leaf chlorosis, and gene expression. Many of the Boechera species were more tolerant to heat and high light stress than A. thaliana. Gene expression data indicates that two important marker genes for stress responses: APX2 (Ascorbate peroxidase 2) and HsfA2 (Heat shock transcription factor A2) have distinct species-specific expression patterns. The findings of species-specific responses and tolerance to stress indicate that stress pathways are evolutionarily labile even among closely related species. PMID:26030823

  20. Species-specific effects of pigmentation negation on the neural response to faces

    PubMed Central

    Balas, Benjamin; Stevenson, Kate

    2013-01-01

    Face processing is limited in scope as a function of experience – discrimination ability and face-specific behavioral effects are reduced in out-group faces. Nonetheless, other-species faces phylogenetically close to our own may be processed by similar mechanisms as human faces. Presently, we asked whether or not the well-known effect of contrast-negation on face recognition (Galper, 1970) was exclusive to human faces or generalized to monkey faces. Negation disrupts face pigmentation substantially, allowing us to examine species-specific use of surface cues as a function of expertise. We tested adult observers behaviorally and electrophysiologically: Participants completed a 4AFC discrimination task subject to manipulations of face species and independent negation of image luminance and image chroma, and the same stimuli were used to collect event-related potentials in a go/no-go task. We predicted that expertise for human faces would lead to larger deleterious effects of negation for human faces in both tasks, reflected in longer RTs for correct responses in the discrimination task and species-specific modulation of the N170 and P200 by contrast-negation. Our results however, indicate that behaviorally, luminance and chroma negation affect discrimination performance in a species-independent manner, while similar effects of contrast-negation effects are evident in each species at different components of the ERP response. PMID:23792327

  1. Human MD-2 confers on mouse Toll-like receptor 4 species-specific lipopolysaccharide recognition.

    PubMed

    Akashi, S; Nagai, Y; Ogata, H; Oikawa, M; Fukase, K; Kusumoto, S; Kawasaki, K; Nishijima, M; Hayashi, S; Kimoto, M; Miyake, K

    2001-12-01

    Toll-like receptor 4 (TLR4) recognizes lipopolysaccharide (LPS). MD-2 is associated with TLR4 and imparts LPS responsiveness to it. Little is known, however, as to whether MD-2 directly regulates LPS recognition by TLR4. To address the issue, we took advantage of a species-specific pharmacology of lipid IVa, an analogue of lipid A. Lipid IVa acted agonistically on mouse (m) TLR4/MD-2 but not on human (h) TLR4/MD-2. Lipid IVa antagonized the agonistic effect of lipid A on hTLR4/MD-2. We examined the chimeric complex consisting of mTLR4 and hMD-2 to ask whether species specificity is conferred by TLR4 or MD-2. hMD-2 was clearly distinct from mMD-2 in the way of influencing LPS recognition by mTLR4. hMD-2 conferred on mTLR4 responsiveness to lipid A but not to lipid IVa. Moreover, lipid IVa acted as a lipid A antagonist on mTLR4 that is associated with hMD-2. Collectively, MD-2 directly influences the fine specificity of TLR4.

  2. Identification of hare meat by a species-specific marker of mitochondrial origin.

    PubMed

    Santos, Cristina G; Melo, Vitor S; Amaral, Joana S; Estevinho, Letícia; Oliveira, M Beatriz P P; Mafra, Isabel

    2012-03-01

    Meat species identification in food has gained increasing interest in recent years due to public health, economic and legal concerns. Following the consumer trend towards high quality products, game meat has earned much attention. The aim of the present work was to develop a DNA-based technique able to identify hare meat. Mitochondrial cytochrome b gene was used to design species-specific primers for hare detection. The new primers proved to be highly specific to Lepus species, allowing the detection of 0.01% of hare meat in pork meat by polymerase chain reaction (PCR). A real-time PCR assay with the new intercalating EvaGreen dye was further proposed as a specific and fast tool for hare identification with increased sensitivity (1pg) compared to end-point PCR (10pg). It can be concluded that the proposed new primers can be used by both species-specific end-point PCR or real-time PCR to accurately authenticate hare meat.

  3. A new Brucella canis species-specific PCR assay for the diagnosis of canine brucellosis.

    PubMed

    Kang, Sung-Il; Lee, Sang-Eun; Kim, Ji-Yeon; Lee, Kichan; Kim, Jong-Wan; Lee, Hyang-Keun; Sung, So-Ra; Heo, Young-Ran; Jung, Suk Chan; Her, Moon

    2014-09-01

    Brucellosis is a zoonotic disease that is transmitted from animals to humans, and the development of a rapid, accurate, and widely available identification method is essential for diagnosing this disease. In this study, we developed a new Brucella canis species-specific (BcSS) PCR assay and evaluated its specificity and sensitivity. A specific PCR primer set was designed based on the BCAN_B0548-0549 region in chromosome II of B. canis. The PCR detection for B. canis included amplification of a 300-bp product that is, not found on other Brucella species or, genetically or serologically related bacteria. The detection limit of BcSS-PCR assay was 6pg/μl by DNA dilution, or 3×10(3) colony-forming units (CFU) in the buffy coats separated from whole blood experimentally inoculated with B. canis. Using the buffy coat in this PCR assay resulted in approximately 100-times higher sensitivity for B. canis as compared to detect directly from whole blood. This is the first report of a species-specific PCR assay to detect B. canis, and the new assay will provide a valuable tool for the diagnosis of B. canis infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Identification and authentication of Rosa species through development of species-specific SCAR marker(s).

    PubMed

    Bashir, K M I; Awan, F S; Khan, I A; Khan, A I; Usman, M

    2014-05-30

    Roses (Rosa indica) belong to one of the most crucial groups of plants in the floriculture industry. Rosa species have special fragrances of interest to the perfume and pharmaceutical industries. The genetic diversity of plants based on morphological characteristics is difficult to measure under natural conditions due to the influence of environmental factors, which is why a reliable fingerprinting method was developed to overcome this problem. The development of molecular markers will enable the identification of Rosa species. In the present study, randomly amplified polymorphic DNA (RAPD) analysis was done on four Rosa species, Rosa gruss-an-teplitz (Surkha), Rosa bourboniana, Rosa centifolia, and Rosa damascena. A polymorphic RAPD fragment of 391 bp was detected in R. bourboniana, which was cloned, purified, sequenced, and used to design a pair of species-specific sequence-characterized amplified region (SCAR) primers (forward and reverse). These SCAR primers were used to amplify the specific regions of the rose genome. These PCR amplifications with specific primers are less sensitive to reaction conditions, and due to their high reproducibility, these species-specific SCAR primers can be used for marker-assisted selection and identification of Rosa species.

  5. Species-specific responses to landscape fragmentation: implications for management strategies.

    PubMed

    Blanchet, Simon; Rey, Olivier; Etienne, Roselyne; Lek, Sovan; Loot, Géraldine

    2010-05-01

    Habitat fragmentation affects the integrity of many species, but little is known about species-specific sensitivity to fragmentation. Here, we compared the genetic structure of four freshwater fish species differing in their body size (Leuciscus cephalus; Leuciscus leuciscus; Gobio gobio and Phoxinus phoxinus) between a fragmented and a continuous landscape. We tested if, overall, fragmentation affected the genetic structure of these fish species, and if these species differed in their sensitivity to fragmentation. Fragmentation negatively affected the genetic structure of these species. Indeed, irrespective of the species identity, allelic richness and heterozygosity were lower, and population divergence was higher in the fragmented than in the continuous landscape. This response to fragmentation was highly species-specific, with the smallest fish species (P. phoxinus) being slightly affected by fragmentation. On the contrary, fish species of intermediate body size (L. leuciscus and G. gobio) were highly affected, whereas the largest fish species (L. cephalus) was intermediately affected by fragmentation. We discuss the relative role of dispersal ability and effective population size on the responses to fragmentation we report here. The weirs studied here are of considerable historical importance. We therefore conclude that restoration programmes will need to consider both this societal context and the biological characteristics of the species sharing this ecosystem.

  6. Boechera species exhibit species-specific responses to combined heat and high light stress.

    PubMed

    Gallas, Genna; Waters, Elizabeth R

    2015-01-01

    As sessile organisms, plants must be able to complete their life cycle in place and therefore tolerance to abiotic stress has had a major role in shaping biogeographical patterns. However, much of what we know about plant tolerance to abiotic stresses is based on studies of just a few plant species, most notably the model species Arabidopsis thaliana. In this study we examine natural variation in the stress responses of five diverse Boechera (Brassicaceae) species. Boechera plants were exposed to basal and acquired combined heat and high light stress. Plant response to these stresses was evaluated based on chlorophyll fluorescence measurements, induction of leaf chlorosis, and gene expression. Many of the Boechera species were more tolerant to heat and high light stress than A. thaliana. Gene expression data indicates that two important marker genes for stress responses: APX2 (Ascorbate peroxidase 2) and HsfA2 (Heat shock transcription factor A2) have distinct species-specific expression patterns. The findings of species-specific responses and tolerance to stress indicate that stress pathways are evolutionarily labile even among closely related species.

  7. Species-specific seed dispersal in an obligate ant-plant mutualism.

    PubMed

    Youngsteadt, Elsa; Baca, Jeniffer Alvarez; Osborne, Jason; Schal, Coby

    2009-01-01

    Throughout lowland Amazonia, arboreal ants collect seeds of specific plants and cultivate them in nutrient-rich nests, forming diverse yet obligate and species-specific symbioses called Neotropical ant-gardens (AGs). The ants depend on their symbiotic plants for nest stability, and the plants depend on AGs for substrate and nutrients. Although the AGs are limited to specific participants, it is unknown at what stage specificity arises, and seed fate pathways in AG epiphytes are undocumented. Here we examine the specificity of the ant-seed interaction by comparing the ant community observed at general food baits to ants attracted to and removing seeds of the AG plant Peperomia macrostachya. We also compare seed removal rates under treatments that excluded vertebrates, arthropods, or both. In the bait study, only three of 70 ant species collected P. macrostachya seeds, and 84% of observed seed removal by ants was attributed to the AG ant Camponotus femoratus. In the exclusion experiment, arthropod exclusion significantly reduced seed removal rates, but vertebrate exclusion did not. We provide the most extensive empirical evidence of species specificity in the AG mutualism and begin to quantify factors that affect seed fate in order to understand conditions that favor its departure from the typical diffuse model of plant-animal mutualism.

  8. Species-specific antennal responses to tibial fragrances by male orchid bees.

    PubMed

    Eltz, Thomas; Ayasse, Manfred; Lunau, Klaus

    2006-01-01

    Male neotropical orchid bees (Euglossini) collect odoriferous substances from orchids and other sources and store them in tibial pouches, accumulating complex and species-specific bouquets. These fragrances are later exposed at display sites, presumably to attract females or conspecific males or both. We hypothesized that the necessity to detect and recognize specific fragrance bouquets has led to peripheral chemosensory specializations in different species of orchid bees. To test this, excised male antennae of four species of Euglossa were stimulated with complete tibial extracts of the same four species in a crosswise experiment. In the majority of the tested extracts, the amplitude of the electroantennogram (EAG) response was significantly different between species and always maximal in males of the extracted species. This effect did not appear to result from a given species' increased sensitivity toward certain attractive components: gas chromatography with electroantennographic detection (GC-EAD) of one extract of Euglossa tridentata evoked similar and generalized response patterns in all four species, encompassing a total of 34 peaks that elicited antennal responses. Therefore, the species effect in EAG responses to complete extracts likely resulted from species-specific interactions of compounds at the receptor level. Antennal specialization to conspecific bouquets adds additional strength to the argument that specificity is an important evolutionary aspect of euglossine tibial fragrances.

  9. Structure-based studies on species-specific inhibition of thymidylate synthase.

    PubMed

    Costi, M Paola; Tondi, Donatella; Rinaldi, Marcella; Barlocco, Daniela; Pecorari, Piergiorgio; Soragni, Fabrizia; Venturelli, Alberto; Stroud, Robert M

    2002-07-18

    Thymidylate synthase (TS) is a well-recognized target for anticancer chemotherapy. Due to its key role in the sole de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is an essential enzyme in all life forms. As such, it has been recently recognized as a valuable new target against infectious diseases. There is also a pressing need for new antimicrobial agents that are able to target strains that are drug resistant toward currently used drugs. In this context, species specificity is of crucial importance to distinguish between the invading microorganism and the human host, yet thymidylate synthase is among the most highly conserved enzymes. We combine structure-based drug design with rapid synthetic techniques and mutagenesis, in an iterative fashion, to develop novel antifolates that are not derived from the substrate and cofactor, and to understand the molecular basis for the observed species specificity. The role of structural and computational studies in the discovery of nonanalog antifolate inhibitors of bacterial TS, naphthalein and dansyl derivatives, and in the understanding of their biological activity profile, are discussed.

  10. Thin layers and species-specific characterization of the phytoplankton community in Monterey Bay, California, USA

    NASA Astrophysics Data System (ADS)

    Rines, J. E. B.; McFarland, M. N.; Donaghay, P. L.; Sullivan, J. M.

    2010-01-01

    During the summers of 2005 and 2006, experiments designed to understand the properties of densely concentrated, thin layers of plankton and the processes governing their dynamics were conducted in Monterey Bay, California, USA. Our goal was to elucidate the role that species-specific properties of phytoplankton play in thin layer dynamics. Using adaptive sampling, we collected water samples from inside and outside bio-optical features of the water column. Characterization of the phytoplankton was compiled from live and preserved samples, and analyzed within a framework of physical, optical, chemical and acoustical data. In both years, Monterey Bay was home to an extraordinarily diverse assemblage of phytoplankton and other protists. Bioluminescent dinoflagellates, and Harmful Algal Bloom (HAB) taxa were common. In 2005, community assemblages were widespread, thus advection of water through the experimental mooring array did not result in floristic changes. In 2006 phytoplankton were very patchy in horizontal distribution, and advection of water through the array was at times accompanied by dramatic shifts in community composition. Individual taxa often exhibited disparate patterns of vertical distribution, with some found throughout the water column, whereas others were restricted to narrow depth intervals. Thin layers were observed in both years. In 2005, the dinoflagellate Akashiwo sanguinea formed intense thin layers near the pycnocline at night, and migrated to near surface waters at dawn. In 2006, layer composition was more complex, and related to the water mass present at the time of sampling. Optically detected thin layers of phytoplankton can be studied from the perspective of the impact their high biomass has on both ecological processes, and ocean optics. But thin layers can also be studied from the species-specific perspective of each organism, its role within the thin layer habitat, and the impact that life within a thin layer has on its life history

  11. Proposed Hydrodynamic Model Improves Resolution of Species-Specific Responses to Drought and Disturbance

    NASA Astrophysics Data System (ADS)

    Matheny, A. M.; Bohrer, G.; Fiorella, R.; Mirfenderesgi, G.

    2015-12-01

    Plant functional types in land surface models (LSMs) are broadly defined, and often represent species with different physiologies within the same category. For example, trees of opposing hydraulic strategies and traits are commonly grouped together, as is the case of red oak and red maple. As a result, LSMs generate typical patterns of errors in predictions of transpiration and production. We studied sap flux, stem water storage, stomatal conductance, photosynthesis, rooting depth, and bole growth of these species at disturbed and undisturbed field sites in Michigan. Species-specific differences significantly impact temporal patterns of stomatal conductance and overall transpiration responses to both drought and disturbance. During drought, maples relied heavily on stem-stored water, while oaks did not. After disturbance, oaks increased stomatal conductance while maple conductance declined. Isotopic analysis of xylem water revealed that oak roots can access a deep groundwater source, which maple roots cannot. This deep rooting strategy permits transpiration and growth to continue in oaks during periods of water limitation, even when maples cease transpiration. Using 16 years of bole growth data, we show that maple growth is strongly correlated with mean annual precipitation, yet oak growth is not. We propose a framework to incorporate these species-specific differences into LSMs using the Finite-Element Tree-Crown Hydrodynamics model version 2 (FETCH2) that resolves the fast dynamics and diurnal hysteresis of stomatal conductance at the tree level. FETCH2 uses atmospheric and biological forcings from the LSM, simulates water movement through trees as flow through a system of porous media conduits, and calculates realistic hydraulic restrictions to stomatal conductance. This model replaces the current, non-physical link which empirically connects soil moisture to stomatal conductance in LSMs. FETCH2 resolved transpiration is then easily scaled to the plot level

  12. Species-Specific Chromosome Engineering Greatly Improves Fully Human Polyclonal Antibody Production Profile in Cattle.

    PubMed

    Matsushita, Hiroaki; Sano, Akiko; Wu, Hua; Wang, Zhongde; Jiao, Jin-An; Kasinathan, Poothappillai; Sullivan, Eddie J; Kuroiwa, Yoshimi

    2015-01-01

    Large-scale production of fully human IgG (hIgG) or human polyclonal antibodies (hpAbs) by transgenic animals could be useful for human therapy. However, production level of hpAbs in transgenic animals is generally very low, probably due to the fact that evolutionarily unique interspecies-incompatible genomic sequences between human and non-human host species may impede high production of fully hIgG in the non-human environment. To address this issue, we performed species-specific human artificial chromosome (HAC) engineering and tested these engineered HAC in cattle. Our previous study has demonstrated that site-specific genomic chimerization of pre-B cell receptor/B cell receptor (pre-BCR/BCR) components on HAC vectors significantly improves human IgG expression in cattle where the endogenous bovine immunoglobulin genes were knocked out. In this report, hIgG1 class switch regulatory elements were subjected to site-specific genomic chimerization on HAC vectors to further enhance hIgG expression and improve hIgG subclass distribution in cattle. These species-specific modifications in a chromosome scale resulted in much higher production levels of fully hIgG of up to 15 g/L in sera or plasma, the highest ever reported for a transgenic animal system. Transchromosomic (Tc) cattle containing engineered HAC vectors generated hpAbs with high titers against human-origin antigens following immunization. This study clearly demonstrates that species-specific sequence differences in pre-BCR/BCR components and IgG1 class switch regulatory elements between human and bovine are indeed functionally distinct across the two species, and therefore, are responsible for low production of fully hIgG in our early versions of Tc cattle. The high production levels of fully hIgG with hIgG1 subclass dominancy in a large farm animal species achieved here is an important milestone towards broad therapeutic applications of hpAbs.

  13. Species-Specific Chromosome Engineering Greatly Improves Fully Human Polyclonal Antibody Production Profile in Cattle

    PubMed Central

    Wu, Hua; Wang, Zhongde; Jiao, Jin-an; Kasinathan, Poothappillai; Sullivan, Eddie J.; Kuroiwa, Yoshimi

    2015-01-01

    Large-scale production of fully human IgG (hIgG) or human polyclonal antibodies (hpAbs) by transgenic animals could be useful for human therapy. However, production level of hpAbs in transgenic animals is generally very low, probably due to the fact that evolutionarily unique interspecies-incompatible genomic sequences between human and non-human host species may impede high production of fully hIgG in the non-human environment. To address this issue, we performed species-specific human artificial chromosome (HAC) engineering and tested these engineered HAC in cattle. Our previous study has demonstrated that site-specific genomic chimerization of pre-B cell receptor/B cell receptor (pre-BCR/BCR) components on HAC vectors significantly improves human IgG expression in cattle where the endogenous bovine immunoglobulin genes were knocked out. In this report, hIgG1 class switch regulatory elements were subjected to site-specific genomic chimerization on HAC vectors to further enhance hIgG expression and improve hIgG subclass distribution in cattle. These species-specific modifications in a chromosome scale resulted in much higher production levels of fully hIgG of up to 15 g/L in sera or plasma, the highest ever reported for a transgenic animal system. Transchromosomic (Tc) cattle containing engineered HAC vectors generated hpAbs with high titers against human-origin antigens following immunization. This study clearly demonstrates that species-specific sequence differences in pre-BCR/BCR components and IgG1 class switch regulatory elements between human and bovine are indeed functionally distinct across the two species, and therefore, are responsible for low production of fully hIgG in our early versions of Tc cattle. The high production levels of fully hIgG with hIgG1 subclass dominancy in a large farm animal species achieved here is an important milestone towards broad therapeutic applications of hpAbs. PMID:26107496

  14. Determination of methionine and selenomethionine in yeast by species-specific isotope dilution GC/MS.

    PubMed

    Yang, Lu; Mester, Zoltán; Sturgeon, Ralph E

    2004-09-01

    A method for the simultaneous determination of methionine (Met) and selenomethionine (SeMet) in yeast using species-specific isotope dilution (ID) gas chromatography/mass spectrometry (GC/MS) is described. Samples were digested by refluxing for 16 h with 4 M methanesulfonic acid. Analytes were derivatized with methyl chloroformate and extracted into chloroform for GC/MS analysis. In addition to use of commercially available 13C-enriched Met and SeMet spikes for species specific ID analysis, a 74Se-enriched SeMet spike was also available for comparison of results. In selective ion monitoring mode, the intensities of ions at m/z 221, 222, 269, 270, and 263 were used to calculate the 221/222, 269/270, and 269/263 ion ratios for quantification of Met and SeMet. Concentrations of 5959 +/- 33 and 3404 +/- 12 microg g(-1) (one standard deviation, n = 6) with relative standard deviations of 0.55 and 0.36% for Met and SeMet, respectively, were obtained using 13C-enriched spikes. A concentration of 3417 +/- 8 microg g(-1) (one standard deviation, n = 6) was obtained using the 74Se-enriched SeMet spike. The concentration of SeMet measured in the yeast is equivalent to 66.43 +/- 0.24% of total Se and 30.31 +/- 0.11% of total Met is in the form of SeMet. Method detection limits (three times the standard deviation) of 3.4 and 1.0 microg g(-1) were estimated for Met and SeMet, respectively, based on a 0.25-g subsample of yeast with 1 mL of extract used for derivatization. A similar concentration of 5930 +/- 29 microg g(-1) (one standard deviation, n = 4) for Met and a lower concentration of 2787 +/- 49 microg g(-1) (one standard deviation, n = 4) for SeMet were obtained for this yeast sample using species-specific ID analysis based on GC/MS with 13C-enriched Met and SeMet spikes when a 2-h open microwave digestion approach using 8 M methanesulfonic acid was used.

  15. A species-specific approach to the use of non-antimony treatments for cutaneous leishmaniasis.

    PubMed

    Ramanathan, Roshan; Talaat, Kawsar R; Fedorko, Daniel P; Mahanty, Siddhartha; Nash, Theodore E

    2011-01-01

    We used a species-specific approach to treat 10 patients with cutaneous leishmaniasis diagnosed using polymerase chain reaction. Non-antimony treatments (oral miltefosine, ketoconazole, and liposomal amphotericin B) were chosen as an alternative to pentavalent antimony drugs based on likely or proven drug efficacy against the infecting species. Leishmania Viannia panamensis was diagnosed in three patients and treated successfully with oral ketoconazole. Miltefosine treatment cured two patients with L. infantum chagasi. A wide variety of Leishmania responded to liposomal amphotericin B administered for 5-7 days. Three patients with L. V. braziliensis, one patient with L. tropica, and two patients with L. infantum chagasi were treated successfully. One person with L. V. braziliensis healed slowly because of a resistant bacterial superinfection, and a second patient with L. infantum chagasi relapsed and was retreated with miltefosine. These drugs were reasonably well-tolerated. In this limited case series, alternative non-antimony-based regimens were convenient, safe, and effective.

  16. A Species-Specific Approach to the Use of Non-Antimony Treatments for Cutaneous Leishmaniasis

    PubMed Central

    Ramanathan, Roshan; Talaat, Kawsar R.; Fedorko, Daniel P.; Mahanty, Siddhartha; Nash, Theodore E.

    2011-01-01

    We used a species-specific approach to treat 10 patients with cutaneous leishmaniasis diagnosed using polymerase chain reaction. Non-antimony treatments (oral miltefosine, ketoconazole, and liposomal amphotericin B) were chosen as an alternative to pentavalent antimony drugs based on likely or proven drug efficacy against the infecting species. Leishmania Viannia panamensis was diagnosed in three patients and treated successfully with oral ketoconazole. Miltefosine treatment cured two patients with L. infantum chagasi. A wide variety of Leishmania responded to liposomal amphotericin B administered for 5–7 days. Three patients with L. V. braziliensis, one patient with L. tropica, and two patients with L. infantum chagasi were treated successfully. One person with L. V. braziliensis healed slowly because of a resistant bacterial superinfection, and a second patient with L. infantum chagasi relapsed and was retreated with miltefosine. These drugs were reasonably well-tolerated. In this limited case series, alternative non-antimony–based regimens were convenient, safe, and effective. PMID:21212212

  17. Design of primer pairs for species-specific diagnosis of Leishmania (Leishmania) infantum chagasi using PCR.

    PubMed

    da Silveira Neto, Osvaldo José; Duarte, Sabrina Castilho; da Costa, Hérika Xavier; Linhares, Guido Fontgalland Coelho

    2012-01-01

    The objective of this study was to design and evaluate new primers for species-specific detection of L. infantum chagasi using PCR. Two combinations of primer pairs were established with the aim of obtaining specific amplification products from the L. infantum chagasi 18S rRNA gene. The combinations of the primer pairs and the respective sizes of the PCR products, based on the U422465 GenBank reference sequence of L. infantum chagasi, were: LCS1/LCS3 (259 bp) and LCS2/LCS3 (820 bp). It was concluded that the new PCR assays optimized using the primer pairs LCS1/LCS3 and LCS2/LCS3 were effective for specific detection of L. infantum chagasi, with analytical sensitivity to detect 1 pg/µL of DNA.

  18. Molecular basis for species-specific sensitivity to "hot" chili peppers.

    PubMed

    Jordt, Sven-Eric; Julius, David

    2002-02-08

    Chili peppers produce the pungent vanilloid compound capsaicin, which offers protection from predatory mammals. Birds are indifferent to the pain-producing effects of capsaicin and therefore serve as vectors for seed dispersal. Here, we determine the molecular basis for this species-specific behavioral response by identifying a domain of the rat vanilloid receptor that confers sensitivity to capsaicin to the normally insensitive chicken ortholog. Like its mammalian counterpart, the chicken receptor is activated by heat or protons, consistent with the fact that both mammals and birds detect noxious heat and experience thermal hypersensitivity. Our findings provide a molecular basis for the ecological phenomenon of directed deterence and suggest that the capacity to detect capsaicin-like inflammatory substances is a recent acquisition of mammalian vanilloid receptors.

  19. [Species specificity of the isoenzyme profile of lactate dehydrogenase in organs of rodents of various ecogenesis].

    PubMed

    Kozhevnikova, L K; Tiutiunnik, N N; Unzhakov, A R; Meldo, Kh I

    2004-02-01

    Separation of isoenzymes of lactate dehydrogenase (LDH, EC. 1.1.1.27) in extracts of heart, kidney, liver, spleen, lungs of nutrias, chinchillas by agar gel electrophoresis reveals a species specificity in ratio of electrophoretic fractions of the enzyme. The isoenzymes of LDH were seem to play an important role in adaptation of fur animals to environmental conditions. It has been shown that in semiaquatic mammals--nutrias, the relative content of the A-subunits in the isoenzymatic spectrum of LDH in organs was increased as compared with terrestrial animals--chinchillas, whereas relative content of B-subunits in these organs of chinchillas was very high. This is an example of subtle biochemical specialisation of function at molecular level to environmental conditions.

  20. Major outer membrane protein of Legionella pneumophila carries a species-specific epitope.

    PubMed Central

    Nolte, F S; Conlin, C A

    1986-01-01

    A monoclonal antibody (LP3IIG2) directed against a species-specific epitope of Legionella pneumophila is available from Genetic Systems Corp., Seattle, Wash., for use as a diagnostic reagent. Outer membrane protein-rich fractions were prepared from L. pneumophila serogroups 1 to 8 by treatment of cell envelopes with 2% Triton X-100. Immunoblots of sodium dodecyl sulfate-polyacrylamide gels demonstrated that each membrane fraction contained two bands that reacted with LP3IIG2. The monoclonal antibody bound preferentially to a 26,000-molecular-weight band that appears to result from modification of the 29,000-molecular-weight major outer membrane protein. Images PMID:2420824

  1. Species-Specific Secondary Metabolite Production in Marine Actinomycetes of the Genus Salinispora▿

    PubMed Central

    Jensen, Paul R.; Williams, Philip G.; Oh, Dong-Chan; Zeigler, Lisa; Fenical, William

    2007-01-01

    Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community. PMID:17158611

  2. Emergence of Species-Specific Transporters During Evolution of the Hemiascomycete Phylum

    PubMed Central

    De Hertogh, Benoît; Hancy, Frédéric; Goffeau, André; Baret, Philippe V.

    2006-01-01

    We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB classification system has allowed the identification within the Hemiascomycete phylum of 97 small phylogenetic transporter subfamilies comprising a total of 355 transporters submitted to four distinct evolution patterns named “ubiquitous,” “species specific,” “phylum gains and losses,” or “homoplasic.” This analysis identifies the transporters that contribute to the emergence of species during the evolution of the Hemiascomycete phylum and may aid in establishing novel phylogenetic criteria for species classification. PMID:16118182

  3. A species-specific periplasmic flagellar protein of Serpulina (Treponema) hyodysenteriae.

    PubMed Central

    Li, Z; Dumas, F; Dubreuil, D; Jacques, M

    1993-01-01

    We have previously reported that a 46-kDa protein present in an outer membrane protein preparation seemed to be a species-specific antigen of Serpulina hyodysenteriae (Z. S. Li, N. S. Jensen, M. Bélanger, M.-C. L'Espérance, and M. Jacques, J. Clin. Microbiol. 30:2941-2947, 1992). The objective of this study was to further characterize this antigen. A Western blot (immunoblot) analysis and immunogold labeling with a monospecific antiserum against this protein confirmed that the protein was present in all S. hyodysenteriae reference strains but not in the nonpathogenic organism Serpulina innocens. The immunogold labeling results also indicated that the protein was associated with the periplasmic flagella of S. hyodysenteriae. N-terminal amino acid sequencing confirmed that the protein was in fact a periplasmic flagellar sheath protein. The molecular mass of this protein, first estimated to be 46 kDa by Western blotting, was determined to be 44 kDa when the protein was evaluated more precisely by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the protein was glycosylated, as determined by glycoprotein staining and also by N-glycosidase F treatment. Five other periplasmic flagellar proteins of S. hyodysenteriae, which may have been the core proteins and had molecular masses of 39, 35, 32, 30, and 29 kDa, were antigenically related and cross-reacted with the periplasmic flagellar proteins of S. innocens. Finally, serum from a pig experimentally infected with S. hyodysenteriae recognized the 44-kDa periplasmic flagellar sheath protein. Our results suggest that the 44-kDa periplasmic flagellar sheath protein of S. hyodysenteriae is a species-specific glycoprotein antigen. Images PMID:8253687

  4. Environmental Drivers of Culicoides Phenology: How Important Is Species-Specific Variation When Determining Disease Policy?

    PubMed Central

    Searle, Kate R.; Barber, James; Stubbins, Francesca; Labuschagne, Karien; Carpenter, Simon; Butler, Adam; Denison, Eric; Sanders, Christopher; Mellor, Philip S.; Wilson, Anthony; Nelson, Noel; Gubbins, Simon; Purse, Bethan V.

    2014-01-01

    Since 2006, arboviruses transmitted by Culicoides biting midges (Diptera: Ceratopogonidae) have caused significant disruption to ruminant production in northern Europe. The most serious incursions involved strains of bluetongue virus (BTV), which cause bluetongue (BT) disease. To control spread of BTV, movement of susceptible livestock is restricted with economic and animal welfare impacts. The timing of BTV transmission in temperate regions is partly determined by the seasonal presence of adult Culicoides females. Legislative measures therefore allow for the relaxation of ruminant movement restrictions during winter, when nightly light-suction trap catches of Culicoides fall below a threshold (the ‘seasonally vector free period’: SVFP). We analysed five years of time-series surveillance data from light-suction trapping in the UK to investigate whether significant inter-specific and yearly variation in adult phenology exists, and whether the SVFP is predictable from environmental factors. Because female vector Culicoides are not easily morphologically separated, inter-specific comparisons in phenology were drawn from male populations. We demonstrate significant inter-specific differences in Culicoides adult phenology with the season of Culicoides scoticus approximately eight weeks shorter than Culicoides obsoletus. Species-specific differences in the length of the SVFP were related to host density and local variation in landscape habitat. When the Avaritia Culicoides females were modelled as a group (as utilised in the SFVP), we were unable to detect links between environmental drivers and phenological metrics. We conclude that the current treatment of Avaritia Culicoides as a single group inhibits understanding of environmentally-driven spatial variation in species phenology and hinders the development of models for predicting the SVFP from environmental factors. Culicoides surveillance methods should be adapted to focus on concentrated assessments of species-specific

  5. Environmental drivers of Culicoides phenology: how important is species-specific variation when determining disease policy?

    PubMed

    Searle, Kate R; Barber, James; Stubbins, Francesca; Labuschagne, Karien; Carpenter, Simon; Butler, Adam; Denison, Eric; Sanders, Christopher; Mellor, Philip S; Wilson, Anthony; Nelson, Noel; Gubbins, Simon; Purse, Bethan V

    2014-01-01

    Since 2006, arboviruses transmitted by Culicoides biting midges (Diptera: Ceratopogonidae) have caused significant disruption to ruminant production in northern Europe. The most serious incursions involved strains of bluetongue virus (BTV), which cause bluetongue (BT) disease. To control spread of BTV, movement of susceptible livestock is restricted with economic and animal welfare impacts. The timing of BTV transmission in temperate regions is partly determined by the seasonal presence of adult Culicoides females. Legislative measures therefore allow for the relaxation of ruminant movement restrictions during winter, when nightly light-suction trap catches of Culicoides fall below a threshold (the 'seasonally vector free period': SVFP). We analysed five years of time-series surveillance data from light-suction trapping in the UK to investigate whether significant inter-specific and yearly variation in adult phenology exists, and whether the SVFP is predictable from environmental factors. Because female vector Culicoides are not easily morphologically separated, inter-specific comparisons in phenology were drawn from male populations. We demonstrate significant inter-specific differences in Culicoides adult phenology with the season of Culicoides scoticus approximately eight weeks shorter than Culicoides obsoletus. Species-specific differences in the length of the SVFP were related to host density and local variation in landscape habitat. When the Avaritia Culicoides females were modelled as a group (as utilised in the SFVP), we were unable to detect links between environmental drivers and phenological metrics. We conclude that the current treatment of Avaritia Culicoides as a single group inhibits understanding of environmentally-driven spatial variation in species phenology and hinders the development of models for predicting the SVFP from environmental factors. Culicoides surveillance methods should be adapted to focus on concentrated assessments of species-specific

  6. Fingerprinting the Asterid Species Using Subtracted Diversity Array Reveals Novel Species-Specific Sequences

    PubMed Central

    Mantri, Nitin; Olarte, Alexandra; Li, Chun Guang; Xue, Charlie; Pang, Edwin C. K.

    2012-01-01

    Background Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade. Methodology/Principal Findings Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants. Conclusions/Significance Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve

  7. Ants Learn Aphid Species as Mutualistic Partners: Is the Learning Behavior Species-Specific?

    PubMed

    Hayashi, Masayuki; Nakamuta, Kiyoshi; Nomura, Masashi

    2015-12-01

    In ant-aphid associations, many aphid species provide ants with honeydew and are tended by ants, whereas others are never tended and are frequently preyed upon by ants. In these relationships, ants must have the ability to discriminate among aphid species, with mutualistic aphids being accepted as partners rather than prey. Although ants reportedly use cuticular hydrocarbons (CHCs) of aphids to differentiate between mutualistic and non-mutualistic species, it is unclear whether the ability to recognize mutualistic aphid species as partners is innate or involves learning. Therefore, we tested whether aphid recognition by ants depends on learning, and whether the learning behavior is species-specific. When workers of the ant Tetramorium tsushimae had previously tended the cowpea aphid, Aphis craccivora, they were less aggressive toward this species. In addition, ants also reduced their aggressiveness toward another mutualistic aphid species, Aphis fabae, after tending A. craccivora, whereas ants remained aggressive toward the non-mutualistic aphid, Acyrthosiphon pisum, regardless of whether or not they had previous experience in tending A. craccivora. When ants were offered glass dummies treated with CHCs of these aphid species, ants that had tended A. craccivora displayed reduced aggression toward CHCs of A. craccivora and A. fabae. Chemical analyses showed the similarity of the CHC profiles between A. craccivora and A. fabae but not with A. pisum. These results suggest that aphid recognition of ants involves learning, and that the learning behavior may not be species-specific because of the similarity of CHCs between different aphid species with which they form mutualisms.

  8. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges.

    PubMed

    Schmitt, Susanne; Tsai, Peter; Bell, James; Fromont, Jane; Ilan, Micha; Lindquist, Niels; Perez, Thierry; Rodrigo, Allen; Schupp, Peter J; Vacelet, Jean; Webster, Nicole; Hentschel, Ute; Taylor, Michael W

    2012-03-01

    Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.

  9. Species-Specific Traits Rather Than Resource Partitioning Mediate Diversity Effects on Resource Use

    PubMed Central

    Godbold, Jasmin A.; Rosenberg, Rutger; Solan, Martin

    2009-01-01

    Background The link between biodiversity and ecosystem processes has firmly been established, but the mechanisms underpinning this relationship are poorly documented. Most studies have focused on terrestrial plant systems where resource use can be difficult to quantify as species rely on a limited number of common resources. Investigating resource use at the bulk level may not always be of sufficient resolution to detect subtle differences in resource use, as species-specific nutritional niches at the biochemical level may also moderate diversity effects on resource use. Methodology/Principal Findings Here we use three co-occurring marine benthic echinoderms (Brissopsis lyrifera, Mesothuria intestinalis, Parastichopus tremulus) that feed on the same phytodetrital food source, to determine whether resource partitioning is the principal mechanism underpinning diversity effects on resource use. Specifically we investigate the use of phytodetrital pigments (chlorophylls and carotenoids) because many of these are essential for biological functions, including reproduction. Pigments were identified and quantified using reverse-phase high performance liquid Chromatography (HPLC) and data were analysed using a combination of extended linear regression with generalised least squares (GLS) estimation and standard multivariate techniques. Our analyses reveal no species-specific selectivity for particular algal pigments, confirming that these three species do not partition food resources at the biochemical level. Nevertheless, we demonstrate increased total resource use in diverse treatments as a result of selection effects and the dominance of one species (B. lyrifera). Conclusion Overall, we found no evidence for resource partitioning at the biochemical level, as pigment composition was similar between individuals, which is likely due to plentiful food availability. Reduced intra-specific competition in the species mixture combined with greater adsorption efficiency and

  10. Species-specific temporal variation in photosynthesis as a moderator of peatland carbon sequestration

    NASA Astrophysics Data System (ADS)

    Korrensalo, Aino; Alekseychik, Pavel; Hájek, Tomáš; Rinne, Janne; Vesala, Timo; Mehtätalo, Lauri; Mammarella, Ivan; Tuittila, Eeva-Stiina

    2017-01-01

    In boreal bogs plant species are low in number, but they differ greatly in their growth forms and photosynthetic properties. We assessed how ecosystem carbon (C) sink dynamics were affected by seasonal variations in the photosynthetic rate and leaf area of different species. Photosynthetic properties (light response parameters), leaf area development and areal cover (abundance) of the species were used to quantify species-specific net and gross photosynthesis rates (PN and PG, respectively), which were summed to express ecosystem-level PN and PG. The ecosystem-level PG was compared with a gross primary production (GPP) estimate derived from eddy covariance (EC) measurements.Species areal cover, rather than differences in photosynthetic properties, determined the species with the highest PG of both vascular plants and Sphagna. Species-specific contributions to the ecosystem PG varied over the growing season, which, in turn, determined the seasonal variation in ecosystem PG. The upscaled growing season PG estimate, 230 g C m-2, agreed well with the GPP estimated by the EC (243 g C m-2).Sphagna were superior to vascular plants in ecosystem-level PG throughout the growing season but had a lower PN. PN results indicated that areal cover of the species, together with their differences in photosynthetic parameters, shape the ecosystem-level C balance. Species with low areal cover but high photosynthetic efficiency appear to be potentially important for the ecosystem C sink. Results imply that functional diversity, i.e., the presence of plant groups with different seasonal timing and efficiency of photosynthesis, may increase the stability of C sinks of boreal bogs.

  11. Species-specific escape of Plasmodium sporozoites from oocysts of avian, rodent, and human malarial parasites.

    PubMed

    Orfano, Alessandra S; Nacif-Pimenta, Rafael; Duarte, Ana P M; Villegas, Luis M; Rodrigues, Nilton B; Pinto, Luciana C; Campos, Keillen M M; Pinilla, Yudi T; Chaves, Bárbara; Barbosa Guerra, Maria G V; Monteiro, Wuelton M; Smith, Ryan C; Molina-Cruz, Alvaro; Lacerda, Marcus V G; Secundino, Nágila F C; Jacobs-Lorena, Marcelo; Barillas-Mury, Carolina; Pimenta, Paulo F P

    2016-08-02

    Malaria is transmitted when an infected mosquito delivers Plasmodium sporozoites into a vertebrate host. There are many species of Plasmodium and, in general, the infection is host-specific. For example, Plasmodium gallinaceum is an avian parasite, while Plasmodium berghei infects mice. These two parasites have been extensively used as experimental models of malaria transmission. Plasmodium falciparum and Plasmodium vivax are the most important agents of human malaria, a life-threatening disease of global importance. To complete their life cycle, Plasmodium parasites must traverse the mosquito midgut and form an oocyst that will divide continuously. Mature oocysts release thousands of sporozoites into the mosquito haemolymph that must reach the salivary gland to infect a new vertebrate host. The current understanding of the biology of oocyst formation and sporozoite release is mostly based on experimental infections with P. berghei, and the conclusions are generalized to other Plasmodium species that infect humans without further morphological analyses. Here, it is described the microanatomy of sporozoite escape from oocysts of four Plasmodium species: the two laboratory models, P. gallinaceum and P. berghei, and the two main species that cause malaria in humans, P. vivax and P. falciparum. It was found that sporozoites have species-specific mechanisms of escape from the oocyst. The two model species of Plasmodium had a common mechanism, in which the oocyst wall breaks down before sporozoites emerge. In contrast, P. vivax and P. falciparum sporozoites show a dynamic escape mechanism from the oocyst via polarized propulsion. This study demonstrated that Plasmodium species do not share a common mechanism of sporozoite escape, as previously thought, but show complex and species-specific mechanisms. In addition, the knowledge of this phenomenon in human Plasmodium can facilitate transmission-blocking studies and not those ones only based on the murine and avian models.

  12. Species-specific variation in nesting and postfledging resource selection for two forest breeding migrant songbirds.

    PubMed

    Jenkins, Julianna M A; Thompson, Frank R; Faaborg, John

    2017-01-01

    Habitat selection is a fundamental component of community ecology, population ecology, and evolutionary biology and can be especially important to species with complex annual habitat requirements, such as migratory birds. Resource preferences on the breeding grounds may change during the postfledging period for migrant songbirds, however, the degree to which selection changes, timing of change, and whether all or only a few species alter their resource use is unclear. We compared resource selection for nest sites and resource selection by postfledging juvenile ovenbirds (Seiurus aurocapilla) and Acadian flycatchers (Empidonax virescens) followed with radio telemetry in Missouri mature forest fragments from 2012-2015. We used Bayesian discrete choice modeling to evaluate support for local vegetation characteristics on the probability of selection for nest sites and locations utilized by different ages of postfledging juveniles. Patterns of resource selection variation were species-specific. Resource selection models indicated that Acadian flycatcher habitat selection criteria were similar for nesting and dependent postfledging juveniles and selection criteria diverged when juveniles became independent from adults. After independence, flycatcher resource selection was more associated with understory foliage density. Ovenbirds differed in selection criteria between the nesting and postfledging periods. Fledgling ovenbirds selected areas with higher densities of understory structure compared to nest sites, and the effect of foliage density on selection increased as juveniles aged and gained independence. The differences observed between two sympatric forest nesting species, in both the timing and degree of change in resource selection criteria over the course of the breeding season, illustrates the importance of considering species-specific traits and postfledging requirements when developing conservation efforts, especially when foraging guilds or prey bases differ

  13. A crowd-sourcing approach for the construction of species-specific cell signaling networks.

    PubMed

    Bilal, Erhan; Sakellaropoulos, Theodore; Melas, Ioannis N; Messinis, Dimitris E; Belcastro, Vincenzo; Rhrissorrakrai, Kahn; Meyer, Pablo; Norel, Raquel; Iskandar, Anita; Blaese, Elise; Rice, John J; Peitsch, Manuel C; Hoeng, Julia; Stolovitzky, Gustavo; Alexopoulos, Leonidas G; Poussin, Carine

    2015-02-15

    Animal models are important tools in drug discovery and for understanding human biology in general. However, many drugs that initially show promising results in rodents fail in later stages of clinical trials. Understanding the commonalities and differences between human and rat cell signaling networks can lead to better experimental designs, improved allocation of resources and ultimately better drugs. The sbv IMPROVER Species-Specific Network Inference challenge was designed to use the power of the crowds to build two species-specific cell signaling networks given phosphoproteomics, transcriptomics and cytokine data generated from NHBE and NRBE cells exposed to various stimuli. A common literature-inspired reference network with 220 nodes and 501 edges was also provided as prior knowledge from which challenge participants could add or remove edges but not nodes. Such a large network inference challenge not based on synthetic simulations but on real data presented unique difficulties in scoring and interpreting the results. Because any prior knowledge about the networks was already provided to the participants for reference, novel ways for scoring and aggregating the results were developed. Two human and rat consensus networks were obtained by combining all the inferred networks. Further analysis showed that major signaling pathways were conserved between the two species with only isolated components diverging, as in the case of ribosomal S6 kinase RPS6KA1. Overall, the consensus between inferred edges was relatively high with the exception of the downstream targets of transcription factors, which seemed more difficult to predict. ebilal@us.ibm.com or gustavo@us.ibm.com. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  14. Site-specific structural analysis of a yeast prion strain with species-specific seeding activity

    PubMed Central

    Marcelino-Cruz, Anna Marie; Bhattacharya, Moumita; Anselmo, Aaron C

    2011-01-01

    Prion proteins misfold and aggregate into multiple infectious strain variants that possess unique abilities to overcome prion species barriers, yet the structural basis for the species-specific infectivities of prion strains is poorly understood. Therefore, we have investigated the site-specific structural properties of a promiscuous chimeric form of the yeast prion Sup35 from Saccharomyces cerevisiae and Candida albicans. The Sup35 chimera forms two strain variants, each of which selectively infect one species but not the other. Importantly, the N-terminal and middle domains of the Sup35 chimera (collectively referred to as Sup35NM) contain two prion recognition elements (one from each species) that regulate the nucleation of each strain. Mutations in either prion recognition element significantly bias nucleation of one strain conformation relative to the other. Here we have investigated the folding of each prion recognition element for the serine-to-arginine mutant at residue 17 of the Sup35NM chimera known to promote nucleation of C. albicans strain conformation. Using cysteine-specific labeling analysis, we find that residues in the C. albicans prion recognition element are solvent-shielded, while those outside the recognition sequence (including most of those in the S. cerevisiae recognition element) are solvent-exposed. Moreover, we find that proline mutations in the C. albicans recognition sequence disrupt the prion templating activity of this strain conformation. Our structural findings reveal that differential folding of complementary and non-complementary prion recognition elements within the prion amyloid core of the Sup35NM chimera is the structural basis for its species-specific templating activity. PMID:22048721

  15. Connections between circadian clocks and carbon metabolism reveal species-specific effects on growth control.

    PubMed

    Müller, Lukas M; von Korff, Maria; Davis, Seth J

    2014-06-01

    The plant circadian system exists in a framework of rhythmic metabolism. Much has been learned about the transcriptional machinery that generates the clock rhythm. Interestingly, these components are largely conserved between monocots and dicots, but key differences in physiological and developmental output processes have been found. How the clock coordinates carbon metabolism to drive plant growth performance is described with a focus on starch breakdown in Arabidopsis. It is proposed that clock effects on plant growth and fitness are more complex than just matching internal with external rhythms. Interesting recent findings support that the products of photosynthesis, probably sucrose, in turn feeds back to the clock to set its rhythm. In this way, the clock both controls and is controlled by carbon fluxes. This has an interesting connection to stress signalling and water-use efficiency, and it is now known that the clock and abscisic acid pathways are reciprocally coordinated. These processes converge to drive growth in a species-specific context such that predictions from the Arabidopsis model to other species can be restricted. This has been seen from phenotypic growth studies that revealed that dicot shoot growth is rhythmic whereas monocot shoot growth is continuous. Taken together, emerging evidence suggests reciprocal interactions between metabolism, the circadian clock, and stress signalling to control growth and fitness in Arabidopsis, but transferability to other species is not always possible due to species-specific effects. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. Effect of prenatal species-specific and music stimulation on the postnatal auditory preference of domestic chick.

    PubMed

    Jain, Suman; Sharma, Ratna; Wadhwa, Shashi

    2004-04-01

    Perinatal sensory experience plays an important role in the development of perceptual preferences. In the present study prenatal enrichment with sound stimulus was given to see its effect on the development of postnatal auditory preference. Auditory stimulation with either species-specific (chicken maternal and hatching calls) or music (slow and fast sitar music) sounds was provided to two separate sets of fertilized eggs from the day 10 of incubation. The postnatal auditory preference of the chicks to either species-specific or music sounds was then tested at different time periods after hatching. All the chicks, irrespective of the type of prenatal exposure, showed preference for species-specific maternal calls. Notably, the music stimulated chicks did not show preference for either slow or fast music. In both the experimental groups, the number of chicks responding to the species-specific maternal calls was significantly (P<0.001) more at 24 h and 48 h post hatch, when compared with the unstimulated control group. Comparison of the species-specific stimulated group with the music stimulated group, for auditory preference to the maternal calls, did not show any significant difference. Further, in the species-specific sound stimulated groups, there was a significant (P<0.001) increase in the number of chicks responding to maternal calls at 60 h of age with repeated testing. However, there was no effect of peer imprinting on the auditory preference of the chicks, in both the experimental groups. The results indicate that prenatal auditory experience with either species-specific or non-specific music enhances the postnatal auditory preference of chicks for the species-specific sounds.

  17. Advances in microspeciation of drugs and biomolecules: Species-specific concentrations, acid-base properties and related parameters.

    PubMed

    Mazák, Károly; Noszál, Béla

    2016-10-25

    The pharmacokinetic and pharmacodynamic behaviour of drugs and the interacting biomolecules are highly influenced by their species-specific physico-chemical properties. The first of such bio-relevant, structure-dependent properties were the species-specific acid-base constants and the co-dependent concentrations, but the past decade brought significant advances to previously uncharted territories, including the experimental determination of species-specific partition coefficients, solubilities and redox equilibrium constants. This review gives an overview of the types and definitions of species-specific physico-chemical and analytical properties. We survey the pertinent literature, the fundamental relationships, and summarize some of our recent work that enabled the determination of species-specific partition coefficients for coexisting, inseparable protonation isomers and pH-independent, microscopic redox equilibrium constants. The thorough insight provided by these species-specific properties improves our understanding of the submolecular mechanism of pharmacokinetic processes. As a result, there are some pieces of clear-cut evidence of practical significance. A few of them are as follows: - passive diffusion into lipophilic media is not necessarily predominated by the non-charged species, contrary to the widespread misbelief. - the reactive microspecies in structure-controlled, highly specific biochemical reactions is not necessarily the major one. - a preventive defence system against oxidative stress can be based upon thiol-disulfide equilibria of custom-tailored redox potentials. Copyright © 2016. Published by Elsevier B.V.

  18. Nesting behaviour influences species-specific gas exchange across avian eggshells

    PubMed Central

    Portugal, Steven J.; Maurer, Golo; Thomas, Gavin H.; Hauber, Mark E.; Grim, Tomáš; Cassey, Phillip

    2014-01-01

    Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (GH2O) across the shell, typically measured as mass loss during incubation, has been demonstrated to optimally ensure the healthy development of the embryo while avoiding desiccation. Accordingly, eggs exposed to sub-optimal gas exchange have reduced hatching success. We tested the association between eggshell GH2O and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in GH2O has evolved to maintain optimal water loss across a diverse set of nest environments. We measured gas exchange through eggshell fragments in 151 British breeding bird species and fitted phylogenetically controlled, general linear models to test the relationship between GH2O and potential predictor parameters of each species. Of our 17 life-history traits, only two were retained in the final model: wet-incubating parent and nest type. Eggs of species where the parent habitually returned to the nest with wet plumage had significantly higher GH2O than those of parents that returned to the nest with dry plumage. Eggs of species nesting in ground burrows, cliffs and arboreal cups had significantly higher GH2O than those of species nesting on the ground in open nests or cups, in tree cavities and in shallow arboreal nests. Phylogenetic signal (measured as Pagel's λ) was intermediate in magnitude, suggesting that differences observed in the GH2O are dependent upon a combination of shared ancestry and species-specific life history and ecological traits. Although these data are correlational by nature, they are consistent with the hypothesis that parents constrained to return to the nest with wet plumage will increase the humidity of the nest environment, and the eggs of these species have evolved a higher GH2O to overcome this constraint and still achieve optimal water

  19. Nesting behaviour influences species-specific gas exchange across avian eggshells.

    PubMed

    Portugal, Steven J; Maurer, Golo; Thomas, Gavin H; Hauber, Mark E; Grim, Tomáš; Cassey, Phillip

    2014-09-15

    Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (G(H2O)) across the shell, typically measured as mass loss during incubation, has been demonstrated to optimally ensure the healthy development of the embryo while avoiding desiccation. Accordingly, eggs exposed to sub-optimal gas exchange have reduced hatching success. We tested the association between eggshell G(H2O) and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in G(H2O) has evolved to maintain optimal water loss across a diverse set of nest environments. We measured gas exchange through eggshell fragments in 151 British breeding bird species and fitted phylogenetically controlled, general linear models to test the relationship between G(H2O) and potential predictor parameters of each species. Of our 17 life-history traits, only two were retained in the final model: wet-incubating parent and nest type. Eggs of species where the parent habitually returned to the nest with wet plumage had significantly higher G(H2O) than those of parents that returned to the nest with dry plumage. Eggs of species nesting in ground burrows, cliffs and arboreal cups had significantly higher G(H2O) than those of species nesting on the ground in open nests or cups, in tree cavities and in shallow arboreal nests. Phylogenetic signal (measured as Pagel's λ) was intermediate in magnitude, suggesting that differences observed in the G(H2O) are dependent upon a combination of shared ancestry and species-specific life history and ecological traits. Although these data are correlational by nature, they are consistent with the hypothesis that parents constrained to return to the nest with wet plumage will increase the humidity of the nest environment, and the eggs of these species have evolved a higher G(H2O) to overcome this constraint and still

  20. Species-specific intrinsic water use efficiency and its mediation of carbon assimilation during the drought

    NASA Astrophysics Data System (ADS)

    Yi, K.; Wenzel, M. K.; Maxwell, J. T.; Novick, K. A.; Gray, A.; Roman, D. T.

    2015-12-01

    Drought is expected to occur more frequently and intensely in the future, and many studies have suggested frequent and intense droughts can significantly alter carbon and water cycling in forest ecosystems, consequently decreasing the ability of forests to assimilate carbon. Predicting the impact of drought on forest ecosystem processes requires an understanding of species-specific responses to drought, especially in eastern US where species composition is highly dynamic. An emerging approach for describing species-specific drought response is to classify the plant water use strategy into isohydric and anisohydric behaviors. Trees utilizing isohydric behavior regulate water potential by closing stomata to reduce water loss during drought conditions, while anisohydric trees allow water potential to drop by sustaining stomatal conductance, but with the risk of hydraulic failure caused by cavitation of xylem tissues. Since catastrophic cavitation occurs infrequently in the relatively wet eastern U.S., we hypothesize that 1) tree growth of isohydric trees will be more limited during the drought than the anisohydric trees due to decreased stomatal conductance, but 2) variation in intrinsic water use efficient (iWUE) during drought in isohydric trees will mediate the effects of drought on carbon assimilation. We will test these hypotheses by 1) analyzing tree-ring chronologies and dendrometer data on productivity, and 2) estimating intrinsic water use efficiency (iWUE) at multiple scales by analyzing gas exchange data for the leaf-level, inter-annual variability of d13C in tree stem cores for the tree-level, and eddy covariance technique for the stand-level. Our study site is the Morgan-Monroe State Forest (Indiana, USA). A 46 m flux tower has been continuously recording the carbon, water and energy fluxes, and tree diameter has been measured every 2 weeks using dendrometers, since 1998. Additional research, including gas exchange measurements performed during the

  1. Species-Specific Immunity Induced by Infection with Entamoeba histolytica and Entamoeba moshkovskii in Mice

    PubMed Central

    Shimokawa, Chikako; Culleton, Richard; Imai, Takashi; Suzue, Kazutomo; Hirai, Makoto; Taniguchi, Tomoyo; Kobayashi, Seiki; Hisaeda, Hajime; Hamano, Shinjiro

    2013-01-01

    Entamoeba histolytica, the parasitic amoeba responsible for amoebiasis, causes approximately 100,000 deaths every year. There is currently no vaccine against this parasite. We have previously shown that intracecal inoculation of E. histolytica trophozoites leads to chronic and non-healing cecitis in mice. Entamoeba moshkovskii, a closely related amoeba, also causes diarrhea and other intestinal disorders in this model. Here, we investigated the effect of infection followed by drug-cure of these species on the induction of immunity against homologous or heterologous species challenge. Mice were infected with E. histolytica or E. moshkovskii and treated with metronidazole 14 days later. Re-challenge with E. histolytica or E. moshkovskii was conducted seven or 28 days following confirmation of the clearance of amoebae, and the degree of protection compared to non-exposed control mice was evaluated. We show that primary infection with these amoebae induces a species-specific immune response which protects against challenge with the homologous, but not a heterologous species. These findings pave the way, therefore, for the identification of novel amoebae antigens that may become the targets of vaccines and provide a useful platform to investigate host protective immunity to Entamoeba infections. PMID:24312397

  2. Enzyme-linked immunosorbent assay for detection of filovirus species-specific antibodies.

    PubMed

    Nakayama, Eri; Yokoyama, Ayaka; Miyamoto, Hiroko; Igarashi, Manabu; Kishida, Noriko; Matsuno, Keita; Marzi, Andrea; Feldmann, Heinz; Ito, Kimihito; Saijo, Masayuki; Takada, Ayato

    2010-11-01

    Several enzyme-linked immunosorbent assays (ELISAs) for the detection of filovirus-specific antibodies have been developed. However, diagnostic methods to distinguish antibodies specific to the respective species of filoviruses, which provide the basis for serological classification, are not readily available. We established an ELISA using His-tagged secreted forms of the transmembrane glycoproteins (GPs) of five different Ebola virus (EBOV) species and one Marburg virus (MARV) strain as antigens for the detection of filovirus species-specific antibodies. The GP-based ELISA was evaluated by testing antisera collected from mice immunized with virus-like particles as well as from humans and nonhuman primates infected with EBOV or MARV. In our ELISA, little cross-reactivity of IgG antibodies was observed in most of the mouse antisera. Although sera and plasma from some patients and monkeys showed notable cross-reactivity with the GPs from multiple filovirus species, the highest reactions of IgG were uniformly detected against the GP antigen homologous to the virus species that infected individuals. We further confirmed that MARV-specific IgM antibodies were specifically detected in specimens collected from patients during the acute phase of infection. These results demonstrate the usefulness of our ELISA for diagnostics as well as ecological and serosurvey studies.

  3. Fluorescent banding pattern and species-specific DNA marker in Rumex thyrsiflorus Fingerh.

    PubMed

    Grabowska-Joachimiak, A; Kwolek, D; Kula, A; Marciniuk, P

    2012-01-01

    The object of this work was to analyze the karyotype structure of Rumex thyrsiflorus using differential fluorescent methods of chromosome staining (C-banding/DAPI and CMA3/DA/DAPI) and molecular sex markers. The results obtained were compared with data on the structure of the sex chromosomes and autosomes in R. acetosa, a model species in studies of sex determination and sex chromosome evolution in plants with an XX/XY1Y2 system. A high level of similarity was found in the sex chromosome structure of the 2 species, along with small differences in their autosomal complexes. It suggests that differentiation of these 2 closely related species was not accompanied by major structural changes within their sex chromosomes. Molecular tests, however, revealed differences in the composition of male-specific repetitive sequence RAYSII, occurring in the Y1 chromosome. Amplification of this sequence showed the presence of a single product (∼700 bp) in R. acetosa and of 2 products (∼600 bp and ∼700 bp) in R. thyrsiflorus. The longer product (∼700 bp) was also revealed in R. arifolius, another species closely related to R. acetosa. The shorter DNA fragment, characteristic of R. thyrsiflorus, differed from the common product by of a large indel with a length of 110 bp. This fragment may serve as a species-specific molecular marker useful in taxonomical and population studies as well as in further research on the sex chromosome differentiation in R. thyrsiflorus. Copyright © 2012 S. Karger AG, Basel.

  4. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

    PubMed

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

    Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

  5. Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF mass spectrometry.

    PubMed

    Stephan, Roger; Cernela, Nicole; Ziegler, Dominik; Pflüger, Valentin; Tonolla, Mauro; Ravasi, Damiana; Fredriksson-Ahomaa, Maria; Hächler, Herbert

    2011-11-01

    Yersinia enterocolitica are Gram-negative pathogens and known as important causes of foodborne infections. Rapid and reliable identification of strains of the species Y. enterocolitica within the genus Yersinia and the differentiation of the pathogenic from the non-pathogenic biotypes has become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid species identification and subtyping of Y. enterocolitica. To this end, we developed a reference MS database library including 19 Y. enterocolitica (non-pathogenic biotype 1A and pathogenic biotypes 2 and 4) as well as 24 non-Y. enterocolitica strains, belonging to eleven different other Yersinia spp. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2000 to 30,000 Da). Species-specific and biotype-specific biomarker protein mass patterns were determined for Y. enterocolitica. The defined biomarker mass patterns (SARAMIS SuperSpectrum™) were validated using 117 strains from various Y. enterocolitica bioserotypes in a blind-test. All strains were correctly identified and for all strains the mass spectrometry-based identification scheme yielded identical results compared to a characterization by a combination of biotyping and serotyping. Our study demonstrates that MALDI-TOF-MS is a reliable and powerful tool for the rapid identification of Y. enterocolitica strains to the species level and allows subtyping of strains to the biotype level. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

    PubMed Central

    Paralkar, Vikram R.; Mishra, Tejaswini; Luan, Jing; Yao, Yu; Kossenkov, Andrew V.; Anderson, Stacie M.; Dunagin, Margaret; Pimkin, Maxim; Gore, Meghneel; Sun, Diana; Konuthula, Neeraja; Raj, Arjun; An, Xiuli; Mohandas, Narla; Bodine, David M.; Hardison, Ross C.

    2014-01-01

    Mammals express thousands of long noncoding (lnc) RNAs, a few of which are known to function in tissue development. However, the entire repertoire of lncRNAs in most tissues and species is not defined. Indeed, most lncRNAs are not conserved, raising questions about function. We used RNA sequencing to identify 1109 polyadenylated lncRNAs expressed in erythroblasts, megakaryocytes, and megakaryocyte-erythroid precursors of mice, and 594 in erythroblasts of humans. More than half of these lncRNAs were unannotated, emphasizing the opportunity for new discovery through studies of specialized cell types. Analysis of the mouse erythro-megakaryocytic polyadenylated lncRNA transcriptome indicates that ∼75% arise from promoters and 25% from enhancers, many of which are regulated by key transcription factors including GATA1 and TAL1. Erythroid lncRNA expression is largely conserved among 8 different mouse strains, yet only 15% of mouse lncRNAs are expressed in humans and vice versa, reflecting dramatic species-specificity. RNA interference assays of 21 abundant erythroid-specific murine lncRNAs in primary mouse erythroid precursors identified 7 whose knockdown inhibited terminal erythroid maturation. At least 6 of these 7 functional lncRNAs have no detectable expression in human erythroblasts, suggesting that lack of conservation between mammalian species does not predict lack of function. PMID:24497530

  7. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea.

    PubMed

    Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2011-04-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

  8. Hepatitis B Virus and Hepatitis D Virus Entry, Species Specificity, and Tissue Tropism.

    PubMed

    Watashi, Koichi; Wakita, Takaji

    2015-08-03

    Entry of hepatitis B (HBV) and hepatitis D viruses (HDV) into a host cell represents the initial step of infection. This process requires multiple steps, including the low-affinity attachment of the virus to the cell surface, followed by high-affinity attachment to specific receptor(s), and subsequent endocytosis-mediated internalization. Within the viral envelope, the preS1 region is involved in receptor binding. Recently, sodium taurocholate cotransporting polypeptide (NTCP) has been identified as an entry receptor of HBV and HDV by affinity purification using a preS1 peptide. NTCP is mainly or exclusively expressed in the liver, and this membrane protein is at least one of the factors determining the narrow species specificity and hepatotropism of HBV and HDV. However, there are likely other factors that mediate the species and tissue tropism of HBV. This review summarizes the current understanding of the mechanisms of HBV/HDV entry. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  9. Diastereoisomer- and species-specific distribution of hexabromocyclododecane (HBCD) in fish and marine invertebrates.

    PubMed

    Son, Min-Hui; Kim, Jongchul; Shin, Eun-Su; Seo, Sung-hee; Chang, Yoon-Seok

    2015-12-30

    The levels and distributional characteristics of hexabromocyclododecane (HBCD) diastereoisomers have been largely reported for various fish and select shellfish. In this study, we reclassified a number and variety of marine invertebrates, including shellfish, to further contribute to the comprehensive understanding of the effects and assessment of human exposure to HBCD. Overall, 30 marine invertebrate species (n=188) were investigated and the following order of ∑2HBCD (α- and γ-HBCD) was observed: fish>chordata>cephalopoda>echinodermata>bivalve>crustacea. The marine invertebrates that were reclassified into nektonic and benthic organisms showed similar concentration of ∑2HBCD. The feeding habits and modes of the marine organisms were considered to compare the degree of bioaccumulation and diastereoisomer-specific distribution of HBCD due to the effects of the environment in and around pollution sources, as well as the organisms' metabolic capacities. To the best of our knowledge, this is the first study to examine the species-specific distribution patterns of HBCD for both fish and marine invertebrates. We expect to significantly expand the understanding of the environmental fate of HBCD for marine organisms. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Hantaviruses induce cell type- and viral species-specific host microRNA expression signatures.

    PubMed

    Shin, Ok Sarah; Kumar, Mukesh; Yanagihara, Richard; Song, Jin-Won

    2013-11-01

    The mechanisms of hantavirus-induced modulation of host cellular immunity remain poorly understood. Recently, microRNAs (miRNAs) have emerged as a class of essential regulators of host immune response genes. To ascertain if differential host miRNA expression toward representative hantavirus species correlated with immune response genes, miRNA expression profiles were analyzed in human endothelial cells, macrophages and epithelial cells infected with pathogenic and nonpathogenic rodent- and shrew-borne hantaviruses. Distinct miRNA expression profiles were observed in a cell type- and viral species-specific pattern. A subset of miRNAs, including miR-151-5p and miR-1973, were differentially expressed between Hantaan virus and Prospect Hill virus. Pathway analyses confirmed that the targets of selected miRNAs were associated with inflammatory responses and innate immune receptor-mediated signaling pathways. Our data suggest that differential immune responses following hantavirus infection may be regulated in part by cellular miRNA through dysregulation of genes critical to the inflammatory process.

  11. Antispasmodic activity of licochalcone A, a species-specific ingredient of Glycyrrhiza inflata roots.

    PubMed

    Nagai, Hidemasa; He, Ju-Xiu; Tani, Tadato; Akao, Teruaki

    2007-10-01

    Licochalcone A, a species-specific and characteristic retrochalcone ingredient of Glycyrrhiza inflata root, has been shown to possess multiple bioactive properties. However, its muscle relaxant activity has not been reported previously. Licochalcone A showed a concentration-dependent relaxant effect on the contraction induced by carbachol (50% effective concentration (EC50) = 5.64 +/- 1.61 microM), KCl (EC50 5.12 +/- 1.68 microM), BaCl2 (EC50 1.97 +/- 0.48 microM) and A23187 (EC50 2.63 +/- 2.05 microM). Pretreatment with licochalcone A enhanced the relaxant effect of forskolin, an adenylyl cyclase activator, on the contraction in a similar manner to 3-isobutyl-1-methylxanthine (IBMX), a phosphodiesterase (PDE) inhibitor. Furthermore, the IC50 (22.1 +/- 10.9 microM) of licochalcone A against cAMP PDE was similar to that of IBMX (26.2 +/- 7.4 microM). These results indicated that licochalcone A may have been responsible for the relaxant activity of G. inflata root and acted through the inhibition of cAMP PDE.

  12. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

    PubMed Central

    Shmakov, Sergey A.; Sitnik, Vassilii; Makarova, Kira S.; Wolf, Yuri I.; Severinov, Konstantin V.

    2017-01-01

    ABSTRACT Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. PMID:28928211

  13. Species-specific identification of seven vegetable oils based on suspension bead array.

    PubMed

    Li, Yuanyuan; Wu, Yajun; Han, Jianxun; Wang, Bin; Ge, Yiqiang; Chen, Ying

    2012-03-07

    Species adulteration of vegetable oils has become a main form of adulteration in vegetable oils, severely violating consumer rights and causing disorder in the market. A reliable method of species authentication of vegetable oils is desirable. This paper reports a novel method for identification of seven species of vegetable oils based on suspension bead array. One pair of universal primers and seven species-specific probes were designed targeting rbcl gene of the chloroplast. Each probe was coupled to a unique color-coded microsphere. Biotinylated PCR amplicons of seven oils were hybridized to the complementary probes on microsphere sets. Bound amplicons were detected fluorometrically using a reporter dye, streptavidin-R-phycoeryt hrin (SA-PE). A sample could be analyzed less than 1 h after PCR amplification. With the exception of olive probe, all probes showed no cross-reactivity with other species. Absolute detection limit of the seven probes ranged from 0.01 ng/μL to 0.0001 ng/μL. Detection limit in DNA mixture was from 10% to 5%. Detection of vegetable oils validated the effectiveness of the method. The suspension bead array as a rapid, sensitive, and high-throughput technology has potential to identify more species of vegetable oils with increased species of probes.

  14. Identification of Mycobacterium bovis in bovine clinical samples by PCR species-specific primers.

    PubMed Central

    Romero, R E; Garzón, D L; Mejía, G A; Monroy, W; Patarroyo, M E; Murillo, L A

    1999-01-01

    Tuberculosis, caused by Mycobacterium bovis is emerging as the most important disease affecting cattle. Furthermore, it results in a major public health problem when transmitted to humans. Due to its difficult and non-specific diagnosis, M. bovis has been declared to be one of the etiologic agents causing significant economic loss in the cattle industry. Our group evaluated a more rapid and specific method, based on a new polymerase chain reaction species-specific primers, which amplifies a 470-base pair fragment of the M. bovis genome. A total of 275 milk-producing cows were studied by intradermal tuberculin test (ITT) which gave 184 positive and 91 negative cases. From them, 50 animals were taken from a cattle ranch free of tuberculosis. Three different samples were collected from each animal (blood, nasal mucus, and milk). Positive results were obtained from 26 animals by PCR (11.4%), 1 by bacteriological culturing (0.4%) and 1 by bacilloscopy (0.4%). This finding suggests, as in previous reports, that ITT, normally used for bovine tuberculosis detection, has the inconvenience of having a broad range of specificity and sensitivity, and the PCR technique is a more specific and sensitive test to detect infection associated with M. bovis. Therefore, we propose this PCR assay as a useful tool in the epidemiological characterization of infected animals in areas considered to be at high risk of transmission. Images Figure 1. PMID:10369566

  15. Experimental evidence for species-specific habitat preferences in two flycatcher species in their hybrid zone.

    PubMed

    Adamík, Peter; Bures, Stanislav

    2007-10-01

    Hybrid zones are often found in areas where the environmental characteristics of native habitat of both parental species meet. One of the plausible mechanisms that maintain species distinctiveness, or limit hybridization, is the existence of local species-specific preferences for the natal habitat type. We evaluated this hypothesis for two passerine bird species, the pied Ficedula hypoleuca and collared flycatcher F. albicollis, in their narrow hybrid zone in Central Europe. Both species have quite distinct habitat distributions, and they have also been reported to differ in their foraging niches. In a series of aviary experiments, we demonstrated that both species show distinct preferences for trees from their native area. The pied flycatcher preferred coniferous vegetation, while the collared flycatcher favored deciduous vegetation. In addition, both species differed in foraging substrate preferences. The pied flycatcher preferred to forage in the lower strata on the ground than the canopy, whereas the collared flycatcher foraged more at the canopy level. Both males and females of each species were highly consistent in their preference patterns. Due to the widespread nature of hybrid zones as places with transitional habitat features and the well-known habitat tight associations of various animal taxa with particular habitat types, we propose that habitat preferences might be an important and common mechanism that enhances the formation of conspecific pairs.

  16. Magnetic compass orientation in two strictly subterranean rodents: learned or species-specific innate directional preference?

    PubMed

    Oliveriusová, Ludmila; Nĕmec, Pavel; Králová, Zuzana; Sedláček, František

    2012-10-15

    Evidence for magnetoreception in mammals remains limited. Magnetic compass orientation or magnetic alignment has been conclusively demonstrated in only a handful of mammalian species. The functional properties and underlying mechanisms have been most thoroughly characterized in Ansell's mole-rat, Fukomys anselli, which is the species of choice due to its spontaneous drive to construct nests in the southeastern sector of a circular arena using the magnetic field azimuth as the primary orientation cue. Because of the remarkable consistency between experiments, it is generally believed that this directional preference is innate. To test the hypothesis that spontaneous southeastern directional preference is a shared, ancestral feature of all African mole-rats (Bathyergidae, Rodentia), we employed the same arena assay to study magnetic orientation in two other mole-rat species, the social giant mole-rat, Fukomys mechowii, and the solitary silvery mole-rat, Heliophobius argenteocinereus. Both species exhibited spontaneous western directional preference and deflected their directional preference according to shifts in the direction of magnetic north, clearly indicating that they were deriving directional information from the magnetic field. Because all of the experiments were performed in total darkness, our results strongly suggest that all African mole-rats use a light-independent magnetic compass for near-space orientation. However, the spontaneous directional preference is not common and may be either innate (but species-specific) or learned. We propose an experiment that should be performed to distinguish between these two alternatives.

  17. Studies on genome relationship and species-specific PCR marker for Dasypyrum breviaristatum in Triticeae.

    PubMed

    Yang, Zu-Jun; Liu, Cheng; Feng, Juan; Li, Guang-Rong; Zhou, Jian-Ping; Deng, Ke-Jun; Ren, Zheng-Long

    2006-12-01

    Dasypyrum breviaristatum and nine related species in Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique, in order to understand the genetic relationship and to develop species specific markers. The genome relationship dendrogram shows that D. breviaristatum and D. villosum could not be grouped together, indicating that D. breviaristatum was unlikely to be directly derived from D. villosum, while D. breviaristatum was closest to Thinopyrum intermedium, which implied that they might have similar breeding behaviors when introducing their chromatins into wheat. A D. breviaristatum genome specific RAPD product of 1182bp, was cloned and designated as pDb12H. Sequence analysis revealed that pDb12H was strongly homologuos to a long terminal repeat (LTR) Sabrina retrotransposon newly reported in Hordeum. The pDb12H was converted into a PCR based marker, which allows effectively monitoring the D. breviaristatum chromatin introgression into wheat. Fluorescence in situ hybridization (FISH) suggested that pDb12H was specifically hybridized throughout all D. breviaristatum chromosomes arms except for the terminal and centromeric regions, which can be used to characterize wheat -D. breviaristatum chromosome translocation. The genomes repetitive element will also be useful to study gene interactions between the wheat and alien genomes after the polyploidization.

  18. Identification and characterization of species-specific nanobodies for the detection of Listeria monocytogenes in milk.

    PubMed

    Tu, Zhui; Chen, Qi; Li, Yanping; Xiong, Yonghua; Xu, Yang; Hu, Na; Tao, Yong

    2016-01-15

    Listeria monocytogenes (LM), one of the eight species belonging to the genus Listeria, is pathogenic for both humans and animals. In this study, two novel LM-specific clones, designated L5-78 and L5-79, were isolated from a phage display antibody library that was derived from the variable domain of heavy-chain antibodies (VHHs) of non-immunized alpaca. These two clones were expressed, purified, and characterized. Results showed that both isolated VHHs recognize three serotypes (1/2a, 1/2b, and 4b), which are responsible for more than 95% of documented human listeriosis cases. The recombinant VHHs possess high thermal stability, pH tolerance, and urea resistance. A sandwich enzyme-linked immunosorbent assay (ELISA) based on the VHH clone L5-79 and a monoclonal antibody was developed to detect LM in pasteurized milk, with a detection limit of 1 × 10(4) colony-forming units (CFU)/ml. These findings indicated that the species-specific VHHs could be directly isolated from the non-immunized library with a properly designed panning strategy and VHH could be a new source for possible diagnosis/detection of foodborne pathogens in food because it was shown to be highly specific and stable.

  19. Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)

    PubMed Central

    Zhong, Yan; Li, Yingjun; Huang, Kaihui; Cheng, Zong-Ming

    2015-01-01

    The disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting the purifying selection operated during the evolutionary history of NBS-encoding genes. A minority (4/34) of Ka/Ks in non-TIR gene families were greater than 1, showing that some genes were under positive selection pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4–0.5. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree. Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes. PMID:26559332

  20. Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set

    PubMed Central

    Wuyun, Qiqige; Zheng, Wei; Zhang, Yanping; Ruan, Jishou; Hu, Gang

    2016-01-01

    Lysine acetylation is a major post-translational modification. It plays a vital role in numerous essential biological processes, such as gene expression and metabolism, and is related to some human diseases. To fully understand the regulatory mechanism of acetylation, identification of acetylation sites is first and most important. However, experimental identification of protein acetylation sites is often time consuming and expensive. Therefore, the alternative computational methods are necessary. Here, we developed a novel tool, KA-predictor, to predict species-specific lysine acetylation sites based on support vector machine (SVM) classifier. We incorporated different types of features and employed an efficient feature selection on each type to form the final optimal feature set for model learning. And our predictor was highly competitive for the majority of species when compared with other methods. Feature contribution analysis indicated that HSE features, which were firstly introduced for lysine acetylation prediction, significantly improved the predictive performance. Particularly, we constructed a high-accurate structure dataset of H.sapiens from PDB to analyze the structural properties around lysine acetylation sites. Our datasets and a user-friendly local tool of KA-predictor can be freely available at http://sourceforge.net/p/ka-predictor. PMID:27183223

  1. Species-specific immunity induced by infection with Entamoeba histolytica and Entamoeba moshkovskii in mice.

    PubMed

    Shimokawa, Chikako; Culleton, Richard; Imai, Takashi; Suzue, Kazutomo; Hirai, Makoto; Taniguchi, Tomoyo; Kobayashi, Seiki; Hisaeda, Hajime; Hamano, Shinjiro

    2013-01-01

    Entamoeba histolytica, the parasitic amoeba responsible for amoebiasis, causes approximately 100,000 deaths every year. There is currently no vaccine against this parasite. We have previously shown that intracecal inoculation of E. histolytica trophozoites leads to chronic and non-healing cecitis in mice. Entamoeba moshkovskii, a closely related amoeba, also causes diarrhea and other intestinal disorders in this model. Here, we investigated the effect of infection followed by drug-cure of these species on the induction of immunity against homologous or heterologous species challenge. Mice were infected with E. histolytica or E. moshkovskii and treated with metronidazole 14 days later. Re-challenge with E. histolytica or E. moshkovskii was conducted seven or 28 days following confirmation of the clearance of amoebae, and the degree of protection compared to non-exposed control mice was evaluated. We show that primary infection with these amoebae induces a species-specific immune response which protects against challenge with the homologous, but not a heterologous species. These findings pave the way, therefore, for the identification of novel amoebae antigens that may become the targets of vaccines and provide a useful platform to investigate host protective immunity to Entamoeba infections.

  2. Glycoproteins are species-specific markers and major IgE reactants in grass pollens.

    PubMed

    Manduzio, Hélène; Fitchette, Anne-Catherine; Hrabina, Maud; Chabre, Henri; Batard, Thierry; Nony, Emmanuel; Faye, Loïc; Moingeon, Philippe; Gomord, Véronique

    2012-02-01

    Grass pollen allergic patients are concomitantly exposed and sensitized to pollens from multiple Pooideae (i.e. common grass) species. As such, they are currently desensitized by allergen-specific immunotherapy using extracts made from mixes of pollens from Anthoxanthum odoratum, Dactylis glomerata, Lolium perenne, Phleum pratense and Poa pratensis. Herein, we demonstrate that species-specific glycoprotein patterns are documented by 1D and 2D electrophoresis and Western blotting analysis, which can be used as an identity test for such pollens. Most allergens are glycoproteins bearing complex N-glycans encompassing β1,2 xylose and α1,3 fucose glycoepitopes. Glycoepitope destruction using periodate oxidation has no impact on seric IgE reactivity in 75% atopic patients (n = 24). The latter have thus no significant IgE responses to carbohydrate-containing epitopes. In contrast, periodate treatment strongly impairs IgE recognition of glycoallergens in 25% of patients tested, demonstrating the presence of carbohydrate-specific IgE in those patients. While the clinical impact of carbohydrate-specific IgE is still a matter of controversy, the presence of these IgE in the serum of many allergic patients illustrates the need for cross-reacting carbohydrate epitope-free recombinant allergens to develop relevant diagnostic tests. These data also support the pertinence of mixing multiple grass pollens to desensitize atopic patients, with the aim to broaden the repertoire of glycoepitopes in the vaccine, thus mimicking natural exposure conditions.

  3. Species-specific acquisition and consolidation of long-term memory in parasitic wasps

    PubMed Central

    Smid, Hans M; Wang, Guohong; Bukovinszky, Tibor; Steidle, Johannes L.M; Bleeker, Maartje A.K; van Loon, Joop J.A; Vet, Louise E.M

    2007-01-01

    Long-term memory (LTM) formation usually requires repeated, spaced learning events and is achieved by the synthesis of specific proteins. Other memory forms require a single learning experience and are independent of protein synthesis. We investigated in two closely related parasitic wasp species, Cotesia glomerata and Cotesia rubecula, whether natural differences in foraging behaviour are correlated with differences in LTM acquisition and formation. These parasitic wasp species lay their eggs in young caterpillars of pierid butterflies and can learn to associate plant odours with a successful egg laying experience on caterpillars on the odour-producing plant. We used a classical conditioning set-up, while interfering with LTM formation through translation or transcription inhibitors. We show here that C. rubecula formed LTM after three spaced learning trials, whereas C. glomerata required only a single trial for LTM formation. After three spaced learning trials, LTM formation was complete within 4 h in C. glomerata, whereas in C. rubecula, LTM formation took 3 days. Linking neurobiology with ecology, we argue that this species-specific difference in LTM acquisition and formation is adaptive given the extreme differences in both the number of foraging decisions of the two wasp species and in the spatial distributions of their respective hosts in nature. PMID:17439855

  4. Physiological inputs regulate species-specific anatomy during embryogenesis and regeneration

    PubMed Central

    Sullivan, Kelly G.; Emmons-Bell, Maya; Levin, Michael

    2016-01-01

    ABSTRACT A key problem in evolutionary developmental biology is identifying the sources of instructive information that determine species-specific anatomical pattern. Understanding the inputs to large-scale morphology is also crucial for efforts to manipulate pattern formation in regenerative medicine and synthetic bioengineering. Recent studies have revealed a physiological system of communication among cells that regulates pattern during embryogenesis and regeneration in vertebrate and invertebrate models. Somatic tissues form networks using the same ion channels, electrical synapses, and neurotransmitter mechanisms exploited by the brain for information-processing. Experimental manipulation of these circuits was recently shown to override genome default patterning outcomes, resulting in head shapes resembling those of other species in planaria and Xenopus. The ability to drastically alter macroscopic anatomy to that of other extant species, despite a wild-type genomic sequence, suggests exciting new approaches to the understanding and control of patterning. Here, we review these results and discuss hypotheses regarding non-genomic systems of instructive information that determine biological growth and form. PMID:27574538

  5. Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

    PubMed Central

    Heinken, Almut

    2015-01-01

    The human gut is inhabited by thousands of microbial species, most of which are still uncharacterized. Gut microbes have adapted to each other's presence as well as to the host and engage in complex cross feeding. Constraint-based modeling has been successfully applied to predicting microbe-microbe interactions, such as commensalism, mutualism, and competition. Here, we apply a constraint-based approach to model pairwise interactions between 11 representative gut microbes. Microbe-microbe interactions were computationally modeled in conjunction with human small intestinal enterocytes, and the microbe pairs were subjected to three diets with various levels of carbohydrate, fat, and protein in normoxic or anoxic environments. Each microbe engaged in species-specific commensal, parasitic, mutualistic, or competitive interactions. For instance, Streptococcus thermophilus efficiently outcompeted microbes with which it was paired, in agreement with the domination of streptococci in the small intestinal microbiota. Under anoxic conditions, the probiotic organism Lactobacillus plantarum displayed mutualistic behavior toward six other species, which, surprisingly, were almost entirely abolished under normoxic conditions. This finding suggests that the anoxic conditions in the large intestine drive mutualistic cross feeding, leading to the evolvement of an ecosystem more complex than that of the small intestinal microbiota. Moreover, we predict that the presence of the small intestinal enterocyte induces competition over host-derived nutrients. The presented framework can readily be expanded to a larger gut microbial community. This modeling approach will be of great value for subsequent studies aiming to predict conditions favoring desirable microbes or suppressing pathogens. PMID:25841013

  6. Molecular cloning and characterization of ligand- and species-specificity of amphibian estrogen receptors.

    PubMed

    Katsu, Yoshinao; Taniguchi, Ena; Urushitani, Hiroshi; Miyagawa, Shinichi; Takase, Minoru; Kubokawa, Kaoru; Tooi, Osamu; Oka, Tomohiro; Santo, Noriaki; Myburgh, Jan; Matsuno, Akira; Iguchi, Taisen

    2010-09-01

    Estrogens are essential for normal reproductive activity in both males and females as well as for ovarian differentiation during a critical developmental stage in most vertebrates. To understand the molecular mechanisms of estrogen action and to evaluate estrogen receptor ligand interactions in amphibians, we isolated cDNAs encoding the estrogen receptors (ERalpha and ERbeta) from the Japanese firebelly newt (Cynops pyrrhogaster), Tokyo salamander (Hynobius tokyoensis), axolotl (Ambystoma mexicanum), and Raucous toad (Bufo rangeri). Full-length amphibian ER cDNAs were obtained using 5' and 3' rapid amplification of cDNA ends. The predicted amino acid sequences of these amphibian ERs showed a high degree of amino acid sequence identity (over 70%) to each other. We analyzed the relationships of these amphibian ER sequences to other vertebrate ER sequences by constructing a phylogenetic tree. We verified that these were bona fide estrogen receptors using receptor dependent reporter gene assays. We analyzed the effects of natural estrogens, ethinylestradiol, and DDT and its metabolites on the transactivation of the four amphibian species listed above, and Xenopus tropicalis ERs and found that there were species-specific differences in the sensitivity of these ERs to hormones and environmental chemicals. These findings will expand our knowledge of endocrine-disrupting events in amphibians.

  7. Species-specific calls evoke asymmetric activity in the monkey's temporal poles.

    PubMed

    Poremba, Amy; Malloy, Megan; Saunders, Richard C; Carson, Richard E; Herscovitch, Peter; Mishkin, Mortimer

    2004-01-29

    It has often been proposed that the vocal calls of monkeys are precursors of human speech, in part because they provide critical information to other members of the species who rely on them for survival and social interactions. Both behavioural and lesion studies suggest that monkeys, like humans, use the auditory system of the left hemisphere preferentially to process vocalizations. To investigate the pattern of neural activity that might underlie this particular form of functional asymmetry in monkeys, we measured local cerebral metabolic activity while the animals listened passively to species-specific calls compared with a variety of other classes of sound. Within the superior temporal gyrus, significantly greater metabolic activity occurred on the left side than on the right, only in the region of the temporal pole and only in response to monkey calls. This functional asymmetry was absent when these regions were separated by forebrain commissurotomy, suggesting that the perception of vocalizations elicits concurrent interhemispheric interactions that focus the auditory processing within a specialized area of one hemisphere.

  8. Steroid control of steroidogenesis in isolated adrenocortical cells: molecular and species specificity.

    PubMed

    Carsia, R V; Macdonald, G J; Malamed, S

    1983-06-01

    The molecular and species specificity of glucocorticoid suppression of corticosteroidogenesis was investigated in isolated adrenocortical cells. Trypsin-isolated cells from male rat, domestic fowl and bovine adrenal glands were incubated with or without steroidogenic agents and with or without steroids. Glucocorticoids were measured by radioimmunoassay or fluorometric assay after 1-2 h incubation. Glucocorticoids suppressed ACTH-induced steroidogenesis of isolated rat cells with the following relative potencies: corticosterone greater than cortisol = cortisone greater than dexamethasone. The mineralocorticoid, aldosterone did not affect steroidogenesis. Suppression by glucocorticoids was acute (within 1-2 h), and varied directly with the glucocorticoid concentration. Testosterone also suppressed ACTH-induced steroidogenesis. Glucocorticoid-type steroids have equivalent suppressive potencies, thus suggesting that these steroids may induce suppression at least partly by a common mechanism. Although corticosterone caused the greatest suppression, testosterone was more potent. The steroid specificity of suppression of cyclic AMP (cAMP)-induced and ACTH-induced steroidogenesis were similar, suggesting that suppression is not solely the result of interference with ACTH receptor function or the induction of adenylate cyclase activity. Exogenous glucocorticoids also suppressed ACTH-induced steroidogenesis of cells isolated from domestic fowl and beef adrenal glands, thus suggesting that this observed suppression may be a general mechanism of adrenocortical cell autoregulation.

  9. Molecular evolution and species-specific expansion of the NAP members in plants.

    PubMed

    Fan, Kai; Shen, Hao; Bibi, Noreen; Li, Feng; Yuan, Shuna; Wang, Ming; Wang, Xuede

    2015-08-01

    The NAP (NAC-Like, Activated by AP3 /PI) subfamily is one of the important plant-specific transcription factors, and controls many vital biological processes in plants. In the current study, 197 NAP proteins were identified from 31 vascular plants, but no NAP members were found in eight non-vascular plants. All NAP proteins were phylogenetically classified into two groups (NAP I and NAP II), and the origin time of the NAP I group might be relatively later than that of the NAP II group. Furthermore, species-specific gene duplications, caused by segmental duplication events, resulted in the expansion of the NAP subfamily after species-divergence. Different groups have different expansion rates, and the NAP group preference was found during the expansion in plants. Moreover, the expansion of NAP proteins may be related to the gain and loss of introns. Besides, functional divergence was limited after the gene duplication. Abscisic acid (ABA) might play an important role in leaf senescence, which is regulated by NAP subfamily. These results could lay an important foundation for expansion and evolutionary analysis of NAP subfamily in plants.

  10. Plants of the fynbos biome harbour host species-specific bacterial communities.

    PubMed

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.

  11. Species-specific response to human infant faces in the premotor cortex.

    PubMed

    Caria, Andrea; Falco, Simona de; Venuti, Paola; Lee, Sangkyun; Esposito, Gianluca; Rigo, Paola; Birbaumer, Niels; Bornstein, Marc H

    2012-04-02

    The human infant face represents an essential source of communicative signals on the basis of which adults modulate their interactions with infants. Behavioral studies demonstrate that infants' faces activate sensitive and attuned responses in adults through their gaze, face expression, voice, and gesture. In this study we aimed to identify brain responses that underlie adults' general propensity to respond to infant faces. We recorded fMRI during adults' (non-parents) processing of unfamiliar infant faces compared to carefully matched adult faces and infrahuman mammal infant and adult faces. Human infant faces activated several brain systems including the lateral premotor cortex, supplementary motor area, cingulate cortex, anterior insula and the thalamus. Activation of these brain circuits suggests adults' preparation for communicative behavior with infants as well as attachment and caregiving. The same brain regions preferentially responded to human infant faces when compared to animal infant faces, indicating species-specific adult brain responses. Moreover, results of support vector machine based classification analysis indicated that these regions allowed above chance-level prediction of brain state during perception of human infant faces. The complex of brain responses to human infant faces appears to include biological mechanisms that underlie responsiveness and a caring inclination toward young children which appear to transcend adult's biological relationship to the baby. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations

    PubMed Central

    Moura, Gabriela R.; Pinheiro, Miguel; Freitas, Adelaide; Oliveira, José L.; Frommlet, Jörg C.; Carreto, Laura; Soares, Ana R.; Bezerra, Ana R.; Santos, Manuel A. S.

    2011-01-01

    Background Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution. Methodologies/Principal Findings Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases. Conclusions Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life. PMID:22046369

  13. Different functions for homologous serotonergic interneurons and serotonin in species-specific rhythmic behaviours.

    PubMed

    Newcomb, James M; Katz, Paul S

    2009-01-07

    Closely related species can exhibit different behaviours despite homologous neural substrates. The nudibranch molluscs Tritonia diomedea and Melibe leonina swim differently, yet their nervous systems contain homologous serotonergic neurons. In Tritonia, the dorsal swim interneurons (DSIs) are members of the swim central pattern generator (CPG) and their neurotransmitter serotonin is both necessary and sufficient to elicit a swim motor pattern. Here it is shown that the DSI homologues in Melibe, the cerebral serotonergic posterior-A neurons (CeSP-As), are extrinsic to the swim CPG, and that neither the CeSP-As nor their neurotransmitter serotonin is necessary for swim motor pattern initiation, which occurred when the CeSP-As were inactive. Furthermore, the serotonin antagonist methysergide blocked the effects of both the serotonin and CeSP-As but did not prevent the production of a swim motor pattern. However, the CeSP-As and serotonin could influence the Melibe swim circuit; depolarization of a cerebral serotonergic posterior-A was sufficient to initiate a swim motor pattern and hyperpolarization of a CeSP-A temporarily halted an ongoing swim motor pattern. Serotonin itself was sufficient to initiate a swim motor pattern or make an ongoing swim motor pattern more regular. Thus, evolution of species-specific behaviour involved alterations in the functions of identified homologous neurons and their neurotransmitter.

  14. CG dinucleotide clustering is a species-specific property of the genome.

    PubMed

    Glass, Jacob L; Thompson, Reid F; Khulan, Batbayar; Figueroa, Maria E; Olivier, Emmanuel N; Oakley, Erin J; Van Zant, Gary; Bouhassira, Eric E; Melnick, Ari; Golden, Aaron; Fazzari, Melissa J; Greally, John M

    2007-01-01

    Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters.

  15. The GHKL ATPase MORC1 Modulates Species-Specific Plant Immunity in Solanaceae.

    PubMed

    Manosalva, Patricia; Manohar, Murli; Kogel, Karl-Heinz; Kang, Hong-Gu; Klessig, Daniel F

    2015-08-01

    The microrchidia (MORC) proteins, a subset of the GHKL ATPase superfamily, were recently described as components involved in transcriptional gene silencing and plant immunity in Arabidopsis. To assess the role of MORC1 during resistance to Phytophthora infestans in solanaceous species, we altered the expression of the corresponding MORC1 homologs in potato, tomato, and Nicotiana benthamiana. Basal resistance to P. infestans was compromised in StMORC1-silenced potato and enhanced in overexpressing lines, indicating that StMORC1 positively affects immunity. By contrast, silencing SlMORC1 expression in tomato or NbMORC1 expression in N. benthamiana enhanced basal resistance to this oomycete pathogen. In addition, silencing SlMORC1 further enhanced resistance conferred by two resistance genes in tomato. Transient expression of StMORC1 in N. benthamiana accelerated cell death induced by infestin1 (INF1), whereas SlMORC1 or NbMORC1 suppressed it. Domain-swapping and mutational analyses indicated that the C-terminal region dictates the species-specific effects of the solanaceous MORC1 proteins on INF1-induced cell death. This C-terminal region also was required for homodimerization and phosphorylation of recombinant StMORC1 and SlMORC1, and its transient expression induced spontaneous cell death in N. benthamiana. Thus, this C-terminal region likely plays important roles in both determining and modulating the biological activity of MORC1 proteins.

  16. Species-specific effects of soil fauna on fungal foraging and decomposition.

    PubMed

    Crowther, Thomas W; Boddy, Lynne; Jones, T Hefin

    2011-10-01

    Decomposer fungi are primary decomposing agents in terrestrial soils. Their mycelial networks play an important role in nutrient mineralisation and distribution, but are also nutritious resources for various soil invertebrates. Global climate change is predicted to alter the diversity and community composition of these soil fauna. To understand whether changes in invertebrate species diversity are likely to affect fungal-mediated decomposition, this study compared the grazing potentials of different invertebrate taxa and functional groups. Specifically, the grazing impacts of seven invertebrate taxa on the growth and spatial distribution of six basidiomycete fungi growing from beech wood blocks in soil microcosms were explored. Wood decay rates by fungi were also compared. The consequences of grazing were both taxon- and species-specific. Generally, macro-invertebrates caused the greatest damage, while meso- and micro-invertebrates often stimulated mycelial growth. Invertebrate size, preferences and population dynamics are likely to influence grazing potentials. Effects of grazing varied between fungi, with mycelial morphology and biochemistry possibly influencing susceptibility. Heavy grazing indirectly increased fungal-mediated wood decomposition. Changes in invertebrate community composition are predicted to have consequences for fungal growth, activity and community structure in woodland soils. Abiotic climate change factors including CO(2) and temperature affect mycelial productivity directly, but the indirect effects, mediated through changes in the soil invertebrate community, may be equally important in controlling ecosystem functioning.

  17. Serpins prevent granzyme-induced death in a species-specific manner.

    PubMed

    Bots, Michael; VAN Bostelen, Liesbeth; Rademaker, Mirjam Tga; Offringa, Rienk; Medema, Jan Paul

    2006-02-01

    Expression of serine protease inhibitors (serpins) is one of the mechanisms used by tumour cells to escape immune surveillance. Previously, we have shown that expression of serpins SPI-6 and SPI-CI, respectively, renders tumour cells resistant to granzyme B (GrB)-mediated death and granzyme M (GrM)-mediated death. To obtain better insight into the interaction between serpins and their target proteases, we investigated the roles of protease inhibitor (PI)-9 and SPI-6 in the resistance to GrB-mediated and CD95-mediated death in further detail. Neither human PI-9 nor its murine orthologue SPI-6 was capable of preventing CD95-induced apoptosis in murine or human cells, indicating that these serpins do not inhibit the activation of apical caspases in this pathway. High expression of PI-9 or SPI-6 did prevent apoptosis induced by human GrB. Strikingly, only SPI-6, and not PI-9, was capable of inhibiting murine GrB, suggesting that a difference in enzymatic specificity exists between the mouse and the human granzymes. In agreement with this suggestion, murine GrB was clearly less effective in inducing apoptosis in human cells. Similar species specificity was also observed for SPI-CI and GrM when either their capacity to associate or the effectiveness of GrM-induced cytotoxicity was analysed. Our findings therefore indicate a species diversity that has a clear effect on mixed in vitro effector target settings.

  18. Biomarkers for Tuberculosis Based on Secreted, Species-Specific, Bacterial Small Molecules

    PubMed Central

    Pan, Shih-Jung; Tapley, Asa; Adamson, John; Little, Tessa; Urbanowski, Michael; Cohen, Keira; Pym, Alexander; Almeida, Deepak; Dorasamy, Afton; Layre, Emilie; Young, David C.; Singh, Ravesh; Patel, Vinod B.; Wallengren, Kristina; Ndung'u, Thumbi; Wilson, Douglas; Moody, D. Branch; Bishai, William

    2015-01-01

    Improved biomarkers are needed for tuberculosis. To develop tests based on products secreted by tubercle bacilli that are strictly associated with viability, we evaluated 3 bacterial-derived, species-specific, small molecules as biomarkers: 2 mycobactin siderophores and tuberculosinyladenosine. Using liquid chromatography–tandem mass spectrometry, we demonstrated the presence of 1 or both mycobactins and/or tuberculosinyladenosine in serum and whole lung tissues from infected mice and sputum, cerebrospinal fluid (CSF), or lymph nodes from infected patients but not uninfected controls. Detection of the target molecules distinguished host infection status in 100% of mice with both serum and lung as the target sample. In human subjects, we evaluated detection of the bacterial small molecules (BSMs) in multiple body compartments in 3 patient cohorts corresponding to different forms of tuberculosis. We detected at least 1 of the 3 molecules in 90%, 71%, and 40% of tuberculosis patients' sputum, CSF, and lymph node samples, respectively. In paucibacillary forms of human tuberculosis, which are difficult to diagnose even with culture, detection of 1 or more BSM was rapid and compared favorably to polymerase chain reaction–based detection. Secreted BSMs, detectable in serum, warrant further investigation as a means for diagnosis and therapeutic monitoring in patients with tuberculosis. PMID:26014799

  19. Species-specific activation time-lags can explain habitat restrictions in hydrophilic lichens.

    PubMed

    Lidén, Marlene; Jonsson Cabrajić, Anna V; Ottosson-Löfvenius, Mikaell; Palmqvist, Kristin; Lundmark, Tomas

    2010-05-01

    Photosystem II (PSII) activation after hydration with water or humid air was measured in four hydrophilic and a generalist lichen to test the hypothesis that slow activation might explain habitat restriction in the former group. For the hydrophilic species, activation was after 4 h nearly completed in Lobaria amplissima and Platismatia norvegica, while only c. 50% for Bryoria bicolor and Usnea longissima. The generalist Platismatia glauca was activated instantaneously. The effect of this on lichen field performance was investigated using a dynamic model separating the two water sources rain and humid air. Model simulations were made using the species-specific characteristics and climate data from 12 stream microhabitats. For U. longissima, slow PSII activation could reduce realized photosynthesis by a factor of five. Bryoria bicolor was almost as severely affected, while P. norvegica displayed moderate reductions. Lobaria amplissima displayed longer realized activity periods even in unfavourable microclimates, possibly because of a higher water loss resistance. Both close proximity to streams and presence of turbulent water had a positive impact on realized activity among the slowly activated species, coinciding with observed distribution patterns of hydrophilic species. The results presented here may thus partly explain observed habitat restrictions of rare hydrophilic lichens.

  20. Biomarkers for Tuberculosis Based on Secreted, Species-Specific, Bacterial Small Molecules.

    PubMed

    Pan, Shih-Jung; Tapley, Asa; Adamson, John; Little, Tessa; Urbanowski, Michael; Cohen, Keira; Pym, Alexander; Almeida, Deepak; Dorasamy, Afton; Layre, Emilie; Young, David C; Singh, Ravesh; Patel, Vinod B; Wallengren, Kristina; Ndung'u, Thumbi; Wilson, Douglas; Moody, D Branch; Bishai, William

    2015-12-01

    Improved biomarkers are needed for tuberculosis. To develop tests based on products secreted by tubercle bacilli that are strictly associated with viability, we evaluated 3 bacterial-derived, species-specific, small molecules as biomarkers: 2 mycobactin siderophores and tuberculosinyladenosine. Using liquid chromatography-tandem mass spectrometry, we demonstrated the presence of 1 or both mycobactins and/or tuberculosinyladenosine in serum and whole lung tissues from infected mice and sputum, cerebrospinal fluid (CSF), or lymph nodes from infected patients but not uninfected controls. Detection of the target molecules distinguished host infection status in 100% of mice with both serum and lung as the target sample. In human subjects, we evaluated detection of the bacterial small molecules (BSMs) in multiple body compartments in 3 patient cohorts corresponding to different forms of tuberculosis. We detected at least 1 of the 3 molecules in 90%, 71%, and 40% of tuberculosis patients' sputum, CSF, and lymph node samples, respectively. In paucibacillary forms of human tuberculosis, which are difficult to diagnose even with culture, detection of 1 or more BSM was rapid and compared favorably to polymerase chain reaction-based detection. Secreted BSMs, detectable in serum, warrant further investigation as a means for diagnosis and therapeutic monitoring in patients with tuberculosis.

  1. Rapid identification of Candida dubliniensis using a species-specific molecular beacon.

    PubMed

    Park, S; Wong, M; Marras, S A; Cross, E W; Kiehn, T E; Chaturvedi, V; Tyagi, S; Perlin, D S

    2000-08-01

    Candida dubliniensis is an opportunistic fungal pathogen that has been linked to oral candidiasis in AIDS patients, although it has recently been isolated from other body sites. DNA sequence analysis of the internal transcribed spacer 2 (ITS2) region of rRNA genes from reference Candida strains was used to develop molecular beacon probes for rapid, high-fidelity identification of C. dubliniensis as well as C. albicans. Molecular beacons are small nucleic acid hairpin probes that brightly fluoresce when they are bound to their targets and have a significant advantage over conventional nucleic acid probes because they exhibit a higher degree of specificity with better signal-to-noise ratios. When applied to an unknown collection of 23 strains that largely contained C. albicans and a smaller amount of C. dubliniensis, the species-specific probes were 100% accurate in identifying both species following PCR amplification of the ITS2 region. The results obtained with the molecular beacons were independently verified by random amplified polymorphic DNA analysis-based genotyping and by restriction enzyme analysis with enzymes BsmAI and NspBII, which cleave recognition sequences within the ITS2 regions of C. dubliniensis and C. albicans, respectively. Molecular beacons are promising new probes for the rapid detection of Candida species.

  2. Species-specific AFLP markers for identification of Zingiber officinale, Z. montanum and Z. zerumbet (Zingiberaceae).

    PubMed

    Ghosh, S; Majumder, P B; Sen Mandi, S

    2011-02-08

    The Zingiber genus, which includes the herbs known as gingers, commonly used in cooking, is well known for its medicinal properties, as described in the Indian pharmacopoeia. Different members of this genus, although somewhat similar in morphology, differ widely in their pharmacological and therapeutic properties. The most important species of this genus, with maximal therapeutic properties, is Zingiber officinale (garden ginger), which is often adulterated with other less-potent Zingiber sp. There is an existing demand in the herbal drug industry for an authentication system for the Zingiber sp in order to facilitate their commercial use as genuine phytoceuticals. To this end, we used amplified fragment length polymorphism (AFLP) to produce DNA fingerprints for three Zingiber species. Sixteen collections (six of Z. officinale, five of Z. montanum, and five of Z. zerumbet) were used in the study. Seven selective primer pairs were found to be useful for all the accessions. A total of 837 fragments were produced by these primer pairs. Species-specific markers were identified for all three Zingiber species (91 for Z. officinale, 82 for Z. montanum, and 55 for Z. zerumbet). The dendogram analysis generated from AFLP patterns showed that Z. montanum and Z. zerumbet are phylogenetically closer to each other than to Z. officinale. The AFLP fingerprints of the Zingiber species could be used to authenticate Zingiber sp-derived drugs and to resolve adulteration-related problems faced by the commercial users of these herbs.

  3. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    PubMed Central

    Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2011-01-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. PMID:21085196

  4. Species-specific response to human infant faces in the premotor cortex

    PubMed Central

    Caria, Andrea; de Falco, Simona; Venuti, Paola; Lee, Sangkyun; Esposito, Gianluca; Rigo, Paola; Birbaumer, Niels; Bornstein, Marc H.

    2012-01-01

    The human infant face represents an essential source of communicative signals on the basis of which adults modulate their interactions with infants. Behavioral studies demonstrate that infants faces activate sensitive and attuned responses in adults through their gaze, face expression, voice, and gesture. In this study we aimed to identify brain responses that underlie adults’ general propensity to respond to infant faces. We recorded fMRI during adults’ (non-parents) processing of unfamiliar infant faces compared to carefully matched adult faces and infrahuman mammal infant and adult faces. Human infant faces activated several brain systems including the lateral premotor cortex, supplementary motor area, cingulate cortex, anterior insula and the thalamus. Activation of these brain circuits suggests adults’ preparation for communicative behavior with infants as well as attachment and caregiving. The same brain regions preferentially responded to human infant faces when compared to animal infant faces, indicating species-specific adult brain responses. Moreover, results of support vector machine based classification analysis indicated that these regions allowed above chance-level prediction of brain state during perception of human infant faces. The complex of brain responses to human infant faces appear to include biological mechanisms that underlie responsiveness and a caring inclination toward young children which appear to transcend adult’s biological relationship to the baby. PMID:22230948

  5. One-step species-specific high resolution melting analysis for nosocomial bacteria detection.

    PubMed

    Wong, Yeng Pooi; Chua, Kek Heng; Thong, Kwai Lin

    2014-12-01

    Nosocomial infections are a major public health concern worldwide. Early and accurate identification of nosocomial pathogens which are often multidrug resistant is crucial for prompt treatment. Hence, an alternative real-time polymerase chain reaction coupled with high resolution melting-curve analysis (HRMA) was developed for identification of five nosocomial bacteria. This assay targets species-specific regions of each nosocomial bacteria and produced five distinct melt curves with each representing a particular bacterial species. The melting curves were characterized by peaks of 78.8 ± 0.2 °C for Acinetobacter baumannii, 82.7 ± 0.2 °C for Escherichia coli, 86.3 ± 0.3 °C for Klebsiella pneumoniae, 88.8 ± 0.2 °C for Pseudomonas aeruginosa and 74.6 ± 02 °C for methicillin-resistant Staphylococcus aureus. The assay was able to specifically detect the five bacterial species with an overall detection limit of 2 × 10(-2) ng/μL. In conclusion, the HRM assay developed is a simple and rapid method for identification of the selected nosocomial pathogens. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Toxicological and chemical investigation of untreated municipal wastewater: Fraction- and species-specific toxicity.

    PubMed

    Hrubik, Jelena; Glisic, Branka; Tubic, Aleksandra; Ivancev-Tumbas, Ivana; Kovacevic, Radmila; Samardzija, Dragana; Andric, Nebojsa; Kaisarevic, Sonja

    2016-05-01

    Absence of a municipal wastewater (WW) treatment plant results in the untreated WW discharge into the recipient. The present study investigated toxic effects and chemical composition of water extracts and fractions from untreated WW and recipient Danube River (DR). Samples were prepared by solid-phase extraction and silica gel fractionation and screened for EROD activity and cytotoxicity using aquatic models, comprising of fish liver cells (PLHC-1) and a model of the early development of zebrafish embryos, while rat (H4IIE) and human (HepG2) hepatoma cells served as mammalian models. Polar fraction caused cytotoxicity and increased the EROD activity in PLHC-1 cells, and increased mortality and developmental abnormalities in developing zebrafish embryos. In H4IIE, polar fraction induced inhibition of cell growth and increased EROD activity, whereas HepG2 exerted low or no response to the exposure. Non-polar and medium-polar fractions were ineffective. Tentative identification by GC/MS showed that WW is characterized by the hydrocarbons, alkylphenols, plasticizers, and a certain number of benzene derivatives and organic acids. In DR, smaller number of organic compounds was identified and toxicity was less pronounced than in WW treatments. The present study revealed the potent toxic effect of polar fraction of untreated WW, with biological responses varying in sensitivity across organisms. Obtained results confirmed that fraction- and species-specific toxicity should be considered when assessing health risk of environmental pollution.

  7. Diversity of the skin microbiota of fishes: evidence for host species specificity.

    PubMed

    Larsen, Andrea; Tao, Zhen; Bullard, Stephen A; Arias, Covadonga R

    2013-09-01

    Skin microbiota of Gulf of Mexico fishes were investigated by ribosomal internal spacer analysis (RISA) and 16S rRNA gene sequencing. A total of 102 fish specimens representing six species (Mugil cephalus, Lutjanus campechanus, Cynoscion nebulosus, Cynoscion arenarius, Micropogonias undulatus, and Lagodon rhomboides) were sampled at regular intervals throughout a year. The skin microbiota from each individual fish was analyzed by RISA and produced complex profiles with 23 bands on average. Similarities between RISA profiles ranged from 97.5% to 4.0%. At 70% similarity, 11 clusters were defined, each grouping individuals from the same fish species. Multidimensional scaling and analysis of similarity correlated the RISA-defined clusters with geographic locality, date, and fish species. Global R values indicated that fish species was the most indicative variable for group separation. Analysis of 16S rRNA gene sequences (from pooled samples of 10 individual fish for each fish species) showed that the Proteobacteria was the predominant phylum in skin microbiota, followed by the Firmicutes and the Actinobacteria. The distribution and abundance of bacterial sequences were different among all species analyzed. Aeribacillus was found in all fish species representing 19% of all clones sequenced, while some genera were fish species-specific (Neorickettsia in M. cephalus and Microbacterium in L. campechanus). Our data provide evidence for the existence of specific skin microbiota associated with particular fish species. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Species-specific time trends and enantiomer fractions of hexabromocyclododecane (HBCD) in biota from East Greenland.

    PubMed

    Vorkamp, Katrin; Bester, Kai; Rigét, Frank F

    2012-10-02

    Time trends of hexabromocyclododecane (HBCD) isomers were studied for glaucous gull and ringed seal from East Greenland. The ringed seal results extended a previous time trend (1986-2008) to 2010. α-HBCD was the only isomer consistently above quantification limits. For glaucous gull liver, annual median values of α-HBCD (1994-2010) ranged from 22 to 120 ng/g lipid weight (lw) with no significant trend, while HBCD in ringed seal blubber from the same area showed a significant increase from 3.9 to 11 ng/g lw (1986-2010). Reasons for this difference are unknown, but might include different feeding habits and species-specific metabolisation processes. Concentrations of several organochlorine (OC) compounds were determined for glaucous gull and ringed seal samples collected from the same area in 2004. HBCD concentrations in glaucous gull liver appeared relatively low when compared to OC concentrations in the same tissue and to both HBCD and OCs in ringed seal blubber from the same area. Enantiomer fractions (EF) deviated significantly from racemic for all annual mean EFs in glaucous gull suggesting metabolisation processes toward an enrichment of (-)α-HBCD. For ringed seal, this enrichment was less pronounced and only significant for two of the ten years. For neither species, significant changes in EF were found over time.

  9. Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant.

    PubMed Central

    Wakasugi, K; Quinn, C L; Tao, N; Schimmel, P

    1998-01-01

    The genetic code is established in aminoacylation reactions whereby amino acids are joined to tRNAs bearing the anticodons of the genetic code. Paradoxically, while the code is universal there are many examples of species-specific aminoacylations, where a tRNA from one taxonomic domain cannot be acylated by a synthetase from another. Here we consider an example where a human, but not a bacterial, tRNA synthetase charges its cognate eukaryotic tRNA and where the bacterial, but not the human, enzyme charges the cognate bacterial tRNA. While the bacterial enzyme has less than 10% sequence identity with the human enzyme, transplantation of a 39 amino acid peptide from the human into the bacterial enzyme enabled the latter to charge its eukaryotic tRNA counterpart in vitro and in vivo. Conversely, substitution of the corresponding peptide of the bacterial enzyme for that of the human enabled the human enzyme to charge bacterial tRNA. This peptide element discriminates a base pair difference in the respective tRNA acceptor stems. Thus, functionally important co-adaptations of a synthetase to its tRNA act as small modular units that can be moved across taxonomic domains and thereby preserve the universality of the code. PMID:9427763

  10. A comparative evaluation of PCR- based methods for species- specific determination of African animal trypanosomes in Ugandan cattle

    PubMed Central

    2013-01-01

    Background In recent years, PCR has been become widely applied for the detection of trypanosomes overcoming many of the constraints of parasitological and serological techniques, being highly sensitive and specific for trypanosome detection. Individual species-specific multi-copy trypanosome DNA sequences can be targeted to identify parasites. Highly conserved ribosomal RNA (rRNA) genes are also useful for comparisons between closely related species. The internal transcribed spacer regions (ITS) in particular are relatively small, show variability among related species and are flanked by highly conserved segments to which PCR primers can be designed. Individual variations in inter-species length makes the ITS region a useful marker for identification of multiple trypanosome species within a sample. Methods Six hundred blood samples from cattle collected in Uganda on FTA cards were screened using individual species-specific primers for Trypanosoma congolense, Trypanosoma brucei and Trypanosoma vivax and compared to a modified (using eluate extracted using chelex) ITS-PCR reaction. Results The comparative analysis showed that the species-specific primer sets showed poor agreement with the ITS primer set. Using species-specific PCR for Trypanozoon, a prevalence of 10.5% was observed as compared to 0.2% using ITS PCR (Kappa = 0.03). For Trypanosoma congolense, the species-specific PCR reaction indicated a prevalence of 0% compared to 2.2% using ITS PCR (Kappa = 0). For T. vivax, species-specific PCR detected prevalence of 5.7% compared to 2.8% for ITS PCR (Kappa = 0.29). Conclusions When selecting PCR based tools to apply to epidemiological surveys for generation of prevalence data for animal trypanosomiasis, it is recommended that species-specific primers are used, being the most sensitive diagnostic tool for screening samples to identify members of Trypanozoon (T. b. brucei s.l). While ITS primers are useful for studying the prevalence of trypanosomes

  11. The molecular basis for species-specific activation of human TRPA1 protein by protons involves poorly conserved residues within transmembrane domains 5 and 6.

    PubMed

    de la Roche, Jeanne; Eberhardt, Mirjam J; Klinger, Alexandra B; Stanslowsky, Nancy; Wegner, Florian; Koppert, Wolfgang; Reeh, Peter W; Lampert, Angelika; Fischer, Michael J M; Leffler, Andreas

    2013-07-12

    The surveillance of acid-base homeostasis is concerted by diverse mechanisms, including an activation of sensory afferents. Proton-evoked activation of rodent sensory neurons is mainly mediated by the capsaicin receptor TRPV1 and acid-sensing ion channels. In this study, we demonstrate that extracellular acidosis activates and sensitizes the human irritant receptor TRPA1 (hTRPA1). Proton-evoked membrane currents and calcium influx through hTRPA1 occurred at physiological acidic pH values, were concentration-dependent, and were blocked by the selective TRPA1 antagonist HC030031. Both rodent and rhesus monkey TRPA1 failed to respond to extracellular acidosis, and protons even inhibited rodent TRPA1. Accordingly, mouse dorsal root ganglion neurons lacking TRPV1 only responded to protons when hTRPA1 was expressed heterologously. This species-specific activation of hTRPA1 by protons was reversed in both mouse and rhesus monkey TRPA1 by exchange of distinct residues within transmembrane domains 5 and 6. Furthermore, protons seem to interact with an extracellular interaction site to gate TRPA1 and not via a modification of intracellular N-terminal cysteines known as important interaction sites for electrophilic TRPA1 agonists. Our data suggest that hTRPA1 acts as a sensor for extracellular acidosis in human sensory neurons and should thus be taken into account as a yet unrecognized transduction molecule for proton-evoked pain and inflammation. The species specificity of this property is unique among known endogenous TRPA1 agonists, possibly indicating that evolutionary pressure enforced TRPA1 to inherit the role as an acid sensor in human sensory neurons.

  12. The Molecular Basis for Species-specific Activation of Human TRPA1 Protein by Protons Involves Poorly Conserved Residues within Transmembrane Domains 5 and 6*

    PubMed Central

    de la Roche, Jeanne; Eberhardt, Mirjam J.; Klinger, Alexandra B.; Stanslowsky, Nancy; Wegner, Florian; Koppert, Wolfgang; Reeh, Peter W.; Lampert, Angelika; Fischer, Michael J. M.; Leffler, Andreas

    2013-01-01

    The surveillance of acid-base homeostasis is concerted by diverse mechanisms, including an activation of sensory afferents. Proton-evoked activation of rodent sensory neurons is mainly mediated by the capsaicin receptor TRPV1 and acid-sensing ion channels. In this study, we demonstrate that extracellular acidosis activates and sensitizes the human irritant receptor TRPA1 (hTRPA1). Proton-evoked membrane currents and calcium influx through hTRPA1 occurred at physiological acidic pH values, were concentration-dependent, and were blocked by the selective TRPA1 antagonist HC030031. Both rodent and rhesus monkey TRPA1 failed to respond to extracellular acidosis, and protons even inhibited rodent TRPA1. Accordingly, mouse dorsal root ganglion neurons lacking TRPV1 only responded to protons when hTRPA1 was expressed heterologously. This species-specific activation of hTRPA1 by protons was reversed in both mouse and rhesus monkey TRPA1 by exchange of distinct residues within transmembrane domains 5 and 6. Furthermore, protons seem to interact with an extracellular interaction site to gate TRPA1 and not via a modification of intracellular N-terminal cysteines known as important interaction sites for electrophilic TRPA1 agonists. Our data suggest that hTRPA1 acts as a sensor for extracellular acidosis in human sensory neurons and should thus be taken into account as a yet unrecognized transduction molecule for proton-evoked pain and inflammation. The species specificity of this property is unique among known endogenous TRPA1 agonists, possibly indicating that evolutionary pressure enforced TRPA1 to inherit the role as an acid sensor in human sensory neurons. PMID:23709225

  13. Species-specific fine root biomass distribution alters competition in mixed forests under climate change

    NASA Astrophysics Data System (ADS)

    Reyer, Christopher; Gutsch, Martin; Lasch, Petra; Suckow, Felicitas; Sterck, Frank; Mohren, Frits

    2010-05-01

    The importance of mixed forests in European silviculture has increased due to forest conversion policies and multifunctional forest management. Concurrently, evidences for substantial impacts of climate change on forest ecosystems accumulate. Projected drier and warmer conditions alter the water relations of tree species, their growth and ultimately their inter-specific competition in mixed stands. Process-based models are scientific tools to study the impact of climate change on and to deepen the understanding of the functioning of these systems based on ecological mechanisms. They allow for long-term, stand-level studies of forest dynamics which could only be addressed with great difficulty in an experimental or empirical setup. We used the process-based forest model 4C to simulate inter-specific competition in mixed stands of Douglas-fir (Pseudotsuga menziesii) and Common beech (Fagus sylvatica) as well as Scots pine (Pinus sylvestris) and Sessile / Pedunculate oak (Quercus petraea and Quercus robur) under a) historical climate for model verification and b) under climate change scenario realizations of the climate model STAR 2.0 in Brandenburg, Germany. Some of the climate change scenario realizations feature a substantially drier and warmer summer climate which decreases the climatic water balance during the growing season. We assumed species-specific fine root biomass distributions which feature broadleaved fine roots in deeper soil layers and coniferous fine roots in upper soil layers according to several root excavation studies from mixed stands. The stands themselves were constructed from yield tables of the contributing species. The model verification provided good results for the basal area predictions under the historical climate. Under climate change, the number of days when the tree water demand exceeded the soil water supply was higher for the coniferous species than for broadleaved species. Furthermore, after 45 simulation years the basal area

  14. Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

    NASA Astrophysics Data System (ADS)

    Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

    2012-12-01

    Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant

  15. Using species-specific paleotemperature equations with foraminifera: A case study in the Southern California Bight

    USGS Publications Warehouse

    Bemis, B.E.; Spero, H.J.; Thunell, R.C.

    2002-01-01

    Species-specific paleotemperature equations were used to reconstruct a record of temperature from foraminiferal ??18O values over the last 25 kyr in the Southern California Bight. The equations yield similar temperatures for the ??18O values of Globigerina bulloides and Neogloboquadrina pachyderma. In contrast, applying a single paleotemperature equation to G. bulloides and N. pachyderma ??18O yields different temperatures, which has been used to suggest that these species record the surface-to-thermocline temperature gradient. In Santa Barbara Basin, an isotopically distinct morphotype of G. bulloides dominates during glacial intervals and yields temperatures that appear too cold when using a paleotemperature equation calibrated for the morphotype common today. When a more appropriate paleotemperature equation is used for glacial G. bulloides, we obtain more realistic glacial temperatures. Glacial-interglacial temperature differences (G-I ??T) calculated in the present study indicate significant cooling (??? 8-10??C) throughout the Southern California Bight during the last glacial maximum (LGM). The magnitude of glacial cooling varies from ???8??C near the middle of the Southern California Bight (Tanner Basin and San Nicolas Basin) to ???9??C in the north (Santa Barbara Basin) and ???9.5-10??C in the south (Velero Basin and No Name Basin). Our temperature calculations agree well with previous estimates based on the modern analog technique. In contrast, studies using N. pachyderma coiling ratios, U37k??? indices, and transfer functions esfimate considerably warmer LGM temperatures and smaller G-I ??T. ?? 2002 Elsevier Science B.V. All rights reserved.

  16. Species-Specific Effects of Woody Litter on Seedling Emergence and Growth of Herbaceous Plants

    PubMed Central

    Koorem, Kadri; Price, Jodi N.; Moora, Mari

    2011-01-01

    The effect of litter on seedling establishment can influence species richness in plant communities. The effect of litter depends on amount, and also on litter type, but relatively little is known about the species-specific effects of litter. We conducted a factorial greenhouse experiment to examine the effect of litter type, using two woody species that commonly co-occur in boreonemoral forest—evergreen spruce (Picea abies), deciduous hazel (Corylus avellana), and a mixture of the two species—and litter amount—shallow (4 mm), deep (12 mm) and leachate—on seedling emergence and biomass of three understorey species. The effect of litter amount on seedling emergence was highly dependent on litter type; while spruce needle litter had a significant negative effect that increased with depth, seedling emergence in the presence of hazel broadleaf litter did not differ from control pots containing no litter. Mixed litter of both species also had a negative effect on seedling emergence that was intermediate compared to the single-species treatments. Spruce litter had a marginally positive (shallow) or neutral effect (deep) on seedling biomass, while hazel and mixed litter treatments had significant positive effects on biomass that increased with depth. We found non-additive effects of litter mixtures on seedling biomass indicating that high quality hazel litter can reduce the negative effects of spruce. Hazel litter does not inhibit seedling emergence; it increases seedling growth, and creates better conditions for seedling growth in mixtures by reducing the suppressive effect of spruce litter, having a positive effect on understorey species richness. PMID:22028890

  17. Conserved and species-specific molecular denominators in mammalian skeletal muscle aging.

    PubMed

    Mercken, Evi M; Capri, Miriam; Carboneau, Bethany A; Conte, Maria; Heidler, Juliana; Santoro, Aurelia; Martin-Montalvo, Alejandro; Gonzalez-Freire, Marta; Khraiwesh, Husam; González-Reyes, José A; Moaddel, Ruin; Zhang, Yongqing; Becker, Kevin G; Villalba, José M; Mattison, Julie A; Wittig, Ilka; Franceschi, Claudio; de Cabo, Rafael

    2017-01-01

    Aging is a complex phenomenon involving functional decline in multiple physiological systems. We undertook a comparative analysis of skeletal muscle from four different species, i.e. mice, rats, rhesus monkeys, and humans, at three different representative stages during their lifespan (young, middle, and old) to identify pathways that modulate function and healthspan. Gene expression profiling and computational analysis revealed that pathway complexity increases from mice to humans, and as mammals age, there is predominantly an upregulation of pathways in all species. Two downregulated pathways, the electron transport chain and oxidative phosphorylation, were common among all four species in response to aging. Quantitative PCR, biochemical analysis, mitochondrial DNA measurements, and electron microscopy revealed a conserved age-dependent decrease in mitochondrial content, and a reduction in oxidative phosphorylation complexes in monkeys and humans. Western blot analysis of key proteins in mitochondrial biogenesis discovered that (i) an imbalance toward mitochondrial fusion occurs in aged skeletal muscle and (ii) mitophagy is not overtly affected, presumably leading to the observed accumulation of abnormally large, damaged mitochondria with age. Select transcript expression analysis uncovered that the skeletal inflammatory profile differentially increases with age, but is most pronounced in humans, while increased oxidative stress (as assessed by protein carbonyl adducts and 4-hydroxynonenal) is common among all species. Expression studies also found that there is unique dysregulation of the nutrient sensing pathways among the different species with age. The identification of conserved pathways indicates common molecular mechanisms intrinsic to health and lifespan, whereas the recognition of species-specific pathways emphasizes the importance of human studies for devising optimal therapeutic modalities to slow the aging process.

  18. The dynamics of histone H3 modifications is species-specific in plant meiosis.

    PubMed

    Oliver, Cecilia; Pradillo, Mónica; Corredor, Eduardo; Cuñado, Nieves

    2013-07-01

    Different histone modifications often modify DNA-histone interactions affecting both local and global structure of chromatin, thereby providing a vast potential for functional responses. Most studies have focused on the role of several modifications in gene transcription regulation, being scarce on other aspects of eukaryotic chromosome structure during cell division, mainly in meiosis. To solve this issue we have performed a cytological analysis to determine the chromosomal distribution of several histone H3 modifications throughout all phases of both mitosis and meiosis in different plant species. We have chosen Aegilops sp. and Secale cereale (monocots) and Arabidopsis thaliana (dicots) because they differ in their phylogenetic affiliation as well as in content and distribution of constitutive heterochromatin. In the species analyzed, the patterns of H3 acetylation and methylation were held constant through mitosis, including modifications associated with "open chromatin". Likewise, the immunolabeling patterns of H3 methylation remained invariable throughout meiosis in all cases. On the contrary, there was a total loss of acetylated H3 immunosignals on condensed chromosomes in both meiotic divisions, but only in monocot species. Regarding the phosphorylation of histone H3 at Ser10, present on condensed chromosomes, although we did not observe any difference in the dynamics, we found slight differences between the chromosomal distribution of this modification between Arabidopsis and cereals (Aegilops sp. and rye). Thus far, in plants chromosome condensation throughout cell division appears to be associated with a particular combination of H3 modifications. Moreover, the distribution and dynamics of these modifications seem to be species-specific and even differ between mitosis and meiosis in the same species.

  19. Tissue- and species-specific differences in cytochrome c oxidase assembly induced by SURF1 defects

    PubMed Central

    Kovářová, Nikola; Pecina, Petr; Nůsková, Hana; Vrbacký, Marek; Zeviani, Massimo; Mráček, Tomáš; Viscomi, Carlo; Houštěk, Josef

    2016-01-01

    Mitochondrial protein SURF1 is a specific assembly factor of cytochrome c oxidase (COX), but its function is poorly understood. SURF1 gene mutations cause a severe COX deficiency manifesting as the Leigh syndrome in humans, whereas in mice SURF1−/− knockout leads only to a mild COX defect. We used SURF1−/− mouse model for detailed analysis of disturbed COX assembly and COX ability to incorporate into respiratory supercomplexes (SCs) in different tissues and fibroblasts. Furthermore, we compared fibroblasts from SURF1−/− mouse and SURF1 patients to reveal interspecies differences in kinetics of COX biogenesis using 2D electrophoresis, immunodetection, arrest of mitochondrial proteosynthesis and pulse-chase metabolic labeling. The crucial differences observed are an accumulation of abundant COX1 assembly intermediates, low content of COX monomer and preferential recruitment of COX into I–III2–IVn SCs in SURF1 patient fibroblasts, whereas SURF1−/− mouse fibroblasts were characterized by low content of COX1 assembly intermediates and milder decrease in COX monomer, which appeared more stable. This pattern was even less pronounced in SURF1−/− mouse liver and brain. Both the control and SURF1−/− mice revealed only negligible formation of the I–III2–IVn SCs and marked tissue differences in the contents of COX dimer and III2–IV SCs, also less noticeable in liver and brain than in heart and muscle. Our studies support the view that COX assembly is much more dependent on SURF1 in humans than in mice. We also demonstrate markedly lower ability of mouse COX to form I–III2–IVn supercomplexes, pointing to tissue-specific and species-specific differences in COX biogenesis. PMID:26804654

  20. Temperature has species-specific effects on corticosterone in alligator lizards.

    PubMed

    Telemeco, Rory S; Addis, Elizabeth A

    2014-09-15

    In response to conditions that threaten homeostasis and/or life, vertebrates generally increase production of glucocorticoid hormones, such as corticosterone (CORT), which induces an emergency physiological state referred to as the stress response. Given that extreme temperatures pose a threat to performance and survival, glucocorticoid upregulation might be an important component of a vertebrate ectotherm's response to extreme thermal conditions. To address this hypothesis, we experimentally examined the effects of body temperature (10, 20, 28, and 35°C; 5-h exposure) on CORT in two congeneric species of lizard naturally exposed to different thermal environments, northern and southern alligator lizards (Elgaria coerulea and Elgaria multicarinata, respectively). In both species, CORT was similarly elevated at medium and high temperatures (28 and 35°C, respectively), but CORT was only elevated at low temperatures (10°C) in southern alligator lizards. We also examined CORT before and after adrenocorticotrophic hormone (ACTH) challenge. In both species, ACTH induced higher CORT levels than any temperature, suggesting that these animals could respond to further stressors at all experimental temperatures. Finally, we compared our laboratory results to measurements of CORT in field-active southern alligator lizards. Plasma CORT concentrations from our laboratory experiment had the same mean and less variance than the field lizards, suggesting that our laboratory lizards displayed CORT within natural levels. Our results demonstrate that body temperature directly affects CORT in alligator lizards. Moreover, the CORT response of these lizards appears to be adapted to their respective thermal environments. Species-specific differences in the thermal CORT response might be common in vertebrate ectotherms and have implications for species' biogeography and responses to climate change. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. A systems toxicology approach to elucidate the mechanisms involved in RDX species-specific sensitivity.

    PubMed

    Warner, Christopher M; Gust, Kurt A; Stanley, Jacob K; Habib, Tanwir; Wilbanks, Mitchell S; Garcia-Reyero, Natàlia; Perkins, Edward J

    2012-07-17

    Interspecies uncertainty factors in ecological risk assessment provide conservative estimates of risk where limited or no toxicity data is available. We quantitatively examined the validity of interspecies uncertainty factors by comparing the responses of zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) to the energetic compound 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), a known neurotoxicant. Relative toxicity was measured through transcriptional, morphological, and behavioral end points in zebrafish and fathead minnow fry exposed for 96 h to RDX concentrations ranging from 0.9 to 27.7 mg/L. Spinal deformities and lethality occurred at 1.8 and 3.5 mg/L RDX respectively for fathead minnow and at 13.8 and 27.7 mg/L for zebrafish, indicating that zebrafish have an 8-fold greater tolerance for RDX than fathead minnow fry. The number and magnitude of differentially expressed transcripts increased with increasing RDX concentration for both species. Differentially expressed genes were enriched in functions related to neurological disease, oxidative-stress, acute-phase response, vitamin/mineral metabolism and skeletal/muscular disorders. Decreased expression of collagen-coding transcripts were associated with spinal deformity and likely involved in sensitivity to RDX. Our work provides a mechanistic explanation for species-specific sensitivity to RDX where zebrafish responded at lower concentrations with greater numbers of functions related to RDX tolerance than fathead minnow. While the 10-fold interspecies uncertainty factor does provide a reasonable cross-species estimate of toxicity in the present study, the observation that the responses between ZF and FHM are markedly different does initiate a call for concern regarding establishment of broad ecotoxicological conclusions based on model species such as zebrafish.

  2. Detection and identification of species-specific bacteria associated with synanthropic mites.

    PubMed

    Hubert, Jan; Kopecký, Jan; Perotti, M Alejandra; Nesvorná, Marta; Braig, Henk R; Ságová-Marečková, Markéta; Macovei, Lilia; Zurek, Ludek

    2012-05-01

    Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for direct bacterial localization. T-RFLP analysis of 16S rRNA gene revealed distinct species-specific bacterial communities. The results were further confirmed by cloning and sequencing (284 clones). L. destructor and D. farinae showed more diverse communities then A. siro and T. putrescentiae. In the cultivated part of the community, the mean CFUs from four mite species ranged from 5.2 × 10(2) to 1.4 × 10(3) per mite. D. farinae had significantly higher CFUs than the other species. Bacteria were located in the digestive and reproductive tract, parenchymatical tissue, and in bacteriocytes. Among the clones, Bartonella-like bacteria occurring in A. siro and T. putresecentiae represented a distinct group related to Bartonellaceae and to Bartonella-like symbionts of ants. The clones of high similarity to Xenorhabdus cabanillasii were found in L. destructor and D. farinae, and one clone related to Photorhabdus temperata in A. siro. Members of Sphingobacteriales cloned from D. farinae and A. siro clustered with the sequences of "Candidatus Cardinium hertigii" and as a separate novel cluster.

  3. Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2

    PubMed Central

    Ohto, Umeharu; Fukase, Koichi; Miyake, Kensuke; Shimizu, Toshiyuki

    2012-01-01

    Lipopolysaccharide (LPS), also known as endotoxin, activates the innate immune response through toll-like receptor 4 (TLR4) and its coreceptor, MD-2. MD-2 has a unique hydrophobic cavity that directly binds to lipid A, the active center of LPS. Tetraacylated lipid IVa, a synthetic lipid A precursor, acts as a weak agonist to mouse TLR4/MD-2, but as an antagonist to human TLR4/MD-2. However, it remains unclear as to how LPS and lipid IVa show agonistic or antagonistic activities in a species-specific manner. The present study reports the crystal structures of mouse TLR4/MD-2/LPS and TLR4/MD-2/lipid IVa complexes at 2.5 and 2.7 Å resolutions, respectively. Mouse TLR4/MD-2/LPS exhibited an agonistic “m”-shaped 2:2:2 complex similar to the human TLR4/MD-2/LPS complex. Mouse TLR4/MD-2/lipid IVa complex also showed an agonistic structural feature, exhibiting architecture similar to the 2:2:2 complex. Remarkably, lipid IVa in the mouse TLR4/MD-2 complex occupied nearly the same space as LPS, although lipid IVa lacked the two acyl chains. Human MD-2 binds lipid IVa in an antagonistic manner completely differently from the way mouse MD-2 does. Together, the results provide structural evidence of the agonistic property of lipid IVa on mouse TLR4/MD-2 and deepen understanding of the ligand binding and dimerization mechanism by the structurally diverse LPS variants. PMID:22532668

  4. Quantification of ferritin bound iron in human serum using species-specific isotope dilution mass spectrometry.

    PubMed

    Ren, Yao; Walczyk, Thomas

    2014-09-01

    Ferritin is a hollow sphere protein composed of 24 subunits that can store up to 4500 iron atoms in its inner cavity. It is mainly found in the liver and spleen but also in serum at trace levels. Serum ferritin is considered as the best single indicator in assessing body iron stores except liver or bone marrow biopsy. However, it is confounded by other disease conditions. Ferritin bound iron (FBI) and ferritin saturation have been suggested as more robust biomarkers. The current techniques for FBI determination are limited by low antibody specificity, low instrument sensitivity and possible analyte losses during sample preparation. The need for a highly sensitive and reliable method is widely recognized. Here we describe a novel technique to detect serum FBI using species-specific isotope dilution mass spectrometry (SS-IDMS). [(57)Fe]-ferritin was produced by biosynthesis and in vitro labeling with the (57)Fe spike in the form of [(57)Fe]-citrate after cell lysis and heat treatment. [(57)Fe]-ferritin for sample spiking was further purified by fast liquid protein chromatography. Serum ferritin and added [(57)Fe]-ferritin were separated from other iron species by ultrafiltration followed by isotopic analysis of FBI using negative thermal ionization mass spectrometry. Repeatability of our assay is 8% with an absolute detection limit of 18 ng FBI in the sample. As compared to other speciation techniques, SS-IDMS offers maximum control over sample losses and species conversion during analysis. The described technique may therefore serve as a reference technique for clinical applications of FBI as a new biomarker for assessing body iron status.

  5. Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary

    PubMed Central

    Béres, Beatrix; Kánainé Sipos, Dóra; Müller, Tamás; Staszny, Ádám; Farkas, Milán; Bakos, Katalin; Urbányi, Béla

    2017-01-01

    Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation. PMID:28265489

  6. Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary.

    PubMed

    Béres, Beatrix; Kánainé Sipos, Dóra; Müller, Tamás; Staszny, Ádám; Farkas, Milán; Bakos, Katalin; Orbán, László; Urbányi, Béla; Kovács, Balázs

    2017-01-01

    Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s-1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent's indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation.

  7. Species-specific dynamic responses of gut bacteria to a mammalian glycan.

    PubMed

    Raghavan, Varsha; Groisman, Eduardo A

    2015-05-01

    The mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that related Bacteroides species that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certain Bacteroides species display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response. Bacteroides species exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient. Genes mediating a specific task are typically conserved in related microbes. For instance, gut Bacteroides species harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may regulate the same genes

  8. Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

    PubMed Central

    Raghavan, Varsha

    2015-01-01

    ABSTRACT The mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that related Bacteroides species that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certain Bacteroides species display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response. Bacteroides species exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient. IMPORTANCE Genes mediating a specific task are typically conserved in related microbes. For instance, gut Bacteroides species harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may

  9. Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA.

    PubMed

    Cho, Ae-Ri; Dong, Hee-Jin; Cho, Seongbeom

    2014-01-01

    Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be 85.56±0.07℃ for cattle, 84.96±0.08℃ for pig, and 85.99±0.05℃ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); 84.91±0.11℃ for goat and 83.90±0.11℃ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and 86.31±0.23℃ for chicken, 88.66±0.12℃ for duck, and 84.49±0.08℃ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from 10 pg/μL to 100 fg/μL levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

  10. Molecular diagnostic for boll weevil (Coleoptera: Curculionidae) based on amplification of three species-specific microsatellites.

    PubMed

    Kim, Kyung Seok; Szendrei, Zsofia; Rodriguez-Saona, Cesar; Mulder, Phillip G; Sappington, Thomas W

    2009-04-01

    The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by scouts. For example, the congeneric pepper weevil, Anthonomus eugenii Cano, and other superficially similar weevils are attracted to components of the boll weevil lure or trap color. Although morphologically distinguishable by trained personnel, the potential for misidentification is compounded when captured weevils are dismembered or partially consumed by ants or ground beetles that sometimes feed on them in the traps. Because misidentification can have expensive consequences, a molecular diagnostic tool would be of great value to eradication managers. We demonstrate that a cocktail of three primer pairs in a single polymerase chain reaction (PCR) amplify species-specific microsatellites that unambiguously distinguish the boll weevil from three other weevil species tested, including pepper weevil; cranberry weevil, Anthonomus eugenii musculus Say; and pecan weevil, Curculio caryae Horn. However, it does not distinguish the boll weevil from the subspecific "thurberia" weevil. A universal internal transcribed spacer primer pair included in the cocktail cross-amplifies DNA from all species, serving as a positive control. Furthermore, the diagnostic primers amplified the target microsatellites from various boll weevil adult body parts, indicating that the PCR technology using the primer cocktail is sensitive enough to positively identify a boll weevil even when the body is partly degraded.

  11. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

    PubMed Central

    2009-01-01

    Background Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. Results We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome. Conclusion These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation. PMID:19656368

  12. Functional role and species-specific contribution of arginases in pulmonary fibrosis.

    PubMed

    Kitowska, Kamila; Zakrzewicz, Dariusz; Königshoff, Melanie; Chrobak, Izabella; Grimminger, Friedrich; Seeger, Werner; Bulau, Patrick; Eickelberg, Oliver

    2008-01-01

    Lung fibrosis is characterized by increased deposition of ECM, especially collagens, and enhanced proliferation of fibroblasts. l-arginine is a key precursor of nitric oxide, asymmetric dimethylarginine, and proline, an amino acid enriched in collagen. We hypothesized that l-arginine metabolism is altered in pulmonary fibrosis, ultimately affecting collagen synthesis. Expression analysis of key enzymes in the arginine pathway, protein arginine methyltransferases (Prmt), arginine transporters, and arginases by quantitative (q) RT-PCR and Western blot revealed significant upregulation of arginase-1 and -2, but not Prmt or arginine transporters, during bleomycin-induced pulmonary fibrosis in mice. HPLC revealed a concomitant, time-dependent decrease in pulmonary l-arginine levels. Arginase-1 and -2 mRNA and protein expression was increased in primary fibroblasts isolated from bleomycin-treated mice, compared with controls, and assessed by qRT-PCR and Western blot analysis. TGF-beta1, a key profibrotic mediator, induced arginase-1 and -2 mRNA expression in primary and NIH/3T3 fibroblasts. Treatment of fibroblasts with the arginase inhibitor, NG-hydroxy-l-arginine, attenuated TGF-beta1-stimulated collagen deposition, but not collagen mRNA expression or Smad signaling, in fibroblasts. In human lungs derived from patients with idiopathic pulmonary fibrosis, arginase activity was unchanged, but arginase-1 expression significantly decreased when compared with donor lungs. Our results thus demonstrate that arginase-1 is expressed and functionally important for collagen deposition in lung fibroblasts. TGF-beta1-induced upregulation of arginase-1 suggests an interplay between profibrotic agents and l-arginine metabolism during the course of lung fibrosis in the mouse, whereas species-specific regulatory mechanisms may account for the differences observed in mouse and human.

  13. Species-specific responses to community density in an unproductive perennial plant community.

    PubMed

    Treberg, Michael A; Turkington, Roy

    2014-01-01

    Most studies of density dependent regulation in plants consider a single target species, but regulation may also occur at the level of the entire community. Knowing whether a community is at carrying capacity is essential for understanding its behaviour because low density plant communities may behave quite differently than their high density counterparts. Also, because the intensity of density dependence may differ considerably between species and physical environments, generalizations about its effects on community structure requires comparisons under a range of conditions. We tested if: (1) density dependent regulation occurs at the level of an entire plant community as well as within individual species; (2) the intensity (effect of increasing community density on mean plant mass) and importance (the effect of increasing density, relative to other factors, on mean plant mass) of competition increases, decreases or remains unchanged with increasing fertilization; (3) there are species-specific responses to changes in community density and productivity. In 63 1 m2 plots, we manipulated the abundance of the nine most common species by transplanting or removing them to create a series of Initial Community Densities above and below the average natural field density, such that the relative proportion of species was consistent for all densities. Plots were randomly assigned to one of three fertilizer levels. At the community level, negative density dependence of mean plant size was observed for each of the 4 years of the study and both the intensity and importance of competition increased each year. At the species level, most species' mean plant mass were negatively density dependent. Fertilizer had a significant effect only in the final year when it had a negative effect on mean plant mass. Our data demonstrate a yield-density response at the entire community-level using perennial plant species in a multi-year experiment.

  14. Species-Specific Diversity of a Fixed Motor Pattern: The Electric Organ Discharge of Gymnotus

    PubMed Central

    Rodríguez-Cattaneo, Alejo; Pereira, Ana Carolina; Aguilera, Pedro A.; Crampton, William G. R.; Caputi, Angel A.

    2008-01-01

    Understanding fixed motor pattern diversity across related species provides a window for exploring the evolution of their underlying neural mechanisms. The electric organ discharges of weakly electric fishes offer several advantages as paradigmatic models for investigating how a neural decision is transformed into a spatiotemporal pattern of action. Here, we compared the far fields, the near fields and the electromotive force patterns generated by three species of the pulse generating New World gymnotiform genus Gymnotus. We found a common pattern in electromotive force, with the far field and near field diversity determined by variations in amplitude, duration, and the degree of synchronization of the different components of the electric organ discharges. While the rostral regions of the three species generate similar profiles of electromotive force and local fields, most of the species-specific differences are generated in the main body and tail regions of the fish. This causes that the waveform of the field is highly site dependant in all the studied species. These findings support a hypothesis of the relative separation of the electrolocation and communication carriers. The presence of early head negative waves in the rostral region, a species-dependent early positive wave at the caudal region, and the different relationship between the late negative peak and the main positive peak suggest three points of lability in the evolution of the electrogenic system: a) the variously timed neuronal inputs to different groups of electrocytes; b) the appearance of both rostrally and caudally innervated electrocytes, and c) changes in the responsiveness of the electrocyte membrane. PMID:18461122

  15. Warm acclimation and oxygen depletion induce species-specific responses in salmonids.

    PubMed

    Anttila, Katja; Lewis, Mario; Prokkola, Jenni M; Kanerva, Mirella; Seppänen, Eila; Kolari, Irma; Nikinmaa, Mikko

    2015-05-15

    Anthropogenic activities are greatly altering the habitats of animals, whereby fish are already encountering several stressors simultaneously. The purpose of the current study was to investigate the capacity of fish to respond to two different environmental stressors (high temperature and overnight hypoxia) separately and together. We found that acclimation to increased temperature (from 7.7±0.02°C to 14.9±0.05°C) and overnight hypoxia (daily changes from normoxia to 63-67% oxygen saturation), simulating climate change and eutrophication, had both antagonistic and synergistic effects on the capacity of fish to tolerate these stressors. The thermal tolerance of Arctic char (Salvelinus alpinus) and landlocked salmon (Salmo salar m. sebago) increased with warm acclimation by 1.3 and 2.2°C, respectively, but decreased when warm temperature was combined with overnight hypoxia (by 0.2 and 0.4°C, respectively). In contrast, the combination of the stressors more than doubled hypoxia tolerance in salmon and also increased hypoxia tolerance in char by 22%. Salmon had 1.2°C higher thermal tolerance than char, but char tolerated much lower oxygen levels than salmon at a given temperature. The changes in hypoxia tolerance were connected to the responses of the oxygen supply and delivery system. The relative ventricle mass was higher in cold- than in warm-acclimated salmon but the thickness of the compact layer of the ventricle increased with the combination of warm and hypoxia acclimation in both species. Char had also significantly larger hearts and thicker compact layers than salmon. The results illustrate that while fish can have protective responses when encountering a single environmental stressor, the combination of stressors can have unexpected species-specific effects that will influence their survival capacity.

  16. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions.

    PubMed

    Clare, David S; Spencer, Matthew; Robinson, Leonie A; Frid, Christopher L J

    2016-01-01

    Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions) and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions) but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive) or antagonistic (negative) depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed.

  17. Dectin-1 intracellular domain determines species-specific ligand spectrum by modulating receptor sensitivity.

    PubMed

    Takano, Tomotsugu; Motozono, Chihiro; Imai, Takashi; Sonoda, Koh-Hei; Nakanishi, Yoichi; Yamasaki, Sho

    2017-08-28

    C-type lectin receptors (CLRs) comprise a large family of immunoreceptors that recognizes polysaccharide ligands exposed on pathogen surfaces and are conserved among mammals. However, interspecies differences in their ligand spectrums are not fully understood. Dectin-1 is a well-characterized CLR that recognizes β-glucan. We report here that seaweed-derived fucan activates cells expressing human Dectin-1 but not mouse Dectin-1. Low-valency β-glucan components within fucan appeared to be responsible for this activation, as the ligand activity was eliminated by β-glucanase treatment. The low-valency β-glucan laminarin also acted as an agonist for human Dectin-1 but not for mouse Dectin-1, whereas the high-valency β-glucan curdlan activated both human and mouse Dectin-1. Reciprocal mutagenesis analysis revealed that the ligand-binding domain of human Dectin-1 does not determine its unique sensitivity to low-valency β-glucan. Rather, we found that its intracellular domain renders human Dectin-1 reactive to low-valency β-glucan ligand. Substitution with two amino acids, Glu2 and Pro5, located in the human Dectin-1 intracellular domain was sufficient to confer sensitivity to low-valency β-glucan in mouse Dectin-1. Conversely, the introduction of mouse-specific amino acids, Lys2 and Ser5, to human Dectin-1 reduced the reactivity to low-valency β-glucan. Indeed, low-valency ligands induced a set of proinflammatory genes in human but not mouse primary dendritic cells. These results suggest that Dectin-1's intracellular domain, but not its ligand-binding domain, determines the species-specific activation profile of Dectin-1 ligands. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  18. Species-specific effects of herbivory on the oviposition behavior of the moth Manduca sexta.

    PubMed

    Reisenman, Carolina E; Riffell, Jeffrey A; Duffy, Kristin; Pesque, Adrien; Mikles, David; Goodwin, Brenna

    2013-01-01

    In Southwestern USA, the jimsonweed Datura wrightii and the nocturnal sphinx moth Manduca sexta form a pollinator-plant and herbivore-plant association. While certain plant volatile organic compounds (VOCs) attract moths for oviposition, it is likely that other host-derived olfactory cues, such as herbivore-induced VOCs, repel moths for oviposition. Here, we studied the oviposition preference of female M. sexta towards intact and damaged host plants of three species: D. wrightii, D. discolor (a less preferred feeding resource but also used by females for oviposition), and Solanum lycopersicum-tomato-(used by moths as an oviposition resource only). Damage was inflicted to the plants either by larval feeding or artificial damage. Mated females were exposed to an intact plant and a damaged plant and allowed to lay eggs for 10 min. Oviposition preferences of females were highly heterogeneous in all cases, but a larger proportion of moths laid significantly fewer eggs on feeding-damaged and artificially damaged plants of S. lycopersicum. Many females also avoided feeding-damaged D. discolor and D. wrightii plants induced by treatment with methyl jasmonate. Chemical analyses showed a significant increase in the total amount of VOCs released by vegetative tissues of feeding-damaged plants, as well as species-specific increases in emission of certain VOCs. In particular, feeding-damaged S. lycopersicum plants emitted (-)-linalool, an odorant that repels moths for oviposition. Finally, the emission of D. wrightii floral VOCs, which are important in mediating feeding by adult moths (and hence pollination), did not change in plants damaged by larval feeding. We propose that the observed differential effects of herbivory on oviposition choice are due to different characteristics (i.e., mutually beneficial or parasitic) of the insect-plant interaction.

  19. Tissue- and species-specific differences in cytochrome c oxidase assembly induced by SURF1 defects.

    PubMed

    Kovářová, Nikola; Pecina, Petr; Nůsková, Hana; Vrbacký, Marek; Zeviani, Massimo; Mráček, Tomáš; Viscomi, Carlo; Houštěk, Josef

    2016-04-01

    Mitochondrial protein SURF1 is a specific assembly factor of cytochrome c oxidase (COX), but its function is poorly understood. SURF1 gene mutations cause a severe COX deficiency manifesting as the Leigh syndrome in humans, whereas in mice SURF1(-/-) knockout leads only to a mild COX defect. We used SURF1(-/-) mouse model for detailed analysis of disturbed COX assembly and COX ability to incorporate into respiratory supercomplexes (SCs) in different tissues and fibroblasts. Furthermore, we compared fibroblasts from SURF1(-/-) mouse and SURF1 patients to reveal interspecies differences in kinetics of COX biogenesis using 2D electrophoresis, immunodetection, arrest of mitochondrial proteosynthesis and pulse-chase metabolic labeling. The crucial differences observed are an accumulation of abundant COX1 assembly intermediates, low content of COX monomer and preferential recruitment of COX into I-III2-IVn SCs in SURF1 patient fibroblasts, whereas SURF1(-/-) mouse fibroblasts were characterized by low content of COX1 assembly intermediates and milder decrease in COX monomer, which appeared more stable. This pattern was even less pronounced in SURF1(-/-) mouse liver and brain. Both the control and SURF1(-/-) mice revealed only negligible formation of the I-III2-IVn SCs and marked tissue differences in the contents of COX dimer and III2-IV SCs, also less noticeable in liver and brain than in heart and muscle. Our studies support the view that COX assembly is much more dependent on SURF1 in humans than in mice. We also demonstrate markedly lower ability of mouse COX to form I-III2-IVn supercomplexes, pointing to tissue-specific and species-specific differences in COX biogenesis.

  20. Positive selection underlies the species-specific binding of Plasmodium falciparum RH5 to human basigin.

    PubMed

    Forni, Diego; Pontremoli, Chiara; Cagliani, Rachele; Pozzoli, Uberto; Clerici, Mario; Sironi, Manuela

    2015-09-01

    Plasmodium falciparum, the causative agent of the deadliest form of malaria, is a member of the Laverania subgenus, which includes ape-infecting parasites. P. falciparum is thought to have originated in gorillas, although infection is now restricted to humans. Laverania parasites display remarkable host-specificity, which is partially mediated by the interaction between parasite ligands and host receptors. We analyse the evolution of BSG (basigin) and GYPA (glycophorin A) in primates/hominins, as well as of their Plasmodium-encoded ligands, PfRH5 and PfEBA175. We show that, in primates, positive selection targeted two sites in BSG (F27 and H102), both involved in PfRH5 binding. A population genetics-phylogenetics approach detected the strongest selection for the gorilla lineage: one of the positively selected sites (K191) is a major determinant of PfRH5 binding affinity. Analysis of RH5 genes indicated episodic selection on the P. falciparum branch; the positively selected W447 site is known to stabilize the interaction with human basigin. Conversely, we detect no selection in the receptor-binding region of EBA175 in the P. falciparum lineage. Its host receptor, GYPA, shows evidence of positive selection in all hominid lineages; selected codons include glycosylation sites that modulate PfEBA175 binding affinity. Data herein provide an evolutionary explanation for species-specific binding of the PfRH5-BSG ligand-receptor pair and support the hypothesis that positive selection at these genes drove the host shift leading to the emergence of P. falciparum as a human pathogen. © 2015 John Wiley & Sons Ltd.

  1. Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2.

    PubMed

    Ohto, Umeharu; Fukase, Koichi; Miyake, Kensuke; Shimizu, Toshiyuki

    2012-05-08

    Lipopolysaccharide (LPS), also known as endotoxin, activates the innate immune response through toll-like receptor 4 (TLR4) and its coreceptor, MD-2. MD-2 has a unique hydrophobic cavity that directly binds to lipid A, the active center of LPS. Tetraacylated lipid IVa, a synthetic lipid A precursor, acts as a weak agonist to mouse TLR4/MD-2, but as an antagonist to human TLR4/MD-2. However, it remains unclear as to how LPS and lipid IVa show agonistic or antagonistic activities in a species-specific manner. The present study reports the crystal structures of mouse TLR4/MD-2/LPS and TLR4/MD-2/lipid IVa complexes at 2.5 and 2.7 Å resolutions, respectively. Mouse TLR4/MD-2/LPS exhibited an agonistic "m"-shaped 2:2:2 complex similar to the human TLR4/MD-2/LPS complex. Mouse TLR4/MD-2/lipid IVa complex also showed an agonistic structural feature, exhibiting architecture similar to the 2:2:2 complex. Remarkably, lipid IVa in the mouse TLR4/MD-2 complex occupied nearly the same space as LPS, although lipid IVa lacked the two acyl chains. Human MD-2 binds lipid IVa in an antagonistic manner completely differently from the way mouse MD-2 does. Together, the results provide structural evidence of the agonistic property of lipid IVa on mouse TLR4/MD-2 and deepen understanding of the ligand binding and dimerization mechanism by the structurally diverse LPS variants.

  2. Species-Specific Responses to Community Density in an Unproductive Perennial Plant Community

    PubMed Central

    Treberg, Michael A.; Turkington, Roy

    2014-01-01

    Most studies of density dependent regulation in plants consider a single target species, but regulation may also occur at the level of the entire community. Knowing whether a community is at carrying capacity is essential for understanding its behaviour because low density plant communities may behave quite differently than their high density counterparts. Also, because the intensity of density dependence may differ considerably between species and physical environments, generalizations about its effects on community structure requires comparisons under a range of conditions. We tested if: (1) density dependent regulation occurs at the level of an entire plant community as well as within individual species; (2) the intensity (effect of increasing community density on mean plant mass) and importance (the effect of increasing density, relative to other factors, on mean plant mass) of competition increases, decreases or remains unchanged with increasing fertilization; (3) there are species-specific responses to changes in community density and productivity. In 63 1 m2 plots, we manipulated the abundance of the nine most common species by transplanting or removing them to create a series of Initial Community Densities above and below the average natural field density, such that the relative proportion of species was consistent for all densities. Plots were randomly assigned to one of three fertilizer levels. At the community level, negative density dependence of mean plant size was observed for each of the 4 years of the study and both the intensity and importance of competition increased each year. At the species level, most species' mean plant mass were negatively density dependent. Fertilizer had a significant effect only in the final year when it had a negative effect on mean plant mass. Our data demonstrate a yield-density response at the entire community-level using perennial plant species in a multi-year experiment. PMID:25050710

  3. Assessment of mercury speciation in feathers using species-specific isotope dilution analysis.

    PubMed

    Renedo, Marina; Bustamante, Paco; Tessier, Emmanuel; Pedrero, Zoyne; Cherel, Yves; Amouroux, David

    2017-11-01

    Seabirds are considered as effective sentinels of environmental marine contamination and their feathers are extensively used as non-lethal samples for contaminant biomonitoring. This tissue represents the main route for mercury (Hg) elimination in seabirds and contains predominantly methylmercury (MeHg). In this work, we developed a robust analytical technique for precise and accurate simultaneous quantification of MeHg, inorganic Hg (iHg) and consequently total Hg (THg), in feathers by gas-chromatography (GC)-ICPMS analyses using species-specific isotope dilution technique. An optimisation of the extraction method was carried out by testing different extraction systems, reagents and spiking procedures using an internal reference feather sample. The procedure was validated for MeHg and THg concentrations with a human hair certified reference material. Microwave nitric acid extraction with spike addition before the extraction provided the best recovery and was chosen as the most appropriate species simultaneous extraction method (SSE). An additional assessment was performed by comparison of our developed extraction method and a MeHg specific extraction technique (MSE) classically used for Hg speciation studies on feathers. The developed method was applied to feather samples from a large number of seabirds from the Southern Ocean (penguins, albatrosses, petrels and skuas) to investigate the variability of Hg speciation across a large range of Hg exposure conditions and concentrations. In all cases, MeHg accounted for > 90% of THg, thus verifying the predominance of organic Hg over iHg in feathers. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts

    PubMed Central

    Rowley, Paul A.; Ho, Brandon; Bushong, Sarah; Johnson, Arlen; Sawyer, Sara L.

    2016-01-01

    In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1 and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. We find a highly refined, species-specific relationship between Xrn1p and the “L-A” totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, Xrn1p appears to co-evolve with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. We demonstrate that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs. PMID:27711183

  5. Species-Specific Effects on Ecosystem Functioning Can Be Altered by Interspecific Interactions

    PubMed Central

    Spencer, Matthew; Robinson, Leonie A.; Frid, Christopher L. J.

    2016-01-01

    Biological assemblages are constantly undergoing change, with species being introduced, extirpated and experiencing shifts in their densities. Theory and experimentation suggest that the impacts of such change on ecosystem functioning should be predictable based on the biological traits of the species involved. However, interspecific interactions could alter how species affect functioning, with the strength and sign of interactions potentially depending on environmental context (e.g. homogenous vs. heterogeneous conditions) and the function considered. Here, we assessed how concurrent changes to the densities of two common marine benthic invertebrates, Corophium volutator and Hediste diversicolor, affected the ecological functions of organic matter consumption and benthic-pelagic nutrient flux. Complementary experiments were conducted within homogenous laboratory microcosms and naturally heterogeneous field plots. When the densities of the species were increased within microcosms, interspecific interactions enhanced effects on organic matter consumption and reduced effects on nutrient flux. Trait-based predictions of how each species would affect functioning were only consistently supported when the density of the other species was low. In field plots, increasing the density of either species had a positive effect on organic matter consumption (with no significant interspecific interactions) but no effect on nutrient flux. Our results indicate that species-specific effects on ecosystem functioning can be altered by interspecific interactions, which can be either facilitative (positive) or antagonistic (negative) depending on the function considered. The impacts of biodiversity change may therefore not be predictable based solely on the biological traits of the species involved. Possible explanations for why interactions were detected in microcosms but not in the field are discussed. PMID:27812164

  6. Species-specific photosynthetic responses of four coniferous seedlings to open-field experimental warming

    NASA Astrophysics Data System (ADS)

    Han, S.; Yoon, S. J.; Yoon, T. K.; Han, S. H.; Lee, J.; Lee, D.; Kim, S.; Hwang, J.; Cho, M.; Son, Y.

    2014-12-01

    in chlorophyll contents resulted from heat stress were observed for PD and PK. We found the species-specific responses of Pn related to the change in photosynthetic parameters following experimental warming of four 1-year-old coniferous seedlings.

  7. Auditory cortex of bats and primates: managing species-specific calls for social communication.

    PubMed

    Kanwal, Jagmeet S; Rauschecker, Josef P

    2007-05-01

    Individuals of many animal species communicate with each other using sounds or "calls" that are made up of basic acoustic patterns and their combinations. We are interested in questions about the processing of communication calls and their representation within the mammalian auditory cortex. Our studies compare in particular two species for which a large body of data has accumulated: the mustached bat and the rhesus monkey. We conclude that the brains of both species share a number of functional and organizational principles, which differ only in the extent to which and how they are implemented. For instance, neurons in both species use "combination-sensitivity" (nonlinear spectral and temporal integration of stimulus components) as a basic mechanism to enable exquisite sensitivity to and selectivity for particular call types. Whereas combination-sensitivity is already found abundantly at the primary auditory cortical and also at subcortical levels in bats, it becomes prevalent only at the level of the lateral belt in the secondary auditory cortex of monkeys. A parallel-hierarchical framework for processing complex sounds up to the level of the auditory cortex in bats and an organization into parallel-hierarchical, cortico-cortical auditory processing streams in monkeys is another common principle. Response specialization of neurons seems to be more pronounced in bats than in monkeys, whereas a functional specialization into "what" and "where" streams in the cerebral cortex is more pronounced in monkeys than in bats. These differences, in part, are due to the increased number and larger size of auditory areas in the parietal and frontal cortex in primates. Accordingly, the computational prowess of neural networks and the functional hierarchy resulting in specializations is established early and accelerated across brain regions in bats. The principles proposed here for the neural "management" of species-specific calls in bats and primates can be tested by studying

  8. Species-specificity of equine and porcine Lawsonia intracellularis isolates in laboratory animals.

    PubMed

    Sampieri, Francesca; Vannucci, Fabio A; Allen, Andrew L; Pusterla, Nicola; Antonopoulos, Aphroditi J; Ball, Katherine R; Thompson, Julie; Dowling, Patricia M; Hamilton, Don L; Gebhart, Connie J

    2013-10-01

    Lawsonia intracellularis infection causes proliferative enteropathy (PE) in many mammalian species, with porcine and equine proliferative enteropathy (PPE and EPE) known worldwide. Hamsters are a well-published animal model for PPE infection studies in pigs. There is no laboratory animal model for EPE infection studies and it is not known whether there is species-specificity for equine or porcine isolates of L. intracellularis in animal models. The objective of this study was to determine whether it is possible to generate typical EPE lesions in hamsters after inoculation with an equine strain of L. intracellularis (EPE strain) and whether it is comparatively possible to generate PPE lesions in rabbits after inoculation with a porcine strain of L. intracellularis (PPE strain). In 2 separate trials, 4-week-old and 3-week-old weanling golden Syrian hamsters were challenged with EPE strains and compared to uninfected (both trials) and PPE-infected controls (Trial 2 only). Concurrently, 6 female New Zealand white juvenile rabbits were infected with PPE strain and observed concomitantly to 8 similar rabbits infected with EPE strain for a different experiment. Hamsters and rabbits were observed for 21 to 24 days post-infection (DPI), depending on the experiment. Neither infected species developed clinical signs. The presence of disease was assessed with diagnostic techniques classically used for pigs and horses: immune-peroxidase monolayer assay on sera; quantitative polymerase chain reaction (qPCR) detection of molecular DNA in feces; and hematoxylin and eosin (H&E) stain and immunohistochemistry (IHC) on intestinal tissues. Our results showed that EPE-challenged hamsters do not develop infection when compared with PPE controls (IHC, P = 0.009; qPCR, P = 0.0003). Conversely, PPE-challenged rabbits do not develop typical intestinal lesions in comparison to EPE-challenged rabbits, with serological response at 14 DPI being significantly lower (P = 0.0023). In conclusion

  9. Species-specificity of equine and porcine Lawsonia intracellularis isolates in laboratory animals

    PubMed Central

    Sampieri, Francesca; Vannucci, Fabio A.; Allen, Andrew L.; Pusterla, Nicola; Antonopoulos, Aphroditi J.; Ball, Katherine R.; Thompson, Julie; Dowling, Patricia M.; Hamilton, Don L.; Gebhart, Connie J.

    2013-01-01

    Lawsonia intracellularis infection causes proliferative enteropathy (PE) in many mammalian species, with porcine and equine proliferative enteropathy (PPE and EPE) known worldwide. Hamsters are a well-published animal model for PPE infection studies in pigs. There is no laboratory animal model for EPE infection studies and it is not known whether there is species-specificity for equine or porcine isolates of L. intracellularis in animal models. The objective of this study was to determine whether it is possible to generate typical EPE lesions in hamsters after inoculation with an equine strain of L. intracellularis (EPE strain) and whether it is comparatively possible to generate PPE lesions in rabbits after inoculation with a porcine strain of L. intracellularis (PPE strain). In 2 separate trials, 4-week-old and 3-week-old weanling golden Syrian hamsters were challenged with EPE strains and compared to uninfected (both trials) and PPE-infected controls (Trial 2 only). Concurrently, 6 female New Zealand white juvenile rabbits were infected with PPE strain and observed concomitantly to 8 similar rabbits infected with EPE strain for a different experiment. Hamsters and rabbits were observed for 21 to 24 days post-infection (DPI), depending on the experiment. Neither infected species developed clinical signs. The presence of disease was assessed with diagnostic techniques classically used for pigs and horses: immune-peroxidase monolayer assay on sera; quantitative polymerase chain reaction (qPCR) detection of molecular DNA in feces; and hematoxylin and eosin (H&E) stain and immunohistochemistry (IHC) on intestinal tissues. Our results showed that EPE-challenged hamsters do not develop infection when compared with PPE controls (IHC, P = 0.009; qPCR, P = 0.0003). Conversely, PPE-challenged rabbits do not develop typical intestinal lesions in comparison to EPE-challenged rabbits, with serological response at 14 DPI being significantly lower (P = 0.0023). In conclusion

  10. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

    PubMed Central

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David

    2017-01-01

    transport of samples from endemic to non-endemic countries without the requirement of a complete cold chain. The commercially-available ELISA displayed poorer sensitivity, even after adjustment of the positive threshold (65–88%), compared to the sensitivity (91–100%) of the new molecular diagnostic workflow. Conclusions/Significance Species-specific assays for sensitive detection of Fasciola spp. enable ante-mortem diagnosis in both human and animal settings. This includes Southeast Asia where there are potentially many undocumented human cases and where post-mortem examination of production animals can be difficult. The new molecular workflow provides a sensitive and quantitative diagnostic approach for the rapid testing of medium to large sample sizes, potentially superseding the traditional sedimentation and FEC technique and enabling surveillance programs in locations where animal and human health funding is limited. PMID:28915255

  11. Species-Specific TT Viruses and Cross-Species Infection in Nonhuman Primates

    PubMed Central

    Okamoto, Hiroaki; Fukuda, Masako; Tawara, Akio; Nishizawa, Tsutomu; Itoh, Yukio; Hayasaka, Ikuo; Tsuda, Fumio; Tanaka, Takeshi; Miyakawa, Yuzo; Mayumi, Makoto

    2000-01-01

    Viruses resembling human TT virus (TTV) were searched for in sera from nonhuman primates by PCR with primers deduced from well-conserved areas in the untranslated region. TTV DNA was detected in 102 (98%) of 104 chimpanzees, 9 (90%) of 10 Japanese macaques, 4 (100%) of 4 red-bellied tamarins, 5 (83%) of 6 cotton-top tamarins, and 5 (100%) of 5 douroucoulis tested. Analysis of the amplification products of 90 to 106 nucleotides revealed TTV DNA sequences specific for each species, with a decreasing similarity to human TTV in the order of chimpanzee, Japanese macaque, and tamarin/douroucouli TTVs. Full-length viral sequences were amplified by PCR with inverted nested primers deduced from the untranslated region of TTV DNA from each species. All animal TTVs were found to be circular with a genomic length at 3.5 to 3.8 kb, which was comparable to or slightly shorter than human TTV. Sequences closely similar to human TTV were determined by PCR with primers deduced from a coding region (N22 region) and were detected in 49 (47%) of the 104 chimpanzees; they were not found in any animals of the other species. Sequence analysis of the N22 region (222 to 225 nucleotides) of chimpanzee TTV DNAs disclosed four genetic groups that differed by 36.1 to 50.2% from one another; they were 35.0 to 52.8% divergent from any of the 16 genotypes of human TTV. Of the 104 chimpanzees, only 1 was viremic with human TTV of genotype 1a. It was among the 53 chimpanzees which had been used in transmission experiments with human hepatitis viruses. Antibody to TTV of genotype 1a was detected significantly more frequently in the chimpanzees that had been used in transmission experiments than in those that had not (8 of 28 [29%] and 3 of 35 [9%], respectively; P = 0.038). These results indicate that species-specific TTVs are prevalent in nonhuman primates and that human TTV can cross-infect chimpanzees. PMID:10627523

  12. Neural crest-mediated bone resorption is a determinant of species-specific jaw length

    PubMed Central

    Ealba, Erin L.; Jheon, Andrew H.; Hall, Jane; Curantz, Camille; Butcher, Kristin D.; Schneider, Richard A.

    2015-01-01

    Precise control of jaw length during development is crucial for proper form and function. Previously we have shown that in birds, neural crest mesenchyme (NCM) confers species-specific size and shape to the beak by regulating molecular and histological programs for the induction and deposition of cartilage and bone. Here we reveal that a hitherto unrecognized but similarly essential mechanism for establishing jaw length is the ability of NCM to mediate bone resorption. Osteoclasts are considered the predominant cells that resorb bone, although osteocytes have also been shown to participate in this process. In adults, bone resorption is tightly coupled to bone deposition as a means to maintain skeletal homeostasis. Yet, the role and regulation of bone resorption during growth of the embryonic skeleton have remained relatively unexplored. We compare jaw development in short-beaked quail versus long-billed duck and find that quail have substantially higher levels of enzymes expressed by bone-resorbing cells including tartrate-resistant acid phosphatase (TRAP), Matrix metalloproteinase 13 (Mmp13), and Mmp9. Then, we transplant NCM destined to form the jaw skeleton from quail to duck and generate chimeras in which osteocytes arise from quail donor NCM and osteoclasts come exclusively from the duck host. Chimeras develop quail-like jaw skeletons coincident with dramatically elevated expression of TRAP, Mmp13, and Mmp9. To test for a link between bone resorption and jaw length, we block resorption using a bisphosphonate, osteoprotegerin protein, or an MMP13 inhibitor, and this significantly lengthens the jaw. Conversely, activating resorption with RANKL protein shortens the jaw. Finally, we find that higher resorption in quail presages their relatively lower adult jaw bone mineral density (BMD) and that BMD is also NCM-mediated. Thus, our experiments suggest that NCM not only controls bone resorption by its own derivatives but also modulates the activity of mesoderm

  13. Evidence of species specific vascular plant functions as regulators of methane emissions from northern peatlands

    NASA Astrophysics Data System (ADS)

    Oquist, M. G.

    2001-05-01

    Peatlands play an indisputable role in the global carbon cycle by their net accumulation of atmospheric carbon dioxide and storage of carbon in the form of peat. They are also intimately tied into the fundamental processes of the atmospheric greenhouse gas balance through their production and concomitant emission of methane. During the last decade several studies have emphasized the function of vegetation as an important regulator of methane emissions from wetland ecosystems, including northern peatlands. Vascular plants can affect methane emissions either by facilitating transportation of methane over the soil/atmosphere interface, or by supplying the microbial soil communities with readily degradable organic substrates through root activity, stimulating biogeochemical transformation rates including methanogenesis. We found evidence of both these types of vegetation-based interactions in a sub-arctic peatland ecosystem and also indications that the two different processes of vegetation induced stimulation of methane emission rates are species specific with respect to the vascular plant communities. By reducing incoming PAR through shading manipulations and comparing these to ambient light control plots we created an intra-habitat gradient of vascular plant photosynthesis at two contrasting sites, one ombrotrophic (dominated by Eriophorum vaginatum/Carex rotundata) and one minerotrophic (dominated by Eriophorum angustifolium). The position of the water table was found to be the dominating environmental factor controlling methane emission rates in both habitat types. At the ombrotrophic site the photosynthetic rate was the second most important factor, especially during peak vascular plant activity (late June- early August) when this variable could explain ca 15% of the variations in methane flux rates. Furthermore, the photosynthetic rates in the shaded plots were reduced by ca 25% and was accompanied by a significant 20% (P=0.01) reduction in methane emission

  14. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

    PubMed

    Shmakov, Sergey A; Sitnik, Vassilii; Makarova, Kira S; Wolf, Yuri I; Severinov, Konstantin V; Koonin, Eugene V

    2017-09-19

    Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes.IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match

  15. A charge balance approach to understanding the species-specific coccolithophore response to the carbon system

    NASA Astrophysics Data System (ADS)

    Rickaby, R. E.; Henderiks, J.; Zondervan, I.; Young, J. N.; Halloran, P.

    2008-12-01

    Major questions surround the species-specific nature of coccolithophore calcification in response to rising atmospheric carbon dioxide levels and the likely feedback of planktonic calcifiers. Recent evidence from rapidly accumulating sediments implies that some of the larger species of coccolithophore are increasing their calcification in response to anthropogenic change, which appears at odds with the paradigm view that coccolithophores reduce the ratio of calcification to photosynthesis rates and tend towards malformation with increasing levels of atmospheric carbon dioxide and decreased pH. Additional key observations will be presented from new culture experiments performed with the relatively small Gephyrocapsa oceanica, and the large Coccolithus braarudii at constant pH but with increasing and correlated concentrations of dissolved inorganic carbon (DIC), aqueous carbon dioxide, and saturation state. The stable isotopic composition of the coccoliths reveals that C. braarudii calcifies under modern DIC conditions using the carbonate ion but at high DIC, the coccoliths become malformed and the isotopic composition suggests that there is a switch to use of the bicarbonate ion. At high DIC and higher saturation state, the site of calcification appears to become more acidic. By contrast, G. oceanica utilises bicarbonate for calcification in all treatments and shows no sign of malformation. In contrast to C. braarudii, G. oceanica has increasing growth rates with increasing DIC, and even shows decreasing fractionation of carbon isotopes into organic matter with increasing carbon dioxide. This can be explained if G. oceanica relies heavily on the diffusive supply of carbon dioxide for photosynthesis, which is limiting under modern conditions. We hypothesise that the response of coccolithophores to anthropogenic change depends primarily on their mode of accessing carbon for photosynthesis. We have developed a simple model based on the charge balance of a cell, and the

  16. Species Specificity of the Putative Male Antennal Aphrodisiac Pheromone in Leptopilina heterotoma, Leptopilina boulardi, and Leptopilina victoriae.

    PubMed

    Weiss, Ingmar; Ruther, Joachim; Stökl, Johannes

    2015-01-01

    Male antennal aphrodisiac pheromones have been suggested to elicit female receptiveness in several parasitic Hymenoptera, including Leptopilina boulardi. None of the proposed pheromones, however, has been fully identified to date. It is also unknown whether these antennal pheromones are species specific, because the species specificity of mate recognition and courtship elicitation in Leptopilina prevented such experiments. In this study we present an experimental design that allows the investigation of the species specificity of the putative male aphrodisiac pheromone of L. heterotoma, L. boulardi, and L. victoriae. This is achieved by chemical manipulation of the odour profile of heterospecific females, so that males perceive them as conspecifics and show antennal courtship behaviour. Males courted the manipulated heterospecific females and antennal contact between the male and the female was observed. However, males elicited receptiveness only in conspecific females, never in the manipulated heterospecific females. Chemical analysis showed the presence of species specific unsaturated hydrocarbons on the antennae of males. Only trace amounts of these hydrocarbons are found on the antennae of females. Our results are an important step towards the understanding and identification of antennal pheromones of parasitic wasps.

  17. Validation of a TaqMan diagnostic assay for the systematic development of Phytophthora genus and species specific markers

    USDA-ARS?s Scientific Manuscript database

    The genus Phytophthora contains many species that are not native to the USA and have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was developed based on mitochondrial gene order differences that allowed for the systemat...

  18. Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens

    PubMed Central

    2011-01-01

    Background Eimeria parasites can cause the disease coccidiosis in poultry and even subclinical infection can incur economic loss. Diagnosis of infection predominantly relies on traditional techniques including lesion scoring and faecal microscopy despite the availability of sensitive molecular assays, largely due to cost and the requirement for specialist equipment. Despite longstanding proven efficacy these traditional techniques demand time and expertise, can be highly subjective and may under-diagnose subclinical disease. Recognition of the tight economic margins prevailing in modern poultry production and the impact of avian coccidiosis on poverty in many parts of the world has highlighted a requirement for a panel of straightforward and sensitive, but cost-effective, Eimeria species-specific diagnostic assays. Results Loop-mediated isothermal amplification (LAMP) is an uncomplicated, quick and relatively inexpensive diagnostic tool. In this study we have developed a panel of species-specific LAMP assays targeting the seven Eimeria species that infect the chicken. Each assay has been shown to be genuinely species-specific with the capacity to detect between one and ten eimerian genomes, equivalent to less than a single mature schizont. Development of a simple protocol for template DNA preparation from tissue collected post mortem with no requirement for specialist laboratory equipment supports the use of these assays in routine diagnosis of eimerian infection. Preliminary field testing supports this hypothesis. Conclusions Development of a panel of sensitive species-specific LAMP assays introduces a valuable new cost-effective tool for use in poultry husbandry. PMID:22053893

  19. Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

    USDA-ARS?s Scientific Manuscript database

    The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

  20. Systematic development of Phytophthora species-specific mitochondrial diagnostic markers for economically important members of the genus

    USDA-ARS?s Scientific Manuscript database

    The genus Phytophthora contains many invasive species to the USA that have the potential to cause significant damage to agriculture and native ecosystems. A genus and species-specific diagnostic assay was previously reported based on mitochondrial gene order differences that allowed for the systemat...

  1. Species-specific induction of CYP2B by 2,4,6-tryphenyldioxane-1,3 (TPD).

    PubMed

    Pustylnyak, Vladimir; Pivovarova, Elena; Slynko, Nikolai; Gulyaeva, Lyudmila; Lyakhovich, Vyacheslav

    2009-12-16

    The aim of the current study was to investigate the species-specific induction of CYP2B by 2,4,6-tryphenyldioxane-1,3 (TPD) in relation to activation of CAR. 7-Pentoxyresorufin O-dealkylase (PROD) activity, RT-PCR, Western blot, Electrophoretic mobility shift assays (EMSA). Phenobarbital-like inducer administration significantly up-regulated CYP2B activity in rat and mouse liver in a species-specific manner, in contrast to the effects on CYP2B in lungs, kidneys and brains. In parallel, Western blot analysis showed that the species-specific increase of PROD in liver is related to the high content of CYP2B: phenobarbital (PB) and TPD increased CYP2B in rat liver, PB and 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) - in mouse liver. The CYP2B protein level was unchanged in the lungs of rats and mice after inducer treatment, whereas it was not detected in the kidney and brain of control and treated animals. The hepatic CYP2B activity in both species paralleled the increase of CYP2B mRNA. A detectable CYP2B mRNA level was measured in the lungs of untreated mice and rats, though it was unchanged during induction. Noninducibility of CYP2B in extrahepatic tissues accompanied an absence of constitutive androstane receptor (CAR) gene expression in these tissues. In liver CYP2B induction paralleled the high level of CAR expression detected by RT-PCR. Moreover, PB, TPD and TCPOBOP treatment stimulated nuclear accumulation of CAR and increased CAR receptor NR1-binding activity in animal liver in a species-specific manner. We have shown that the increased nuclear accumulation and binding activity of CAR are associated with the species-specific up-regulation of CYP2B by TPD in rat liver.

  2. [The population-and-species-specific structure of anopheles (diptera, culicidae) mosquitoes in the Upper Rhine Valley, Germany].

    PubMed

    Perevozkin, V P; Gordeev, M I; Nikolaeva, N V; Becker, N

    2010-01-01

    The authors studied the population-and-species-specific structure of malaria mosquitoes in the Upper Rhine valley, Germany. Four Anopheles mosquito species were identified. These included An. claviger, An. maculipennis, An. messeae, and An. plumbeus. The predominance coefficients of the species were determined. An. messeae is dominant; An. maculipennis is subdominant, An. plumbeus and An. claviger are rare. The latter two species are ecologically specialized and predominantly develop inthe biotopes that are inaccessible for dominant species. The karyotypes of An. messeae show a high variability in sex chromosome XL and a low rate of homo- and heterozygotes in 3R, inversion. The greatest species-specific and karyotypic variety of malaria mosquitoes is noted for large aquatic biotopes.

  3. Conservation of nif- and species-specific domains within repeated promoter sequences from fast-growing Rhizobium species.

    PubMed Central

    Schofield, P R; Watson, J M

    1985-01-01

    In the fast-growing Rhizobium species, repeated DNA sequences, which include the promoter region of the nif HDK operon have been described. These repeated sequences are promoters which specifically activate transcription in the endosymbiotic state. Hybridization analysis of these sequences from R. trifolii has revealed that they may be involved in the species-specific activation of the various genes whose transcription they promote. Comparative analysis of various copies of these repeated sequences, from R. trifolii (the clover symbiont) and R. meliloti (the alfalfa symbiont), reveals the presence of domains of intra- and interspecific conservation within the promoter regions. We suggest that these promoter elements represent sites which are involved in the species-specific and general, nif-specific activation of Rhizobium symbiotic genes. PMID:3892479

  4. Identification of goose, mule duck, chicken, turkey, and swine in foie gras by species-specific polymerase chain reaction.

    PubMed

    Rodríguez, Miguel A; García, Teresa; González, Isabel; Asensio, Luis; Mayoral, Belén; López-Calleja, Inés; Hernández, Pablo E; Martín, Rosario

    2003-03-12

    A specific Polymerase Chain Reaction (PCR) has been developed for the identification of goose (Anser anser), mule duck (Anas platyrhynchos x Cairina moschata), chicken (Gallus gallus), turkey (Meleagris gallopavo), and swine (Sus scrofa domesticus) in foie gras. A forward common primer was designed on a conserved DNA sequence in the mitochondrial 12S ribosomal RNA gene (rRNA), and reverse primers were designed to hybridize on species-specific DNA sequences of each species considered. The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose, mule duck, chicken, turkey, and swine in foie gras. Analysis of experimental mixtures demonstrated that the detection limit of the assay was approximately 1% for each species analyzed. This genetic marker can be very useful for the accurate identification of these species, avoiding mislabeling or fraudulent species substitution in foie gras.

  5. Phylogenetic Sequence Variations in Bacterial rRNA Affect Species-Specific Susceptibility to Drugs Targeting Protein Synthesis▿‡

    PubMed Central

    Akshay, Subramanian; Bertea, Mihai; Hobbie, Sven N.; Oettinghaus, Björn; Shcherbakov, Dimitri; Böttger, Erik C.; Akbergenov, Rashid

    2011-01-01

    Antibiotics targeting the bacterial ribosome typically bind to highly conserved rRNA regions with only minor phylogenetic sequence variations. It is unclear whether these sequence variations affect antibiotic susceptibility or resistance development. To address this question, we have investigated the drug binding pockets of aminoglycosides and macrolides/ketolides. The binding site of aminoglycosides is located within helix 44 of the 16S rRNA (A site); macrolides/ketolides bind to domain V of the 23S rRNA (peptidyltransferase center). We have used mutagenesis of rRNA sequences in Mycobacterium smegmatis ribosomes to reconstruct the different bacterial drug binding sites and to study the effects of rRNA sequence variations on drug activity. Our results provide a rationale for differences in species-specific drug susceptibility patterns and species-specific resistance phenotypes associated with mutational alterations in the drug binding pocket. PMID:21730122

  6. Cutting edge: Gln22 of mouse MD-2 is essential for species-specific lipopolysaccharide mimetic action of taxol.

    PubMed

    Kawasaki, K; Gomi, K; Nishijima, M

    2001-01-01

    MD-2 associates with the extracellular domain of Toll-like receptor 4 (TLR4) and greatly enhances LPS signaling via TLR4. Taxol, which mimics the action of LPS on murine macrophages, induces signals via mouse TLR4-MD-2, but not via human TLR4-MD-2. Here we investigated the molecular basis for this species-specific action of Taxol. Expression of mouse MD-2 conferred both LPS and Taxol responsiveness on human embryonic kidney 293 cells expressing mouse TLR4, whereas expression of human MD-2 conferred LPS responsiveness alone, suggesting that MD-2 is responsible for the species-specificity as to Taxol responsiveness. Furthermore, mouse MD-2 mutants, in which Gln(22) was changed to other amino acids, showed dramatically reduced ability to confer Taxol responsiveness, although their ability to confer LPS responsiveness was not affected. These results indicated that Gln(22) of mouse MD-2 is essential for Taxol signaling but not for LPS signaling.

  7. Species-specific lifespans: Can it be a lottery based on the mode of mitochondrial DNA replication?

    PubMed

    Khaidakov, Magomed

    2016-04-01

    Accumulating evidence suggests that the aging process is, in part, driven by accumulation of large deletions in mitochondrial DNA (mtDNA). Here, I present a hypothesis that significant variations in lifespans can be explained by species-specific mtDNA sequence features that cause a shift in the mode of mtDNA replication and thus preclude the formation of large deletions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Mining of novel species-specific primers for PCR detection of Listeria monocytogenes based on genomic approach.

    PubMed

    Tao, Tingting; Chen, Qiming; Bie, Xiaomei; Lu, Fengxia; Lu, Zhaoxin

    2015-12-01

    Listeria monocytogenes in contaminated food is considered as a serious health threat for consumers due to its high mortality rate. The objective of this study was to obtain novel species-specific target-genes and primers for the molecular detection of L. monocytogenes using a comparative genomic approach. By comparative analysis of L. monocytogenes and non-L. monocytogenes genome sequences in the GenBank database with BLAST program, 26 specific target sequences were used as candidates and the primers were designed for L. monocytogenes species-specificity verification by using PCR assay. Finally, the three genes LMOf2365_0970, LMOf2365_2721 and mpl were identified to have L. monocytogenes species-specificity and be unique as detection targets for diagnostic application. The species-specific primer Lm8 of gene LMOf2365_0970, Lm13 of gene LMOf2365_2721 and Lm20 of gene mpl showed better specificity and sensitivity than the primers described previously. The PCR detection limits of the three specific primer sets were 430, 43, 4.3 fg/μL for genomic DNA, and 5 × 10(3), 50, 5 cfu/mL for pure culture of L. monocytogenes. There was no interference in specificity of detecting L. monocytogenes by co-culture with other foodborne pathogens in high concentration. Moreover, after 6-8 h of enrichment, L. monocytogenes in the artificially contaminated milk samples at an inoculum dose of 38 cfu/10 mL milk could be detected successfully with the studied three primers. Therefore, the three specific genes and primers can be applied to establish a novel rapid and accurate method for detecting L. monocytogenes in food materials.

  9. A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

    PubMed Central

    Dawson, Wayne; Hör, Jens; Egert, Markus; van Kleunen, Mark; Pester, Michael

    2017-01-01

    Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (<0.1 relative abundance) in this process. In addition, we aimed to determine whether plant phylogeny has an influence on the plant species-specific rhizosphere bacterial community. For this purpose, 19 herbaceous plant species from five different plant orders were grown in a common soil substrate. Bacterial communities in the initial soil substrate and the established rhizosphere soils were compared by 16S rRNA gene amplicon sequencing. Only a small number of bacterial operational taxonomic units (OTUs, 97% sequence identity) responded either positively (ca. 1%) or negatively (ca. 1%) to a specific plant species. On average, 91% of plant-specific positive response OTUs comprised bacteria belonging to the rare biosphere, highlighting that low-abundance populations are metabolically active in the rhizosphere. In addition, low-abundance OTUs were in terms of their summed relative abundance major drivers of the bacterial phyla composition across the rhizosphere of all tested plant species. However, no effect of plant phylogeny could be observed on the established rhizosphere bacterial communities, neither when considering differences in the overall established rhizosphere communities nor when considering plant species-specific responders only. Our study provides a quantitative assessment of the effect of plants on their rhizosphere bacteria across multiple plant orders. Plant species-specific effects on soil bacterial communities involved only 18–111 bacterial OTUs out of several 1000s; this minority may potentially impact plant growth

  10. Timing matters: species-specific interactions between spawning time, substrate quality, and recruitment success in three salmonid species

    PubMed Central

    Sternecker, Katharina; Denic, Marco; Geist, Juergen

    2014-01-01

    Substratum quality and oxygen supply to the interstitial zone are crucial for the reproductive success of salmonid fishes. At present, degradation of spawning grounds due to fine sediment deposition and colmation are recognized as main factors for reproductive failure. In addition, changes in water temperatures due to climate change, damming, and cooling water inlets are predicted to reduce hatching success. We tested the hypothesis that the biological effects of habitat degradation depend strongly on the species-specific spawning seasons and life-history strategies (e.g., fall- vs. spring-spawners, migratory vs. resident species) and assessed temperature as an important species-specific factor for hatching success within river substratum. We studied the species-specific differences in their responses to such disturbances using egg-to-fry survival of Danube Salmon (Hucho hucho), resident brown trout (Salmo trutta fario), and migratory brown trout (Salmo trutta lacustris) as biological endpoint. The egg incubation and hatching success of the salmonids and their dependence on temperature and stream substratum quality were compared. Hatching rates of Danube salmon were lower than of brown trout, probably due to higher oxygen demands and increased interstitial respiration in spring. Increases in maximum water temperature reduced hatching rates of resident and migratory brown trout (both fall-spawners) but were positively correlated with hatching rates of Danube salmon (a spring-spawner). Significantly longer incubation periods of resident and migratory brown trout coincided with relatively low stream substratum quality at the end of the egg incubation. Danube salmon seem to avoid low oxygen concentrations in the hyporheic zone by faster egg development favored by higher water temperatures. Consequently, the prediction of effects of temperature changes and altered stream substratum properties on gravel-spawning fishes and biological communities should consider the

  11. Fast DNA-based identification of the black truffle Tuber melanosporum with direct PCR and species-specific primers.

    PubMed

    Bonito, Gregory

    2009-12-01

    Abstract A quick and sensitive DNA-based assay for identifying the black truffle species Tuber melanosporum is presented. Both direct PCR and species-specific primers are used to amplify a phylogenetically informative region of T. melanosporum rDNA. This method was successfully used to screen fresh and frozen T. melanosporum fruitbodies, and could be modified for the molecular detection of other truffle and mushroom species.

  12. Species-specific SSR alleles for studies of hybrid cattails (Typha latifolia x T. angustifolia; Typhaceae) in North America.

    PubMed

    Snow, Allison A; Travis, Steven E; Wildová, Radka; Fér, Tomás; Sweeney, Patricia M; Marburger, Joy E; Windels, Steven; Kubátová, Barbora; Goldberg, Deborah E; Mutegi, Evans

    2010-12-01

    Studies of hybridizing species are facilitated by the availability of species-specific molecular markers for identifying early- and later-generation hybrids. Cattails are a dominant feature of wetland communities, and a better understanding of the prevalence of hybrids is needed to assess the ecological and evolutionary effects of hybridization. Hybridization between Typha angustifolia and T. latifolia produce long-lived clones, known as Typha ×glauca, which are considered to be invasive. Although morphological variation in cattails makes it difficult to recognize early- and later-generation hybrids, several dominant, species-specific RAPD markers are available. Our goal was to find codominant, species-specific markers with greater polymorphism than RAPDs, to identify later-generation hybrids more efficiently. • We screened nine SSR (simple sequence repeat) loci that were described from populations in Ukraine, and we surveyed 31 cattail populations from the upper Midwest and eastern USA. • Seven SSR loci distinguished the parent taxa and were consistent with known species-specific RAPD markers, allowing easier detection of backcrossing. We used linear discriminant analysis to show that F(1) hybrid phenotypes were intermediate between the parent taxa, while those of backcrossed plants overlapped with the hybrids and their parents. Log(leaf length/leaf width), spike gap length, spike length, and stem diameter explained much of the variation among groups. • We provide the first documentation of backcrossed plants in hybridizing cattail populations in Michigan. The diagnostic SSR loci we identified should be extremely useful for examining the evolutionary and ecology interactions of hybridizing cattails in North America.

  13. A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization.

    PubMed

    Dawson, Wayne; Hör, Jens; Egert, Markus; van Kleunen, Mark; Pester, Michael

    2017-01-01

    Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (<0.1 relative abundance) in this process. In addition, we aimed to determine whether plant phylogeny has an influence on the plant species-specific rhizosphere bacterial community. For this purpose, 19 herbaceous plant species from five different plant orders were grown in a common soil substrate. Bacterial communities in the initial soil substrate and the established rhizosphere soils were compared by 16S rRNA gene amplicon sequencing. Only a small number of bacterial operational taxonomic units (OTUs, 97% sequence identity) responded either positively (ca. 1%) or negatively (ca. 1%) to a specific plant species. On average, 91% of plant-specific positive response OTUs comprised bacteria belonging to the rare biosphere, highlighting that low-abundance populations are metabolically active in the rhizosphere. In addition, low-abundance OTUs were in terms of their summed relative abundance major drivers of the bacterial phyla composition across the rhizosphere of all tested plant species. However, no effect of plant phylogeny could be observed on the established rhizosphere bacterial communities, neither when considering differences in the overall established rhizosphere communities nor when considering plant species-specific responders only. Our study provides a quantitative assessment of the effect of plants on their rhizosphere bacteria across multiple plant orders. Plant species-specific effects on soil bacterial communities involved only 18-111 bacterial OTUs out of several 1000s; this minority may potentially impact plant growth in

  14. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    PubMed

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.

  15. Need for species-specific detection for the diagnosis of amoebiasis in a non-endemic setting.

    PubMed

    Hartmeyer, Gitte N; Høgh, Silje V; Chen, Ming; Holt, Hanne; Skov, Marianne N; Kemp, Michael

    2013-11-01

    The diagnosis of amoebiasis caused by Entamoeba histolytica is traditionally based on microscopy. However, the specificity of this method may be questioned, especially in areas where infections by E. histolytica are rare. In the present study, a species-specific real-time PCR was used for the identification of the morphologically similar species E. histolytica and Entamoeba dispar. Out of 15 microscopy-positive stool samples, all were negative for E. histolytica and positive for E. dispar. In 2 cases, a suspicion of amoebic liver abscesses was confirmed by detection of E. histolytica DNA in stored sample material. Microscopy alone is clearly insufficient for the detection of E. histolytica in a setting where this parasite is rare. Microscopy-positive stool samples should be further tested by species-specific tests to distinguish E. histolytica from the non-pathogenic parasite E. dispar. On specific suspicion of amoebiasis, such as the suspicion of amoebic liver abscesses, species-specific tests can be applied even after storage.

  16. Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes.

    PubMed

    Chaston, John M; Murfin, Kristen E; Heath-Heckman, Elizabeth A; Goodrich-Blair, Heidi

    2013-09-01

    The specificity of a horizontally transmitted microbial symbiosis is often defined by molecular communication between host and microbe during initial engagement, which can occur in discrete stages. In the symbiosis between Steinernema nematodes and Xenorhabdus bacteria, previous investigations focused on bacterial colonization of the intestinal lumen (receptacle) of the nematode infective juvenile (IJ), as this was the only known persistent, intimate and species-specific contact between the two. Here we show that bacteria colonize the anterior intestinal cells of other nematode developmental stages in a species-specific manner. Also, we describe three processes that only occur in juveniles that are destined to become IJs. First, a few bacterial cells colonize the nematode pharyngeal-intestinal valve (PIV) anterior to the intestinal epithelium. Second, the nematode intestine constricts while bacteria initially remain in the PIV. Third, anterior intestinal constriction relaxes and colonizing bacteria occupy the receptacle. At each stage, colonization requires X. nematophila symbiosis region 1 (SR1) genes and is species-specific: X. szentirmaii, which naturally lacks SR1, does not colonize unless SR1 is ectopically expressed. These findings reveal new aspects of Xenorhabdus bacteria interactions with and transmission by theirSteinernema nematode hosts, and demonstrate that bacterial SR1 genes aid in colonizing nematode epithelial surfaces.

  17. Effect of species-specificity in auditory-visual intermodal matching in a chimpanzee (Pan troglodytes) and humans.

    PubMed

    Martinez, L; Matsuzawa, T

    2009-10-01

    The goal of this study was to compare the performance of a chimpanzee and humans on auditory-visual intermodal matching of conspecifics and non-conspecifics. The task consisted of matching vocal samples to facial images of the corresponding vocalizers. We tested the chimpanzee and human subjects with both chimpanzee and human stimuli to assess the involvement of species-specificity in the recognition process. All subjects were highly familiar with the stimuli. The chimpanzee subject, named Pan, had had extensive previous experience in auditory-visual intermodal matching tasks. We found clear evidence of a species-specific effect: the chimpanzee and human subjects both performed better at recognizing conspecifics than non-conspecifics. Our results suggest that Pan's early exposure to human caretakers did not seem to favor a perceptual advantage in better discriminating familiar humans compared to familiar conspecifics. The results also showed that Pan's recognition of non-conspecifics did not significantly improve over the course of the experiment. In contrast, human subjects learned to better discriminate non-conspecific stimuli, suggesting that the processing of recognition might differ across species. Nevertheless, this comparative study demonstrates that species-specificity significantly affects intermodal individual recognition of highly familiar individuals in both chimpanzee and human subjects.

  18. Meristem temperature substantially deviates from air temperature even in moderate environments: is the magnitude of this deviation species-specific?

    PubMed

    Savvides, Andreas; van Ieperen, Wim; Dieleman, Janneke A; Marcelis, Leo F M

    2013-11-01

    Meristem temperature (Tmeristem ) drives plant development but is hardly ever quantified. Instead, air temperature (Tair ) is usually used as its approximation. Meristems are enclosed within apical buds. Bud structure and function may differ across species. Therefore, Tmeristem may deviate from Tair in a species-specific way. Environmental variables (air temperature, vapour pressure deficit, radiation, and wind speed) were systematically varied to quantify the response of Tmeristem . This response was related to observations of bud structure and transpiration. Tomato and cucumber plants were used as model plants as they are morphologically distinct and usually growing in similar environments. Tmeristem substantially deviated from Tair in a species-specific manner under moderate environments. This deviation ranged between -2.6 and 3.8 °C in tomato and between -4.1 and 3.0 °C in cucumber. The lower Tmeristem observed in cucumber was linked with the higher transpiration of the bud foliage sheltering the meristem when compared with tomato plants. We here indicate that for properly linking growth and development of plants to temperature in future applications, for instance in climate change scenarios studies, Tmeristem should be used instead of Tair , as a species-specific trait highly reliant on various environmental factors.

  19. Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes

    PubMed Central

    Chaston, John M.; Murfin, Kristen E.; Heath-Heckman, Elizabeth A.; Goodrich-Blair, Heidi

    2013-01-01

    Summary The specificity of a horizontally transmitted microbial symbiosis is often defined by molecular communication between host and microbe during initial engagement, which can occur in discrete stages. In the symbiosis between Steinernema nematodes and Xenorhabdus bacteria, previous investigations focused on bacterial colonization of the intestinal lumen (receptacle) of the nematode infective juvenile (IJ), as this was the only known persistent, intimate, and species-specific contact between the two. Here we show that bacteria colonize the anterior intestinal cells of other nematode developmental stages in a species-specific manner. Also, we describe three processes that only occur in juveniles that are destined to become IJs. First, a few bacterial cells colonize the nematode pharyngeal-intestinal valve (PIV) anterior to the intestinal epithelium. Second, the nematode intestine constricts while bacteria initially remain in the PIV. Third, anterior intestinal constriction relaxes and colonizing bacteria occupy the receptacle. At each stage, colonization requires X. nematophila symbiosis region 1 (SR1) genes and is species-specific: X. szentirmaii, which naturally lacks SR1, does not colonize unless SR1 is ectopically expressed. These findings reveal new aspects of Xenorhabdus bacteria interactions with and transmission by their Steinernema nematode hosts, and demonstrate that bacterial SR1 genes aid in colonizing nematode epithelial surfaces. PMID:23480552

  20. Synergism between Enantiomers Creates Species-Specific Pheromone Blends and Minimizes Cross-Attraction for Two Species of Cerambycid Beetles.

    PubMed

    Meier, Linnea R; Zou, Yunfan; Millar, Jocelyn G; Mongold-Diers, Judith A; Hanks, Lawrence M

    2016-11-01

    Research over the last decade has revealed extensive parsimony among pheromones within the large insect family Cerambycidae, with males of many species producing the same, or very similar aggregation pheromones. Among some species in the subfamily Cerambycinae, interspecific attraction is minimized by temporal segregation, and/or by minor pheromone components that synergize attraction of conspecifics or inhibit attraction of heterospecifics. Less is known about pheromone-based mechanisms of reproductive isolation among species in the largest subfamily, the Lamiinae. Here, we present evidence that the pheromone systems of two sympatric lamiine species consist of synergistic blends of enantiomers of (E)-6,10-dimethyl-5,9-undecadien-2-ol (fuscumol) and the structurally related (E)-6,10-dimethyl-5,9-undecadien-2-yl acetate (fuscumol acetate), as a mechanism by which species-specific blends of pheromone components can minimize interspecific attraction. Male Astylidius parvus (LeConte) were found to produce (R)- and (S)-fuscumol + (R)-fuscumol acetate + geranylacetone, whereas males of Lepturges angulatus (LeConte) produced (R)- and (S)-fuscumol acetate + geranylacetone. Field experiments confirmed that adult beetles were attracted only by their species-specific blend of the enantiomers of fuscumol and fuscumol acetate, respectively, and not to the individual enantiomers. Because other lamiine species are known to produce single enantiomers or blends of enantiomers of fuscumol and/or fuscumol acetate, synergism between enantiomers, or inhibition by enantiomers, may be a widespread mechanism for forming species-specific pheromone blends in this subfamily.

  1. Species-Specific Effects on Throughfall Kinetic Energy in Subtropical Forest Plantations Are Related to Leaf Traits and Tree Architecture

    PubMed Central

    Bruelheide, Helge; Härdtle, Werner; Kröber, Wenzel; Li, Ying; von Oheimb, Goddert

    2015-01-01

    Soil erosion is a key threat to many ecosystems, especially in subtropical China where high erosion rates occur. While the mechanisms that induce soil erosion on agricultural land are well understood, soil erosion processes in forests have rarely been studied. Throughfall kinetic energy (TKE) is influenced in manifold ways and often determined by the tree’s leaf and architectural traits. We investigated the role of species identity in mono-specific stands on TKE by asking to what extent TKE is species-specific and which leaf and architectural traits account for variation in TKE. We measured TKE of 11 different tree species planted in monocultures in a biodiversity-ecosystem-functioning experiment in subtropical China, using sand-filled splash cups during five natural rainfall events in summer 2013. In addition, 14 leaf and tree architectural traits were measured and linked to TKE. Our results showed that TKE was highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus saponaria, while Schima superba showed lowest TKE. These species-specific effects were mediated by leaf habit, leaf area (LA), leaf pinnation, leaf margin, stem diameter at ground level (GD), crown base height (CBH), tree height, number of branches and leaf area index (LAI) as biotic factors and throughfall as abiotic factor. Among these, leaf habit, tree height and LA showed the highest effect sizes on TKE and can be considered as major drivers of TKE. TKE was positively influenced by LA, GD, CBH, tree height, LAI, and throughfall amount while it was negatively influenced by the number of branches. TKE was lower in evergreen, simple leaved and dentate leaved than in deciduous, pinnated or entire leaved species. Our results clearly showed that soil erosion in forest plantations can be mitigated by the appropriate choice of tree species. PMID:26079260

  2. Molecular differentiation of Nosema apis and Nosema ceranae based on species-specific sequence differences in a protein coding gene.

    PubMed

    Gisder, Sebastian; Genersch, Elke

    2013-05-01

    Nosema apis and Nosema ceranae are two microsporidian pathogens of the European honey bee, Apis mellifera. There is evidence that N. ceranae is more virulent than N. apis subject to environmental factors like climate. This makes N. ceranae one of the suspects in the increasing colony losses recently observed in many regions of the world. Correct differentiation between N. apis and N. ceranae is important and best accomplished by molecular methods. So far only protocols based on species-specific sequence differences in the 16S rRNA gene are available. However, recent studies indicated that these methods may lead to confusing results due to polymorphisms in and recombination between the multi-copy 16S rRNA genes. To solve this problem and to provide a reliable molecular tool for the differentiation between the two bee pathogenic microsporidia we here present and evaluate a duplex-PCR protocol based on species-specific sequence differences in the highly conserved gene coding for the DNA-dependent RNA polymerase II largest subunit. A total of 102 honey bee samples were analyzed by the novel PCR protocol and the results were compared with the results of the originally published PCR-RFLP analysis and two recently published differentiation protocols, based on 16S rRNA sequence differences. Although the novel PCR protocol proved to be as reliable as the 16S rRNA gene based PCR-RFLP it was superior to simple 16S rRNA based PCR protocols which tended to overestimate the rate of N. ceranae infections. Therefore, we propose that species-specific sequence differences of highly conserved protein coding genes should become the preferred molecular tool for differentiation of Nosema spp. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Species-Specific Effects on Throughfall Kinetic Energy in Subtropical Forest Plantations Are Related to Leaf Traits and Tree Architecture.

    PubMed

    Goebes, Philipp; Bruelheide, Helge; Härdtle, Werner; Kröber, Wenzel; Kühn, Peter; Li, Ying; Seitz, Steffen; von Oheimb, Goddert; Scholten, Thomas

    2015-01-01

    Soil erosion is a key threat to many ecosystems, especially in subtropical China where high erosion rates occur. While the mechanisms that induce soil erosion on agricultural land are well understood, soil erosion processes in forests have rarely been studied. Throughfall kinetic energy (TKE) is influenced in manifold ways and often determined by the tree's leaf and architectural traits. We investigated the role of species identity in mono-specific stands on TKE by asking to what extent TKE is species-specific and which leaf and architectural traits account for variation in TKE. We measured TKE of 11 different tree species planted in monocultures in a biodiversity-ecosystem-functioning experiment in subtropical China, using sand-filled splash cups during five natural rainfall events in summer 2013. In addition, 14 leaf and tree architectural traits were measured and linked to TKE. Our results showed that TKE was highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus saponaria, while Schima superba showed lowest TKE. These species-specific effects were mediated by leaf habit, leaf area (LA), leaf pinnation, leaf margin, stem diameter at ground level (GD), crown base height (CBH), tree height, number of branches and leaf area index (LAI) as biotic factors and throughfall as abiotic factor. Among these, leaf habit, tree height and LA showed the highest effect sizes on TKE and can be considered as major drivers of TKE. TKE was positively influenced by LA, GD, CBH, tree height, LAI, and throughfall amount while it was negatively influenced by the number of branches. TKE was lower in evergreen, simple leaved and dentate leaved than in deciduous, pinnated or entire leaved species. Our results clearly showed that soil erosion in forest plantations can be mitigated by the appropriate choice of tree species.

  4. Species-specific lipophilicity of thyroid hormones and their precursors in view of their membrane transport properties.

    PubMed

    Tóth, Gergő; Mazák, Károly; Hosztafi, Sándor; Kökösi, József; Noszál, Béla

    2013-03-25

    A total of 30 species-specific partition coefficients of three thyroid hormones (thyroxine, liothyronine, reverse liothyronine) and their two biological precursors (monoiodotyrosine, diiodotyrosine) are presented. The molecules were studied using combined methods of microspeciation and lipophilicity. Microspeciation was carried out by (1)H NMR-pH and UV-pH titration techniques on the title compounds and their auxiliary derivatives of reduced complexity. Partition of some of the individual microspecies was mimicked by model compounds of the closest possible similarity, then correction factors were determined and introduced. Our data show that the iodinated aromatic ring system is the definitive structural element that fundamentally determines the lipophilicity of thyroid hormones, whereas the protonation state of the aliphatic part plays a role of secondary importance. On the other hand, the lipophilicity of the precursors is highly influenced by the protonation state due to the relative lack of overwhelmingly lipophilic moieties. The different logp values of the positional isomers liothyronine and reverse liothyronine represent the importance of steric and electronic factors in lipophilicity. Our investigations provided clear indication that overall partition, the best membrane transport - predicting physico-chemical parameter depends collectively on the site-specific basicity and species-specific partition coefficient. At physiological pH these biomolecules are strongly amphipathic due to the lipophilic aromatic rings and hydrophilic amino acid side chains which can well be the reason why thyroid hormones cannot cross membranes by passive diffusion and they are constituents of biological membranes. The lipophilicity profile of thyroid hormones and their precursors are calculated and depicted in terms of species-specific lipophilicities over the entire pH range. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Predicting locations of rare aquatic species’ habitat with a combination of species-specific and assemblage-based models

    USGS Publications Warehouse

    McKenna, James E.; Carlson, Douglas M.; Payne-Wynne, Molly L.

    2013-01-01

    Aim: Rare aquatic species are a substantial component of biodiversity, and their conservation is a major objective of many management plans. However, they are difficult to assess, and their optimal habitats are often poorly known. Methods to effectively predict the likely locations of suitable rare aquatic species habitats are needed. We combine two modelling approaches to predict occurrence and general abundance of several rare fish species. Location: Allegheny watershed of western New York State (USA) Methods: Our method used two empirical neural network modelling approaches (species specific and assemblage based) to predict stream-by-stream occurrence and general abundance of rare darters, based on broad-scale habitat conditions. Species-specific models were developed for longhead darter (Percina macrocephala), spotted darter (Etheostoma maculatum) and variegate darter (Etheostoma variatum) in the Allegheny drainage. An additional model predicted the type of rare darter-containing assemblage expected in each stream reach. Predictions from both models were then combined inclusively and exclusively and compared with additional independent data. Results Example rare darter predictions demonstrate the method's effectiveness. Models performed well (R2 ≥ 0.79), identified where suitable darter habitat was most likely to occur, and predictions matched well to those of collection sites. Additional independent data showed that the most conservative (exclusive) model slightly underestimated the distributions of these rare darters or predictions were displaced by one stream reach, suggesting that new darter habitat types were detected in the later collections. Main conclusions Broad-scale habitat variables can be used to effectively identify rare species' habitats. Combining species-specific and assemblage-based models enhances our ability to make use of the sparse data on rare species and to identify habitat units most likely and least likely to support those species

  6. Species-Specific Detection and Identification of Fusarium Species Complex, the Causal Agent of Sugarcane Pokkah Boeng in China

    PubMed Central

    Que, Youxiong; Wang, Jihua; Comstock, Jack C.; Wei, Jinjin; McCord, Per H.; Chen, Baoshan; Chen, Rukai; Zhang, Muqing

    2014-01-01

    Background Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. Methods A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. Result Two Fusarium species (F. verticillioides and F. proliferatum) that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. Conclusions/Significance This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng. PMID:25141192

  7. Sulfated polysaccharides from the egg jelly layer are species-specific inducers of acrosomal reaction in sperms of sea urchins.

    PubMed

    Alves, A P; Mulloy, B; Diniz, J A; Mourão, P A

    1997-03-14

    We have characterized the fine structure of sulfated polysaccharides from the egg jelly layer of three species of sea urchins and tested the ability of these purified polysaccharides to induce the acrosome reaction in spermatozoa. The sea urchin Echinometra lucunter contains a homopolymer of 2-sulfated, 3-linked alpha-L-galactan. The species Arbacia lixula and Lytechinus variegatus contain linear sulfated alpha-L-fucans with regular tetrasaccharide repeating units. Each of these sulfated polysaccharides induces the acrosome reaction in conspecific but not in heterospecific spermatozoa. These results demonstrate that species specificity of fertilization in sea urchins depends in part on the fine structure of egg jelly sulfated polysaccharide.

  8. Bi-parentally inherited species-specific markers identify hybridization between rainbow trout and cutthroat trout subspecies

    USGS Publications Warehouse

    Ostberg, C.O.; Rodriguez, R.J.

    2004-01-01

    Eight polymerase chain reaction primer sets amplifying bi-parentally inherited species-specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F1 and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.

  9. Structural study of the X-ray-induced enzymatic reaction of octahaem cytochrome C nitrite reductase.

    PubMed

    Trofimov, A A; Polyakov, K M; Lazarenko, V A; Popov, A N; Tikhonova, T V; Tikhonov, A V; Popov, V O

    2015-05-01

    Octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens catalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochrome c nitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

  10. X-ray induced alterations in the differentiation and mineralization potential of murine preosteoblastic cells

    NASA Astrophysics Data System (ADS)

    Hu, Yueyuan; Lau, Patrick; Baumstark-Khan, Christa; Hellweg, Christine E.; Reitz, Günther

    2012-05-01

    To evaluate the effects of ionizing radiation (IR) on murine preosteoblastic cell differentiation, we directed OCT-1 cells to the osteoblastic lineage by treatment with a combination of β-glycerophosphate (β-GP), ascorbic acid (AA), and dexamethasone (Dex). In vitro mineralization was evaluated based on histochemical staining and quantification of the hydroxyapatite content of the extracellular bone matrix. Expression of mRNA encoding Runx2, transforming growth factor β1 (TGF-β1), osteocalcin (OCN), and p21CDKN1A was analyzed. Exposure to IR reduced the growth rate and diminished cell survival of OCT-1 cells under standard conditions. Notably, calcium content analysis revealed that deposition of mineralized matrix increased significantly under osteogenic conditions after X-ray exposure in a time-dependent manner. In this study, higher radiation doses exert significant overall effects on TGF-β1, OCN, and p21CDKN1A gene expression, suggesting that gene expression following X-ray treatment is affected in a dose-dependent manner. Additionally, we verified that Runx2 was suppressed within 24 h after irradiation at 2 and 4 Gy. Although further studies are required to verify the molecular mechanism, our observations strongly suggest that treatment with IR markedly alters the differentiation and mineralization process of preosteoblastic cells.

  11. Thermoluminescence characteristics of X-ray induced kyanite mineral and its thermal quenching parameters

    NASA Astrophysics Data System (ADS)

    Kalita, J. M.; Wary, G.

    2014-04-01

    Thermoluminescence (TL) glow curves of X-ray irradiated micro-grain natural kyanite have been recorded under annealed and un-annealed condition at various heating rates (2, 4, 6, 8 and 10 K s-1). TL parameters such as activation energy, order of kinetic and pre-exponential frequency factor have been investigated from the glow peak by a computerized glow curve deconvolution technique. Variation of peak integrals, peak maximum temperatures, FWHM and activation energy with heating rates have been investigated and the glow curves at higher rates have been found to be influenced by presence of thermal quenching. For annealed sample value of thermal quenching activation energy ( W) and pre-exponential factor ( C) are found to be 0.86 ± 0.02 eV and 2.5 × 109 s-1 respectively and for un-annealed sample these values are 1.68 ± 0.03 eV and 3.1 × 1010 s-1 respectively. Experimentally measured value of W and C have been verified by estimating thermal quenching efficiencies η( T) with the help of calculated value of W and C; quenched glow curves have been successfully reconstructed for each heating rate. The dose sensitivity of both types of samples is also reported. Annealed sample shows improved dose response than un-annealed sample.

  12. Defects in sodalite-group minerals determined from X-ray-induced luminescence

    NASA Astrophysics Data System (ADS)

    Finch, Adrian A.; Friis, Henrik; Maghrabi, Mufeed

    2016-07-01

    The luminescence spectra of a suite of natural sodium framework silicates including four different sodalite variants and tugtupite have been collected during X-ray irradiation as a function of temperature between 20 and 673 K. The origin of the emission bands observed in these samples is attributed to F-centres (360 nm), paramagnetic oxygen defects (400 and 450 nm), S2 - ions (620 nm) and tetrahedral Fe3+ (730 nm). Luminescence in the yellow (550 nm) is tentatively attributed to Mn2+, and red luminescence in Cr-rich pink sodalite is possibly from Cr3+ activation. Sudden reduction in luminescence intensities of emission centres was observed for all minerals in the 60-120 K range. Since it is common to all the sodalite-group minerals, we infer it is a feature of the aluminosilicate framework. Sodalite luminescence has responses from substitutions on the framework (e.g. paramagnetic oxygen defects, Fe3+) which give sodalite properties akin to other framework silicates such as feldspar and quartz. However, the presence of the sodalite cage containing anions (such as F-centres, S2 - ions) imparts additional properties akin to alkali halides. The possibility of coupling between Fe3+ and S2 - is discussed. The overall luminescence behaviour of sodalite group can be understood in terms of competition between these centre types.

  13. INVOLVEMENT OF P53 IN X-RAY INDUCED INTRACHROMOSOMAL RECOMBINATION IN MICE. (R825359)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  14. Proton-induces and x-ray induced fluorescence analysis of scoliotic tissue

    SciTech Connect

    Panessa-Warren, B J; Kraner, H W; Jones, K W; Weiss, L S

    1980-02-01

    Adolescent idiopathic scoliosis is characterized by a curvature or assymetry of the spine which may become progressively more severe, with clinical symptoms appearing just prior to, or during, puberty. The incidence for scoliosis in the age group from 12 to 14 years of age has been reported as high as 8 to 10%, with more than 80% of the cases occurring in females. Although pathologic changes exist in muscles from both sides of the spinal curvature, and no statistically significant side differences have been reported, morphologic changes suggest that the concanve side is the most affected. This paper reports our preliminary data on the elemental composition of individual muscle fibers derived from convex, concave and gluteal scoliotic muscle, and erythrocytes from scoliotic and normal patients, analyzed by proton induced x-ray emission (PIXE) and x-ray fluorescence spectroscopy (XRF). A new type of specimen holder was designed for this study which offers low x-ray background, minimal absorption and maintenance of a moist environment around the specimen.

  15. Nuclear apoJ: An X-ray-inducible cell death signal. Final Report

    SciTech Connect

    2003-12-29

    The complex interactions between apoptosis, genomic instability and carcinogenesis induced by low dose ionizing radiation (IR) are poorly understood. Tissues differentially withstand IR based on complex processes that include DNA repair, altered gene expression, and apoptosis. This proposal is based on the investigators' discovery of a protein, apoJ (initially designated xip8/XIP8), that is dramatically IR-induced. The protein is also known as a marker for apoptosis, but its function is unknown. The ''nuclear'' form of the apoJ protein, undergoes dramatic accumulation in the nucleus following IR, and then strongly associates with the C-terminus of Ku70, a key factor in DNA-PK-dependent nonhomologous DNA double strand break (DSB) repair. These studies suggest that the nuclear form of apoJ is a major determinant in the elimination of carcinogenic cells and that it contributes strongly to nonlinearity threshold responses for survival and carcinogenesis.

  16. Observing Femtosecond Fragmentation Using Ultrafast X-ray-Induced Auger Spectra

    DOE PAGES

    Wolf, Thomas; Holzmeier, Fabian; Wagner, Isabella; ...

    2017-07-01

    Molecules often fragment after photoionization in the gas phase. Usually, this process can only be investigated spectroscopically as long as there exists electron correlation between the photofragments. Important parameters, like their kinetic energy after separation, cannot be investigated. We are reporting on a femtosecond time-resolved Auger electron spectroscopy study concerning the photofragmentation dynamics of thymine. We observe the appearance of clearly distinguishable signatures from thymine's neutral photofragment isocyanic acid. Furthermore, we observe a time-dependent shift of its spectrum, which we can attribute to the influence of the charged fragment on the Auger electron. This allows us to map our time-dependentmore » dataset onto the fragmentation coordinate. The time dependence of the shift supports efficient transformation of the excess energy gained from photoionization into kinetic energy of the fragments. Our method is broadly applicable to the investigation of photofragmentation processes.« less

  17. X-ray induced luminescence properties of (Y,Eu)AlO3 single crystals

    NASA Astrophysics Data System (ADS)

    Kuro, Tomoaki; Nakauchi, Daisuke; Okada, Go; Kawaguchi, Noriaki; Yanagida, Takayuki

    2017-02-01

    We investigated photoluminescence, scintillation and dosimeter properties of (Y1-x Eux)AlO3 (x = 0.001, 0.5 and 1) single crystals (hereafter denoted as Eu:YAP for x = 0.001, EYAP for x = 0.5 and EAP for x = 1). The samples were prepared by the Floating Zone method. In photoluminescence (PL), we observed a broad emission around 300-400 nm due to host under excitation of 280 nm, and emissions due to the 4f state transitions of Eu3+ appeared around 590 nm and 615 nm. Scintillation spectra also show emission peaks around 590 and 615 nm due to the 4f state transitions of Eu3+ in all the samples. In addition, emissions around 300-400 nm due to YAP host and around 550-700 nm due to 5d-4f transitions of Eu2+ appeared in Eu:YAP. The PL and scintillation decay time profiles consisted of several exponential decay components. The fast (ns) component group was possibly due to host emission, and especially Eu:YAP demonstrated a very fast PL decay time of 16 ns. The intermediate (μs) component group was due to the 5d-4f transitions of Eu2+. The slow (ms) component group was ascribed to the 4f state transitions of Eu3+ ion. The Eu:YAP sample showed intense thermally-stimulated luminescence (TSL) with peaks at 46, 155, 255 and 443 °C. The intensity was much higher than those of EAP and EYAP. In particular, the peak at 254 °C, which showed the highest intensity, was due to doping with Eu. The TSL dose response function showed a good linearity (R2 > 0.99) over a wide dose range from 0.1 mGy to 100 mGy for Eu:YAP, which showed the highest sensitivity among the present samples.

  18. Antioxidant protects blood-testis barrier against synchrotron radiation X-ray-induced disruption

    PubMed Central

    Zhang, Tingting; Liu, Tengyuan; Shao, Jiaxiang; Sheng, Caibin; Hong, Yunyi; Ying, Weihai; Xia, Weiliang

    2015-01-01

    Synchrotron radiation (SR) X-ray has wide biomedical applications including high resolution imaging and brain tumor therapy due to its special properties of high coherence, monochromaticity and high intensity. However, its interaction with biological tissues remains poorly understood. In this study, we used the rat testis as a model to investigate how SR X-ray would induce tissue responses, especially the blood-testis barrier (BTB) because BTB dynamics are critical for spermatogenesis. We irradiated the male gonad with increasing doses of SR X-ray and obtained the testicles 1, 10 and 20 d after the exposures. The testicle weight and seminiferous tubule diameter reduced in a dose- and time-dependent manner. Cryosections of testes were stained with tight junction (TJ) component proteins such as occludin, claudin-11, JAM-A and ZO-1. Morphologically, increasing doses of SR X-ray consistently induced developing germ cell sloughing from the seminiferous tubules, accompanied by shrinkage of the tubules. Interestingly, TJ constituent proteins appeared to be induced by the increasing doses of SR X-ray. Up to 20 d after SR X-ray irradiation, there also appeared to be time-dependent changes on the steady-state level of these protein exhibiting differential patterns at 20-day after exposure, with JAM-A/claudin-11 still being up-regulated whereas occludin/ZO-1 being down-regulated. More importantly, the BTB damage induced by 40 Gy of SR X-ray could be significantly attenuated by antioxidant N-Acetyl-L-Cysteine (NAC) at a dose of 125 mg/kg. Taken together, our studies characterized the changes of TJ component proteins after SR X-ray irradiation, illustrating the possible protective effects of antioxidant NAC to BTB integrity. PMID:26413412

  19. Evidence of Zinc in Affording Protection Against X-Ray-Induced Brain Injury in Rats.

    PubMed

    Sharma, Priyanka; Singla, Neha; Dhawan, D K

    2017-03-06

    In the present world, X-rays have been regarded as one of the most efficient tools in medicine, industry and research. On the contrary, extensive human exposure to these rays is responsible for causing detrimental effects on physiological system. The aim of the present study was to investigate the role of zinc (Zn), if any, in mitigating the adverse effects induced by fractionated X-irradiation on rat brain. Female Sprague-Dawley rats weighing 170-200 g were divided into four different groups viz.: (a) normal control, (b) X-irradiated (21Gy), (c) zinc treated (227 mg/L in drinking water) and (d) X-irradiated + zinc treated. The skulls of animals belonging to groups (b) and (d) were exposed to X-rays in 30 fractions. Each fraction delivered a radiation dose of 70 rads, and rats were exposed to two fractions every day for 15 days, consecutively. X-ray treatment resulted in significant alterations in the neurobehavior, neurotransmitter levels and neuro-histoarchitecture of rats, whereas zinc co-treatment with X-rays resulted in significant improvement in these parameters. X-ray exposure also caused a significant increase in the levels of lipid peroxidation as well as activities of catalase and superoxide dismutase, which however were decreased upon simultaneous Zn treatment. On the contrary, X-ray treatment down-regulated the glutathione system, which were found to be up-regulated by zinc co-treatment. Further, protein expressions of p53 and NF-ҚB were found to be significantly elevated after X-irradiation, which were reversed following Zn supplementation. Hence, Zn seems to be an effective agent in mitigating the detrimental effects caused by exposure to X-rays.

  20. Time-resolved x-ray imaging of x-ray induced dynamics in Xe clusters

    NASA Astrophysics Data System (ADS)

    Bucher, M.; Ferguson, K.; Gorkhover, T.; Carron, S.; Cryan, J.; Krzywinski, J.; Lutman, A.; Marinelli, A.; Bacellar, C.; Chatterley, A.; Ziemkiewicz, M.; Bernando, C.; Gomez, L.; Jones, C.; Kwok, J.; Tanyag, R. M. P.; Mueller, M.; Rupp, D.; Möller, T.; Gessner, O.; Vilesov, A.; Bostedt, C.

    2016-05-01

    Nanoparticles irradiated by intense x-ray pulses from the LCLS free-electron laser are immediately transformed into a highly excited nanoplasma. Within the first few femtoseconds of the x-ray pulse the particles are ionized and on longer time scales they disintegrate due to Coulomb forces. We performed an x-ray pump / x-ray probe experiment to investigate how the nanoplasma creation and disintegration changes the particle's diffraction response. As samples we used pristine Xe clusters as well as Xe clusters embedded in He droplets. The data show that for pristine clusters the higher diffraction orders diminish first and vanish completely as the nanoplasma expansion progresses. This effect is less prominent in the embedded clusters. We compare our results to previous studies on optically pumped clusters (T. Gorkhover et al., Nat. Photonics, 2016). This work is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under Contract No. DE-AC02-06CH11357.

  1. X-ray induced, substrate-carrier mediated deposition of metal on GaAs

    SciTech Connect

    Ma Qing; Divan, R.; Mancini, D. C.; Rosenberg, R. A.; Quintana, J. P.; Keane, D. T.

    2006-08-21

    A wet metal deposition process on GaAs surfaces is described. The process is induced by high energy x-ray photons and is mediated by photon-generated carriers through the photoelectrochemical mechanism similar to that for light-induced wet etching. The micrometer to submicrometer feature fabrication using this process is demonstrated.

  2. X-ray-induced Cu deposition and patterning on insulators at room temperature.

    PubMed

    Hsu, Pei-Cheng; Chen, Yu-Sheng; Hwu, Yeukuang; Je, J H; Margaritondo, G; Tok, Eng Soon

    2015-11-01

    X-ray irradiation is shown to trigger the deposition of Cu from solution, at room temperature, on a wide variety of insulating substrates: glass, passivated Si, TiN/Ti/SiO2/Si and photoresists like PMMA and SU-8. The process is suitable for patterning and the products can be used as seeds for electroplating of thicker overlayers.

  3. X-ray-induced dominant lethal mutations in mouse oocytes detected by an in vitro assay

    SciTech Connect

    Goldstein, L.S.

    1987-11-01

    Female mice were X-irradiated with 0.5-4.5 Gy 2 h before mating to unirradiated males of the same strain. The dominant lethal frequencies (DLF) were determined by growing the embryos in vitro from the two-cell stage and determining the relative rates of successful embryogenesis to the blastocyst stage and to the trophectoderm outgrowth with proliferated inner cell mass stage. The DLF increased with increasing dose, the two linear aspects having a breakpoint at about 1.5 Gy. The nature of embryo failure was also dose dependent. At doses less than 2.0 Gy embryos failed predominantly after blastocyst formation, but at higher doses the embryos failed both before and after blastocyst formation. Over the dose range tested, the frequency with which lesions leading to dominant lethality were induced (i.e., -ln(1 - DLF)) increased linearly with increasing dose.

  4. Three-dimensional model of x-ray induced microchannel plate output

    SciTech Connect

    Harding, E. C.; Drake, R. P.

    2006-10-15

    Microchannel plates are an important component in a type of imaging diagnostic known as an x-ray framing camera, used in x-ray radiography of high-energy-density physics experiments. A microchannel plate is responsible for detecting x rays and then converting them into amplified bursts of electrons, which are then imaged onto a phosphor-coated fiber optic screen. We present the preliminary development of a three-dimensional model of a single microchannel plate channel in attempt to simulate the pulse height distribution of the microchannel plate electron output. Using a novel technique, initial simulations are compared with experimental data from an ungated x-ray framing camera.

  5. Distribution of X-ray-induced chromosome breakpoints in Down syndrome lymphocytes

    SciTech Connect

    Shafik, H.M.; Au, W.W.; Whorton, E.B. Jr.; Legator, M.S. )

    1990-01-01

    Down syndrome (DS) individuals are known to be predisposed to develop leukemia and their lymphocytes are highly sensitive to the induction of chromosome aberrations by X-rays. A study was conducted to identify the chromosome breakpoints and to evaluate whether site specificity for chromosome breakage and rearrangement may exist which may explain the predisposition phenomenon. DS lymphocytes at the G1 phase of the cell cycle were irradiated with 300, 450, and 600 rad of X-rays. Cells were harvested after 3 days in culture and 193 G-banded karyotypes were analyzed to identify the induced chromosome abnormalities. Out of 273 breakpoints identified, 122 were involved in the formation of stable chromosome rearrangements and 151 in the formation of unstable abnormalities. The Poisson analysis of these breakpoints demonstrated that 16 chromosome bands located in chromosomes 1, 3, 7, 12, 17, 19 and X were preferentially involved in breakage and rearrangement (P less than 0.05). These 16 bands are also found to be locations of cancer breakpoints, oncogenes, or fragile sites. Many abnormal cells were observed to carry stable chromosome rearrangements only. Therefore, these cells are presumed to be compatible with survival and to be initiated in the transformation process. We propose that similar stable and site-specific chromosome rearrangements may exist in proliferating cells in DS individuals after exposure to clastogens and that this abnormality predisposes them to develop leukemia.

  6. Mechanism of the formation of x-ray-induced phosphenes. II. Photochemical investigations

    SciTech Connect

    Doly, M.; Isabelle, D.B.; Vincent, P.; Gaillard, G.; Meyniel, G.

    1980-06-01

    Like visible light, x rays can stimulate the isolated retina and induce an action potential (ERG). To explain the modalities of interaction of incident radiation with the photoreceptor cells, we studied the modifications of the rhodopsin absorption spectrum after x irradiation. For exposures smaller than 5 x 10/sup 5/ R, a large increase in absorption in the uv part of the spectrum is observed. For exposure of 1.25 x 10/sup 6/ R, a 20% decrease is measured in the characteristic peak of rhodopsin (500 nm). In comparison to what is known for visible light, the significant bleaching of rhodopsin by x rays can account for the initiation of an ERG in the isolated retina. By analogy with the enzymatic inactivation after x irradiation, we believe that the x-ray rhodopsin bleaching could be due to an energy transfer from the opsin to the attachment site of the chromophoric group (11-cis retinal). The disorganization of this critical site of the molecule could be at the origin of the rod excitation, then of the ERG.

  7. Studies of soft X-ray-induced Auger effect on the induction of DNA damage.

    PubMed

    Yokoya, A; Fuji, K; Shikazono, N; Akamatsu, K; Urushibara, A; Watanabe, R

    2008-12-01

    To understand the characteristics of DNA damage induced by Auger effect in DNA by ultrasoft X-irradiation. In situ electron paramagnetic resonance (EPR) spectroscopy as well as biochemical analysis has been applied to examine the DNA damage induction in both viewpoints of intermediate species and final products. Unpaired electron species induced in a calf thymus DNA film irradiated with monochromatic ultrasoft X-rays (270-580 eV) was observed using an X-band EPR spectrometer installed in a synchrotron beamline. To determine the yield of single strand break (SSB), pUC18 plasmid DNA was irradiated and then analyzed by agarose gel electrophoresis. To analyze molecular change in a single strand DNA, a new technique using DNA-denaturation-treatment has been applied to quantify multiple SSB arising in both DNA strands. Short-lived EPR spectra were observed during irradiation. The intensity of transient EPR spectrum shows the similar energy dependence with that of the SSB yield around oxygen K-edge in particular. The fraction of the single-strand plasmid DNA (SS-DNA) after irradiation could be determined using a low-temperature-denaturation condition. The obtained slope of the dose-response for SS-DNA shows half of that of closed circular DNA as expected under the diluted solution condition. The availability of an EPR apparatus installed in a synchrotron beamline is demonstrated by detecting very short-lived unpaired electron species. Transient EPR spectra of DNA show the similar energy dependence to that of the SSB yield. The proposed DNA-denaturation assay works as expected using the low-temperature-denaturation condition.

  8. Simulation of ultrasoft X-rays induced DNA damage using the Geant4 Monte Carlo toolkit

    NASA Astrophysics Data System (ADS)

    Tajik, Marjan; Rozatian, Amir S. H.; Semsarha, Farid

    2015-01-01

    In this study, the total yields of SSB and DSB induced by monoenergetic electrons with energies of 0.28-4.55 keV, corresponding to ultrasoft X-rays energies, have been calculated in Charlton and Humm volume model using the Geant4-DNA toolkit and compared with theoretical and experimental data. A reasonable agreement between the obtained results in the present study and experimental and theoretical data of previous studies showed the efficiency of this model in estimating the total yield of strand breaks in spite of its simplicity. Also, it has been found that in the low energy region, the yield of the total SSB remains nearly constant while the DSB yield increases with decreasing energy. Moreover, a direct dependency between DSB induction, RBE value and the mean lineal energy as a microdosimetry quantity has been observed. In addition, it has become clear that the use of the threshold energy of 10.79 eV to calculate the total strand breaks yields results in a better agreement with the experiments, while the threshold of 17.5 eV shows a big difference.

  9. X-ray-induced bystander responses reduce spontaneous mutations in V79 cells

    PubMed Central

    Maeda, Munetoshi; Kobayashi, Katsumi; Matsumoto, Hideki; Usami, Noriko; Tomita, Masanori

    2013-01-01

    The potential for carcinogenic risks is increased by radiation-induced bystander responses; these responses are the biological effects in unirradiated cells that receive signals from the neighboring irradiated cells. Bystander responses have attracted attention in modern radiobiology because they are characterized by non-linear responses to low-dose radiation. We used a synchrotron X-ray microbeam irradiation system developed at the Photon Factory, High Energy Accelerator Research Organization, KEK, and showed that nitric oxide (NO)-mediated bystander cell death increased biphasically in a dose-dependent manner. Here, we irradiated five cell nuclei using 10 × 10 µm2 5.35 keV X-ray beams and then measured the mutation frequency at the hypoxanthine-guanosine phosphoribosyl transferase (HPRT) locus in bystander cells. The mutation frequency with the null radiation dose was 2.6 × 10–5 (background level), and the frequency decreased to 5.3 × 10–6 with a dose of approximately 1 Gy (absorbed dose in the nucleus of irradiated cells). At high doses, the mutation frequency returned to the background level. A similar biphasic dose-response effect was observed for bystander cell death. Furthermore, we found that incubation with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (carboxy-PTIO), a specific scavenger of NO, suppressed not only the biphasic increase in bystander cell death but also the biphasic reduction in mutation frequency of bystander cells. These results indicate that the increase in bystander cell death involves mechanisms that suppress mutagenesis. This study has thus shown that radiation-induced bystander responses could affect processes that protect the cell against naturally occurring alterations such as mutations. PMID:23660275

  10. X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy.

    PubMed

    Ptasińska, Sylwia; Stypczyńska, Agnieszka; Nixon, Tony; Mason, Nigel J; Klyachko, Dimitri V; Sanche, Léon

    2008-08-14

    In this work, the chemical changes in calf thymus DNA samples were analyzed by X-ray photoelectron spectroscopy (XPS). The DNA samples were irradiated for over 5 h and spectra were taken repeatedly every 30 min. In this approach the X-ray beam both damages and probes the samples. In most cases, XPS spectra have complex shapes due to contributions of C, N, and O atoms bonded at several different sites. We show that from a comparative analysis of the modification in XPS line shapes of the C 1s, O 1s, N 1s, and P 2p peaks, one can gain insight into a number of reaction pathways leading to radiation damage to DNA.

  11. Hard X-ray-Induced Valence Tautomeric Interconversion in Cobalt-o-Dioxolene Complexes.

    PubMed

    Francisco, Thiago M; Gee, William J; Shepherd, Helena J; Warren, Mark R; Shultz, David A; Raithby, Paul R; Pinheiro, Carlos B

    2017-10-05

    Valence tautomeric interconversion (VTI) is a reversible process occurring in metal complexes in which an intramolecular metal-ligand electron transfer is accompanied by a change of metal ion spin state, creating two switchable electronic states (redox isomers). Herein, we describe the low-temperature, 30-100 K, single-crystal study of the [Co(diox)2(4-CN-py)2]·benzene complex (1) (diox = 3,5-di-t-butylsemiquinonate (SQ(•-)) and/or 3,5-di-t-butylcatecholate (Cat(2-)) radical; 4-CN-py = 4-cyano-pyridine) using hard synchrotron X-ray radiation with different intensities. We demonstrate for the first time that hard X-rays can induce VTI, and that the interconversion molar fraction is dependent on both intensity and exposure time. This in turn shows that X-rays, as a probe, might be altering the very nature of many structures under investigation at low temperatures, and consequently their properties. Our findings add new perspectives to VTI studies and might be of significant interest to the entire community investigating photoresponsive complexes.

  12. Monochromatic X-Ray Induced Novel Synthesis of Plasmonic Nanostructure for Photovoltaic Application

    PubMed Central

    Bharti, Amardeep; Bhardwaj, Richa; Agrawal, Ashish K.; Goyal, Navdeep; Gautam, Sanjeev

    2016-01-01

    It has been universally delineated that the plasmonic metal nanoparticles can enhance the efficiency of photovoltaic cell by increasing the probability of energetic solar photons capturing phenomena using localized surface plasmonic resonance response. In this paper, we developed a novel in-situ simple approach to synthesize noble plasmonic silver nanoparticles (AgNP) from aqueous poly-vinyl-pyrrolidone solution of metal salt using radiolysis of water via synchrotron monochromatic X-ray irradiation without any chemical reducing agent. X-ray irradiation of water produces hydrated electrons , superoxide and atom radicals , which triggers the reaction and reduces metal salt. X-ray radiolysis based synthesis provides the control over the reaction and prevent the formation of secondary products as occurs in case of chemical reduction route. In the previous studies, synchrotron “white” X-rays had been examined for the synthesis of metal nanoparticles, but that technique limits only upto the material synthesis while in this work we explored the role of “monochromatic” X-rays for the production of bulk amount of nanoparticles which would also provide the feasibility of in-situ characterization. Transmission electron micrographs show that the synthesized AgNP appears spherical with diameter of 2–6 nm and is in agreement with the size estimation from uv-vis spectra by “Mie theory”. PMID:27094793

  13. INVOLVEMENT OF P53 IN X-RAY INDUCED INTRACHROMOSOMAL RECOMBINATION IN MICE. (R825359)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  14. Soft x-ray induced femtosecond solid-to-solid phase transition

    NASA Astrophysics Data System (ADS)

    Tavella, Franz; Höppner, Hauke; Tkachenko, Victor; Medvedev, Nikita; Capotondi, Flavio; Golz, Torsten; Kai, Yun; Manfredda, Michele; Pedersoli, Emanuele; Prandolini, Mark J.; Stojanovic, Nikola; Tanikawa, Takanori; Teubner, Ulrich; Toleikis, Sven; Ziaja, Beata

    2017-09-01

    Soft x-rays were applied to induce graphitization of diamond through a non-thermal solid-to-solid phase transition. This process was observed within poly-crystalline diamond with a time-resolved experiment using ultrashort soft x-ray pulses of duration 52.5 fs and cross correlated by an optical pulse of duration 32.8 fs. This scheme enabled for the first time the measurement of a phase transition on a timescale of ∼150 fs. Excellent agreement between experiment and theoretical predictions was found, using a dedicated code that followed the non-equilibrium evolution of the irradiated diamond including all transient electronic and structural changes. These observations confirm that soft x-rays can induce a non-thermal ultrafast solid-to-solid phase transition on a hundred femtosecond timescale.

  15. Static magnetic fields modulate X-ray-induced DNA damage in human glioblastoma primary cells.

    PubMed

    Teodori, Laura; Giovanetti, Anna; Albertini, Maria Cristina; Rocchi, Marco; Perniconi, Barbara; Valente, Maria Giovanna; Coletti, Dario

    2014-03-01

    Although static magnetic fields (SMFs) are used extensively in the occupational and medical fields, few comprehensive studies have investigated their possible genotoxic effect and the findings are controversial. With the advent of magnetic resonance imaging-guided radiation therapy, the potential effects of SMFs on ionizing radiation (IR) have become increasingly important. In this study we focused on the genotoxic effect of 80 mT SMFs, both alone and in combination with (i.e. preceding or following) X-ray (XR) irradiation, on primary glioblastoma cells in culture. The cells were exposed to: (i) SMFs alone; (ii) XRs alone; (iii) XR, with SMFs applied during recovery; (iv) SMFs both before and after XR irradiation. XR-induced DNA damage was analyzed by Single Cell Gel Electrophoresis assay (comet assay) using statistical tools designed to assess the tail DNA (TD) and tail length (TL) as indicators of DNA fragmentation. Mitochondrial membrane potential, known to be affected by IR, was assessed using the JC-1 mitochondrial probe. Our results showed that exposure of cells to 5 Gy of XR irradiation alone led to extensive DNA damage, which was significantly reduced by post-irradiation exposure to SMFs. The XR-induced loss of mitochondrial membrane potential was to a large extent averted by exposure to SMFs. These data suggest that SMFs modulate DNA damage and/or damage repair, possibly through a mechanism that affects mitochondria.

  16. Low coercive field of polymer ferroelectric via x-ray induced phase transition

    SciTech Connect

    Lee, Hyeon Jun; Kim, Jihong; Lee, Hye Jeong; Kwak, Jeong Hun; Kim, Jae Myung; Lee, Sung Su; Kim, Dong-Yu; Jo, Ji Young; Kwon, Owoong; Kim, Yunseok

    2015-12-28

    We present an experimental strategy via X-ray irradiation combined with time-resolved X-ray diffraction to reduce a coercive field of ferroelectric thin films. We found in real-time that X-ray irradiation enables the irreversible phase transition from a polar to non-polar phase in ferroelectric poly(vinylidene fluoride-trifluoroethylene) thin films. The non-polar regions act as initial nucleation sites for opposite domains thus reducing the coercive field, directly related to the switching of domains, by 48%.

  17. Static magnetic fields modulate X-ray-induced DNA damage in human glioblastoma primary cells

    PubMed Central

    Teodori, Laura; Giovanetti, Anna; Albertini, Maria Cristina; Rocchi, Marco; Perniconi, Barbara; Valente, Maria Giovanna; Coletti, Dario

    2014-01-01

    Although static magnetic fields (SMFs) are used extensively in the occupational and medical fields, few comprehensive studies have investigated their possible genotoxic effect and the findings are controversial. With the advent of magnetic resonance imaging-guided radiation therapy, the potential effects of SMFs on ionizing radiation (IR) have become increasingly important. In this study we focused on the genotoxic effect of 80 mT SMFs, both alone and in combination with (i.e. preceding or following) X-ray (XR) irradiation, on primary glioblastoma cells in culture. The cells were exposed to: (i) SMFs alone; (ii) XRs alone; (iii) XR, with SMFs applied during recovery; (iv) SMFs both before and after XR irradiation. XR-induced DNA damage was analyzed by Single Cell Gel Electrophoresis assay (comet assay) using statistical tools designed to assess the tail DNA (TD) and tail length (TL) as indicators of DNA fragmentation. Mitochondrial membrane potential, known to be affected by IR, was assessed using the JC-1 mitochondrial probe. Our results showed that exposure of cells to 5 Gy of XR irradiation alone led to extensive DNA damage, which was significantly reduced by post-irradiation exposure to SMFs. The XR-induced loss of mitochondrial membrane potential was to a large extent averted by exposure to SMFs. These data suggest that SMFs modulate DNA damage and/or damage repair, possibly through a mechanism that affects mitochondria. PMID:24345558

  18. X-ray induced photocurrent characteristics of CVD diamond detectors with different carbon electrodes

    NASA Astrophysics Data System (ADS)

    Schirru, F.; Lohstroh, A.; Jayawardena, K. D. G. I.; Henley, S. J.; Sellin, P. J.

    2013-12-01

    Diamond has unique properties which make it suitable for a broad range of radiation detection applications ranging from particle timing and spectroscopy, to neutron, UV and X-ray sensors. In X-ray dosimetry, the atomic number of diamond (Z = 6) close to that of the human tissues (Z = 7.42) allows to mimic the real absorbed dose avoiding off-line recalculations. Moreover, its low atomic number and the capability to withstand high radiation fluxes make possible its use as beam monitor without altering significantly the properties of the interacting beam. To preserve the tissue equivalence of the diamond and minimize the perturbation and absorption of the incident beam, diamond detectors based on low thickness and low atomic number electrodes become a requirement. In this paper we present the X-ray detection characteristics of electronic grade CVD diamond sensors prepared in house with thin amorphous carbon electrodes fabricated by Pulsed Laser Deposition (PLD) technique in the fluence range of 2.3-3.6 J·cm-2. The devices showed a linear dependence of the induced photocurrent respect to the dose rate. Also, best dynamic response and better stability of the signals were achieved for applied bias up to ±50 V with signal to noise ratio (SNR) of ~ 300.

  19. X-ray induced synthesis of a novel material: Stable, doped solid CO at ambient conditions

    NASA Astrophysics Data System (ADS)

    Pravica, Michael; Evlyukhin, Egor; Cifligu, Petrika; Harris, Blake; Jae Koh, Jung; Chen, Ning; Wang, Yonggang

    2017-10-01

    We report a novel synthesis of stable doped solid carbon monoxide (p-CO) via hard X-ray irradiation of strontium oxalate at ambient conditions and high pressure. We also show via mid- and far- infrared (IR) techniques that CO2 produced via X-ray photochemistry remained trapped within the recovered sample for many months in contrast to pure p-CO which decomposes in days. Our results demonstrate that p-CO doped with carbonates (as verified with IR and Extended X-ray Absorption Fine Structure spectroscopies) is relatively stable, enabling longer term and practical use of this novel material for CO2 storage or as a novel electrical/optical material.

  20. /sup 20/neon ion- and x-ray-induced mammary carcinogenesis in female rats

    SciTech Connect

    Shellabarger, C.J.; Baum, J.W.; Holtzman, S.; Stone, J.P.

    1983-01-01

    One of the proposed uses of heavy ion irradiation is to image lesions of the human female breast. The rat model system was chosen to assess the carcinogenic potential of heavy ion irradiation in the belief that data obtained from rat studies would have a qualitatively predictive value for the human female. Accordingly, female rats were exposed to /sup 20/Ne ions at the BEVALAC and studied for the development of mammary neoplasia for 312 +- 2 days at Brookhaven along with rats exposed concurrently to x-irradiation or to no irradiation. As the dose of either type of radiation was increased the percent of rats with mammary adenocarcinomas, and the percent of rats with mammary fibroadenomas, tended to increase. At a prevalence of 20%, the RBE for /sup 20/Neon ions for mammary adenocarcinomas was estimated to be larger than 5 and for mammary fibroadenomas the RBE was estimated to be less than 2. No conclusion was reached concerning whether or not the RBE might vary with dose. We suggest that /sup 20/Ne ions do have a carcinogenic potential for rat mammary tissue and that this carcinogenic potential is likely to be greater than for x-irradiation. (DT)

  1. Hard X-ray-induced optical luminescence via biomolecule-directed metal clusters.

    PubMed

    Osakada, Yasuko; Pratx, Guillem; Sun, Conroy; Sakamoto, Masanori; Ahmad, Moiz; Volotskova, Olga; Ong, Qunxiang; Teranishi, Toshiharu; Harada, Yoshie; Xing, Lei; Cui, Bianxiao

    2014-04-07

    Here, we demonstrate that biomolecule-directed metal clusters are applicable in the study of hard X-ray excited optical luminescence, promising a new direction in the development of novel X-ray-activated imaging probes.

  2. Investigation of modification X-ray induced bystander effect in vitro.

    PubMed

    Shemetun, O V; Talan, O O

    2014-09-01

    Objective - to investigate the modification of bystander effect induced by X-irradiation of human peripheral blood in vitro by application of antioxidant vitamin medication. Material and methods. Modeling of radiation-induced bystander effect in vitro in mixed lymphocyte cultures exposed to dose of 1 Gy and non-irradiated blood lymphocytes of persons of different sexes, GTG-staining of metaphase chromosomes and their cytogenetic analysis; application of antioxidant preparation (soluble forms of vitamins E, C and A) in concentration 40 μg/ml. Results. Under the introduction of antioxidant preparation into mixed culture before lymphocytes cultivation frequency of chromosomal aberrations in bystander cells did not significantly different from the control (p > 0.05). application of antioxidant preparation modifies the radiation-induced bystander effect in unirradiated human peripheral blood lymphocytes under their joint cultivation with lymphocytes irradiated in dose of 1 Gy. Antioxidant prevents the development of secondary oxidative stress in unirradiated cells, eliminates the development in them of radiation-induced bystander effect and ensures the preservation of stability of their chromosome apparatus. O. V. Shemetun, O. O. Talan.

  3. Monochromatic X-Ray Induced Novel Synthesis of Plasmonic Nanostructure for Photovoltaic Application

    NASA Astrophysics Data System (ADS)

    Bharti, Amardeep; Bhardwaj, Richa; Agrawal, Ashish K.; Goyal, Navdeep; Gautam, Sanjeev

    2016-04-01

    It has been universally delineated that the plasmonic metal nanoparticles can enhance the efficiency of photovoltaic cell by increasing the probability of energetic solar photons capturing phenomena using localized surface plasmonic resonance response. In this paper, we developed a novel in-situ simple approach to synthesize noble plasmonic silver nanoparticles (AgNP) from aqueous poly-vinyl-pyrrolidone solution of metal salt using radiolysis of water via synchrotron monochromatic X-ray irradiation without any chemical reducing agent. X-ray irradiation of water produces hydrated electrons , superoxide and atom radicals , which triggers the reaction and reduces metal salt. X-ray radiolysis based synthesis provides the control over the reaction and prevent the formation of secondary products as occurs in case of chemical reduction route. In the previous studies, synchrotron “white” X-rays had been examined for the synthesis of metal nanoparticles, but that technique limits only upto the material synthesis while in this work we explored the role of “monochromatic” X-rays for the production of bulk amount of nanoparticles which would also provide the feasibility of in-situ characterization. Transmission electron micrographs show that the synthesized AgNP appears spherical with diameter of 2–6 nm and is in agreement with the size estimation from uv-vis spectra by “Mie theory”.

  4. X-ray-induced sterility in Aedes albopictus (Diptera: Culicidae) and male longevity following irradiation.

    PubMed

    Yamada, H; Parker, A G; Oliva, C F; Balestrino, F; Gilles, J R L

    2014-07-01

    The mosquito Aedes albopictus (Skuse, 1895) is a potent vector of several arboviral diseases, most notably chikungunya and dengue fever. In the context of the sterile insect technique (SIT), the sterilization of the male mosquitoes before their release can be achieved by gamma-ray irradiation. As gamma-ray irradiators are becoming increasingly problematic to purchase and transport, the suitability of an X-ray irradiator as an alternative for the sterilization of Ae. albopictus males was studied. The sterilization of up to 200,000 pupae at one time can be achieved with relative ease, and the sterility results obtained were comparable with those achieved by gamma irradiation, where 99% sterility is induced with a dose of 40 Gy. A significant reduction of longevity was observed in the latter stages of the males' life after irradiation treatments, especially at doses > 40 Gy, which is consistent with the negative effects on longevity induced by similar radiation doses using gamma rays. Females irradiated at 40 Gy were not only 100% sterile, but also failed to oviposit entirely, i.e., all of the females laid 0 eggs. Overall, it was found that the X-ray irradiator is generally suitable for the sterilization process for sterile insect technique programs, as it showed a high processing capacity, practicality, high effectiveness, and reproducibility.

  5. Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli.

    PubMed

    Ferreira, Keila Adriana Magalhães; Fajardo, Emanuella Francisco; Baptista, Rodrigo P; Macedo, Andrea Mara; Lages-Silva, Eliane; Ramírez, Luis Eduardo; Pedrosa, André Luiz

    2014-06-01

    Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.

  6. Species-Specific Standard Redox Potential of Thiol-Disulfide Systems: A Key Parameter to Develop Agents against Oxidative Stress

    PubMed Central

    Mirzahosseini, Arash; Noszál, Béla

    2016-01-01

    Microscopic standard redox potential, a new physico-chemical parameter was introduced and determined to quantify thiol-disulfide equilibria of biological significance. The highly composite, codependent acid-base and redox equilibria of thiols could so far be converted into pH-dependent, apparent redox potentials (E’°) only. Since the formation of stable metal-thiolate complexes precludes the direct thiol-disulfide redox potential measurements by usual electrochemical techniques, an indirect method had to be elaborated. In this work, the species-specific, pH-independent standard redox potentials of glutathione were determined primarily by comparing it to 1-methylnicotinamide, the simplest NAD+ analogue. Secondarily, the species-specific standard redox potentials of the two-electron redox transitions of cysteamine, cysteine, homocysteine, penicillamine, and ovothiol were determined using their microscopic redox equilibrium constants with glutathione. The 30 different, microscopic standard redox potential values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress. PMID:27869189

  7. The molecular mechanism of species-specific recognition of lipopolysaccharides by the MD-2/TLR4 receptor complex.

    PubMed

    Oblak, Alja; Jerala, Roman

    2015-02-01

    Lipid A, a component of bacterial lipopolysaccharide, is a conserved microbe-associated molecular pattern that activates the MD-2/TLR4 receptor complex. Nevertheless, bacteria produce lipid A molecules of considerable structural diversity. The human MD-2/TLR4 receptor most efficiently recognizes hexaacylated bisphosphorylated lipid A produced by enterobacteria, but in some animal species the immune response can be elicited also by alternative lipid A varieties, such as tetraacylated lipid IVa or pentaacylated lipid A of Rhodobacter spheroides. Several crystal structures revealed that hexaacylated lipid A and tetraacylated lipid IVa activate the murine MD-2/TLR4 in a similar manner, but failed to explain the antagonistic vs. agonistic activity of lipid IVa in the human vs. equine receptor, respectively. Targeted mutagenesis studies of the receptor complex revealed intricate combination of electrostatic and hydrophobic interactions primarily within the MD-2 co-receptor, but with a contribution of TLR4 as well, that contribute to species-specific recognition of lipid A. We will review current knowledge regarding lipid A diversity and species-specific activation of the MD-2/TLR4 receptor complex in different species (e.g. human, mouse or equine) by lipid A varieties.

  8. Influence of Species Specificity and Other Factors on Bacteria Associated with the Coral Stylophora pistillata in Taiwan ▿

    PubMed Central

    Hong, Mei-Jhu; Yu, Yi-Ting; Chen, Chaolun A.; Chiang, Pei-Wen; Tang, Sen-Lin

    2009-01-01

    Species of bacteria associated with Stylophora pistillata were determined by analyses of 16S ribosomal genes. Coral samples were taken from two distinct sites at Kenting, in the far south of Taiwan; three coral colonies at each site were tagged and sampled in the winter and summer of 2007. Six hundred 16S rRNA gene clones were selected and sequenced for diversity analysis and community comparison. LIBSHUFF and nonparametric multiple dimensional scaling analyses showed variations in the composition of the coral-associated bacteria in the different samples, suggesting that seasonal and geographic factors and variations in individual coral colonies were all vital drivers of the structure of the S. pistillata-associated bacterial community. To examine the association between species specificity and environmental impacts on the structure of the coral-associated bacterial community, we conducted an integrated, comparative analysis of 44 coral-associated bacterial data sets, including the present study's data. The clustering analysis suggests that the influence of spatial and temporal factors on the coral-associated bacteria population structure is considerable; nonetheless, the effect of species specificity is still detectable in some coral species, especially those from the Caribbean Sea. PMID:19854921

  9. Loop-mediated Isothermal Amplification (LAMP) Assays for the Species-specific Detection of Eimeria that Infect Chickens

    PubMed Central

    Barkway, Christopher P.; Pocock, Rebecca L.; Vrba, Vladimir; Blake, Damer P.

    2015-01-01

    Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm’s anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable. PMID:25741643

  10. Species-specific reversal of stem xylem embolism after a prolonged drought correlates to endpoint concentration of soluble sugars.

    PubMed

    Savi, Tadeja; Casolo, Valentino; Luglio, Jessica; Bertuzzi, Stefano; Trifilo', Patrizia; Lo Gullo, Maria A; Nardini, Andrea

    2016-09-01

    Recent reports on tree mortality associated with anomalous drought and heat have raised interest into processes underlying tree resistance/resilience to water stress. Hydraulic failure and carbon starvation have been proposed as main causes of tree decline, with recent theories treating water and carbon metabolism as interconnected processes. We subjected young plants of two native (Quercus pubescens [Qp] and Prunus mahaleb [Pm]) and two invasive (Robinia pseudoacacia [Rp] and Ailanthus altissima [Aa]) woody angiosperms to a prolonged drought leading to stomatal closure and xylem embolism, to induce carbon starvation and hydraulic failure. At the end of the treatment, plants were measured for embolism rates and NSC content, and re-irrigated to monitor recovery of xylem hydraulics. Data highlight different hydraulic strategies in native vs invasive species under water stress, and provide physiological explanations for species-specific impacts of recent severe droughts. Drought-sensitive species (Qp and Rp) suffered high embolism rates and were unable to completely refill xylem conduits upon restoration of water availability. Species that better survived recent droughts were able to limit embolism build-up (Pm) or efficiently restored hydraulic functionality after irrigation (Aa). Species-specific capacity to reverse xylem embolism correlated to stem-level concentration of soluble carbohydrates, but not to starch content.

  11. Species-specificity of the BamA component of the bacterial outer membrane protein-assembly machinery.

    PubMed

    Volokhina, Elena B; Grijpstra, Jan; Beckers, Frank; Lindh, Erika; Robert, Viviane; Tommassen, Jan; Bos, Martine P

    2013-01-01

    The BamA protein is the key component of the Bam complex, the assembly machinery for outer membrane proteins (OMP) in gram-negative bacteria. We previously demonstrated that BamA recognizes its OMP substrates in a species-specific manner in vitro. In this work, we further studied species specificity in vivo by testing the functioning of BamA homologs of the proteobacteria Neisseria meningitidis, Neisseria gonorrhoeae, Bordetella pertussis, Burkholderia mallei, and Escherichia coli in E. coli and in N. meningitidis. We found that no BamA functioned in another species than the authentic one, except for N. gonorrhoeae BamA, which fully complemented a N. meningitidis bamA mutant. E. coli BamA was not assembled into the N. meningitidis outer membrane. In contrast, the N. meningitidis BamA protein was assembled into the outer membrane of E. coli to a significant extent and also associated with BamD, an essential accessory lipoprotein of the Bam complex.Various chimeras comprising swapped N-terminal periplasmic and C-terminal membrane-embedded domains of N. meningitidis and E. coli BamA proteins were also not functional in either host, although some of them were inserted in the OM suggesting that the two domains of BamA need to be compatible in order to function. Furthermore, conformational analysis of chimeric proteins provided evidence for a 16-stranded β-barrel conformation of the membrane-embedded domain of BamA.

  12. Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels.

    PubMed

    Cho, Anna; Morris, Todd; Wilson, Chris; Freeland, Joanna

    2016-12-01

    Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada. Many of these are potentially sympatric, and 14 species have been formally assessed as endangered, threatened, or special concern. We investigated whether there was sufficient variation within the cytochrome oxidase region (COI) to develop species-specific eDNA markers for at-risk unionids. We developed 32 COI markers for eight unionid species, and tested each of these on the target species plus 29 potentially sympatric unionid taxa. Six of these markers amplified DNA only from the intended target species. We then extracted and amplified mussel eDNA from rearing-tank water samples. We conclude that despite high species diversity, it should be possible to develop eDNA COI markers and screen water samples for habitat occupancy by unionid mussels.

  13. Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates.

    PubMed

    Dalmastri, Claudia; Pirone, Luisa; Tabacchioni, Silvia; Bevivino, Annamaria; Chiarini, Luigi

    2005-05-01

    In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species.

  14. Selective MS screening reveals a sex pheromone in Caenorhabditis briggsae and species-specificity in indole ascaroside signalling.

    PubMed

    Dong, Chuanfu; Dolke, Franziska; von Reuss, Stephan H

    2016-08-14

    The indole ascarosides (icas) represent a highly potent class of nematode-derived modular signalling components that integrate structural inputs from amino acid, carbohydrate, and fatty acid metabolism. Comparative analysis of the crude exo-metabolome of hermaphroditic Caenorhabditis briggsae using a highly sensitive mass spectrometric screen reveals an indole ascaroside blend dominated by two new components. The structures of isolated icas#2 and icas#6.2 were determined by NMR spectroscopy and confirmed by total synthesis and chemical correlation. Low atto- to femtomolar amounts of icas#2 and icas#6.2 act in synergism to attract males indicating a function as sex pheromone. Comparative analysis of 14 Caenorhabditis species further demonstrates that species-specific indole ascaroside biosynthesis is highly conserved in the Elegans group. Functional characterization of the dominating indole ascarosides icas#2, icas#3, and icas#9 reveals a high degree of species-specificity and considerable variability with respect to gender-specificity, thus, confirming that indole ascarosides modulate different biological functions within the Elegans group. Although the nematode response was usually most pronounced towards conspecific signals, Caenorhabditis brenneri, the only species of the Elegans group that does not produce any indole ascarosides, exhibits a robust response to icas#2 suggesting the potential for interspecies interactions.

  15. Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event

    NASA Astrophysics Data System (ADS)

    Diaz, Julia M.; Hansel, Colleen M.; Apprill, Amy; Brighi, Caterina; Zhang, Tong; Weber, Laura; McNally, Sean; Xun, Liping

    2016-12-01

    The reactive oxygen species superoxide (O2.-) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ~120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology.

  16. Physical localisation of repetitive DNA sequences in Alstroemeria: karyotyping of two species with species-specific and ribosomal DNA.

    PubMed

    Kamstra, S A; Kuipers, A G; De Jeu, M J; Ramanna, M S; Jacobsen, E

    1997-10-01

    Fluorescence in situ hybridization (FISH) was used to localise two species-specific repetitive DNA sequences, A001-I and D32-13, and two highly conserved 25S and 5S rDNA sequences on the metaphase chromosomes of two species of Alstroemeria. The Chilean species, Alstroemeria aurea (2n = 16), has abundant constitutive heterochromatin, whereas the Brazilian species, Alstroemeria inodora, has hardly any heterochromatin. The A. aurea specific A001-I probe hybridized specifically to the C-band regions on all chromosomes. The FISH patterns on A. inodora chromosomes using species-specific probe D32-13 resembled the C-banding pattern and the A001-I pattern on A. aurea chromosomes. There were notable differences in number and distribution of rDNA sites between the two species. The 25S rDNA probe revealed 16 sites in A. aurea that closely colocalised with A001-I sites and 12 in A. inodora that were predominantly detected in the centromeric regions. FISH karyotypes of the two Alstroemeria species were constructed accordingly, enabling full identification of all individual chromosomes. These FISH karyotypes will be useful for monitoring the chromosomes of both Alstroemeria species in hybrids and backcross derivatives.

  17. Exchange of Xcp (Gsp) secretion machineries between Pseudomonas aeruginosa and Pseudomonas alcaligenes: species specificity unrelated to substrate recognition.

    PubMed

    de Groot, A; Koster, M; Gérard-Vincent, M; Gerritse, G; Lazdunski, A; Tommassen, J; Filloux, A

    2001-02-01

    Pseudomonas aeruginosa and Pseudomonas alcaligenes are gram-negative bacteria that secrete proteins using the type II or general secretory pathway, which requires at least 12 xcp gene products (XcpA and XcpP to -Z). Despite strong conservation of this secretion pathway, gram-negative bacteria usually cannot secrete exoproteins from other species. Based on results obtained with Erwinia, it has been proposed that the XcpP and/or XcpQ homologs determine this secretion specificity (M. Linderberg, G. P. Salmond, and A. Collmer, Mol. Microbiol. 20:175-190, 1996). In the present study, we report that XcpP and XcpQ of P. alcaligenes could not substitute for their respective P. aeruginosa counterparts. However, these complementation failures could not be correlated to species-specific recognition of exoproteins, since these bacteria could secrete exoproteins of each other. Moreover, when P. alcaligenes xcpP and xcpQ were expressed simultaneously in a P. aeruginosa xcpPQ deletion mutant, complementation was observed, albeit only on agar plates and not in liquid cultures. After growth in liquid culture the heat-stable P. alcaligenes XcpQ multimers were not detected, whereas monomers were clearly visible. Together, our results indicate that the assembly of a functional Xcp machinery requires species-specific interactions between XcpP and XcpQ and between XcpP or XcpQ and another, as yet uncharacterized component(s).

  18. An unusual strain of Haemophilus parasuis that fails to react in a species-specific polymerase chain reaction assay.

    PubMed

    Turni, Conny; Blackall, Patrick J

    2011-03-01

    A total of 30 nasal swabs from pigs preweaned and 11 nasal swabs from sick weaned pigs on a farm in Queensland, Australia, were cultured for the presence of Haemophilus parasuis. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) genotyping and indirect hemagglutination and gel diffusion serotyping were performed on the retrieved H. parasuis isolates. A total of 3 genotypes were recognized among the 42 isolates recovered, and 4 representative isolates of each genotype were found to be nontypeable in the Kielstein/Rapp-Gabrielson serotyping scheme. A total of 20 of the 22 isolates of genotype 1 did not amplify in the species-specific conventional PCR number 1 (cPCR1) based on the 16S ribosomal RNA (rRNA) gene but did give the expected PCR amplicon in 2 other species-specific PCR assays, one of which is also based on the 16S rRNA gene. Nine selected isolates representing all genotypes, both positive and negative in the cPCR1, were sequenced, and all showed a 4-base mutation occurring at the forward primer annealing site. The quadruple base pair substitution from GTGG to TGTT near the 3' end of the forward primer sequence may explain the failure of amplification. Diagnostic laboratories should be aware that such failures can occur and should consider having an alternative PCR available to confirm negative results or, alternatively, use phenotypic characteristics for the identification of suspect H. parasuis isolates.

  19. A transcriptional profile of metallophyte Viola baoshanensis involved in general and species-specific cadmium-defense mechanisms.

    PubMed

    Zhang, Jun; Hu, Min; Li, Jin-Tian; Guan, Jian-Ping; Yang, Bin; Shu, Wen-Sheng; Liao, Bin

    2009-05-15

    Viola baoshanensis Shu, Liu et Lan is a newly identified metallophyte, and its defensive strategies against heavy metals are still unclear. In the present study, we firstly constructed a root cDNA library of the plant subjected to 300muM Cd for 48h by using suppression subtractive hybridization (SSH), and 43 unique cDNA fragments were further isolated from the library. Sequence homology analysis showed that half of the identified genes were involved in general stress defense, such as antioxidative enzymes, protein degradation and stress signal transduction. After RT-PCR and RACE analysis, a Cd-responsive gene Vb40 was identified, which could deduce a novel cysteine-rich mini-protein. Meanwhile, five cyclotide precursor genes (VbCP1-VbCP5) were also identified. The Vb40 and the VbCP1-VbCP5 were further investigated by yeast expression analysis, and they could improve copper (Cu) tolerance in hosted yeast, indicating that these species-specific genes possibly functioned in V. baoshanensis heavy metals tolerance. Our results suggested that heavy metal tolerance in V. baoshanensis relied on both general and species-specific defense.

  20. A comparison between egg trancriptomes of cod and salmon reveals species-specific traits in eggs for each species.

    PubMed

    Wargelius, Anna; Furmanek, Tomasz; Montfort, Jérôme; Le Cam, Aurélie; Kleppe, Lene; Juanchich, Amelie; Edvardsen, Rolf B; Taranger, Geir Lasse; Bobe, Julien

    2015-05-01

    Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if species specific "egg life history traits" can be hidden in the unfertilized egg. This was done by investigating egg transcriptome differences between Atlantic salmon and Atlantic cod. Salmon and cod eggs were selected due to their largely differencing phenotypes. An oligo microarray analysis was performed on ovulated eggs from cod (n = 8) and salmon (n = 7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated with SWISS-Prot and KEGG genes to retrieve an official gene symbol and an orthologous KEGG annotation, in salmon and cod arrays this represented 14,009 and 7,437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score >300, resulting in a total of 2,457 KEGG annotations (genes) being differently expressed between the species (FD > 2). This analysis revealed that immune, signal transduction and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.

  1. Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event

    PubMed Central

    Diaz, Julia M.; Hansel, Colleen M.; Apprill, Amy; Brighi, Caterina; Zhang, Tong; Weber, Laura; McNally, Sean; Xun, Liping

    2016-01-01

    The reactive oxygen species superoxide (O2·−) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ∼120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology. PMID:27924868

  2. MD-2, a novel accessory molecule, is involved in species-specific actions of Salmonella lipid A.

    PubMed

    Muroi, Masashi; Ohnishi, Takahiro; Tanamoto, Ken-ichi

    2002-07-01

    Salmonella lipid A is inactive in human macrophages despite being potently active in murine macrophages. We investigated the molecular basis for this species-specific action of Salmonella lipid A. When murine CD14 (mCD14), mTLR4, and mMD-2 were all expressed in human monocytic THP-1 cells, these cells were capable of responding to Salmonella lipid A. Expressing each of these proteins separately did not impart such responsiveness. Expression of mTLR4 plus mMD-2, but not mCD14 plus mTLR4 or mCD14 plus mMD-2, conferred this responsiveness. In THP-1 cells expressing mCD14, mTLR4, and mMD-2, replacing mCD14 with human CD14 had no effect on responsiveness to Salmonella lipid A or synthetic Salmonella-type lipid A (compound 516). When mTLR4 was replaced with human TLR4, the responses to these lipid A preparations were decreased to half, and the replacement of mMD-2 decreased responsiveness to one-third, although the responses to Escherichia coli lipid A or synthetic E. coli-type lipid A (compound 506) were not affected. These results indicate that both TLR4 and MD-2 participate in the species-specific action of Salmonella lipid A.

  3. Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens.

    PubMed

    Barkway, Christopher P; Pocock, Rebecca L; Vrba, Vladimir; Blake, Damer P

    2015-02-20

    Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm's anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable.

  4. Species-Specific Standard Redox Potential of Thiol-Disulfide Systems: A Key Parameter to Develop Agents against Oxidative Stress

    NASA Astrophysics Data System (ADS)

    Mirzahosseini, Arash; Noszál, Béla

    2016-11-01

    Microscopic standard redox potential, a new physico-chemical parameter was introduced and determined to quantify thiol-disulfide equilibria of biological significance. The highly composite, codependent acid-base and redox equilibria of thiols could so far be converted into pH-dependent, apparent redox potentials (E’°) only. Since the formation of stable metal-thiolate complexes precludes the direct thiol-disulfide redox potential measurements by usual electrochemical techniques, an indirect method had to be elaborated. In this work, the species-specific, pH-independent standard redox potentials of glutathione were determined primarily by comparing it to 1-methylnicotinamide, the simplest NAD+ analogue. Secondarily, the species-specific standard redox potentials of the two-electron redox transitions of cysteamine, cysteine, homocysteine, penicillamine, and ovothiol were determined using their microscopic redox equilibrium constants with glutathione. The 30 different, microscopic standard redox potential values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.

  5. Species specificity in the magnitude and duration of the acute stress response in Mediterranean marine fish in culture.

    PubMed

    Fanouraki, E; Mylonas, C C; Papandroulakis, N; Pavlidis, M

    2011-09-01

    The aim of the present study was to examine the species-specific stress response for seven Mediterranean fishes in culture. Also, to evaluate the method of measuring free cortisol concentration in the rearing water as a non-invasive and reliable indicator of stress in marine species, of aquaculture importance. Gilthead sea bream, Sparus aurata (Sparidae); common dentex, Dentex dentex (Sparidae); common Pandora, Pagellus erythrinus (Sparidae); sharpsnout sea bream, Diplodus puntazzo (Sparidae); dusky grouper, Epinephelus marginatus (Serranidae); meagre, Argyrosomus regius (Sciaenidae) and European sea bass, Dicentrarchus labrax (Moronidae) were subjected to identical acute stress (5-6 min chasing and 1-1.5 min air exposure) under the same environmental conditions and samples were analyzed by the same procedures. Results indicated that there was a clear species-specificity in the magnitude, timing and duration of the stress response in terms of cortisol, glucose and lactate. European sea bass showed a very high response and dusky grouper and meagre a very low response, except plasma glucose concentrations of dusky grouper which was constantly high, while sharpsnout sea bream presented a protracted stress response, up to 8h. The present study confirmed that free cortisol release rate into the water can be used as a reliable stress indicator. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Operational RNA code for amino acids: species-specific aminoacylation of minihelices switched by a single nucleotide.

    PubMed

    Hipps, D; Shiba, K; Henderson, B; Schimmel, P

    1995-06-06

    The genetic code is based on aminoacylation reactions where specific amino acids are attached to tRNAs bearing anticodon trinucleotides. However, the anticodon-independent specific aminoacylation of RNA minihelix substrates by bacterial and yeast tRNA synthetases suggested an operational RNA code for amino acids whereby specific RNA sequences/structures in tRNA acceptor stems correspond to specific amino acids. Because of the possible significance of the operational RNA code for the development of the genetic code, we investigated aminoacylation of synthetic RNA minihelices with a human enzyme to understand the sequences needed for that aminoacylation compared with those needed for a microbial system. We show here that the species-specific aminoacylation of glycine tRNAs is recapitulated by a species-specific aminoacylation of minihelices. Although the mammalian and Escherichia coli minihelices differ at 6 of 12 base pairs, two of the three nucleotides essential for aminoacylation by the E. coli enzyme are conserved in the mammalian minihelix. The two conserved nucleotides were shown to be also important for aminoacylation of the mammalian minihelix by the human enzyme. A simple interchange of the differing nucleotide enabled the human enzyme to now charge the bacterial substrate and not the mammalian minihelix. Conversely, this interchange made the bacterial enzyme specific for the mammalian substrate. Thus, the positional locations (if not the actual nucleotides) for the operational RNA code for glycine appear conserved from bacteria to mammals.

  7. Operational RNA code for amino acids: species-specific aminoacylation of minihelices switched by a single nucleotide.

    PubMed Central

    Hipps, D; Shiba, K; Henderson, B; Schimmel, P

    1995-01-01

    The genetic code is based on aminoacylation reactions where specific amino acids are attached to tRNAs bearing anticodon trinucleotides. However, the anticodon-independent specific aminoacylation of RNA minihelix substrates by bacterial and yeast tRNA synthetases suggested an operational RNA code for amino acids whereby specific RNA sequences/structures in tRNA acceptor stems correspond to specific amino acids. Because of the possible significance of the operational RNA code for the development of the genetic code, we investigated aminoacylation of synthetic RNA minihelices with a human enzyme to understand the sequences needed for that aminoacylation compared with those needed for a microbial system. We show here that the species-specific aminoacylation of glycine tRNAs is recapitulated by a species-specific aminoacylation of minihelices. Although the mammalian and Escherichia coli minihelices differ at 6 of 12 base pairs, two of the three nucleotides essential for aminoacylation by the E. coli enzyme are conserved in the mammalian minihelix. The two conserved nucleotides were shown to be also important for aminoacylation of the mammalian minihelix by the human enzyme. A simple interchange of the differing nucleotide enabled the human enzyme to now charge the bacterial substrate and not the mammalian minihelix. Conversely, this interchange made the bacterial enzyme specific for the mammalian substrate. Thus, the positional locations (if not the actual nucleotides) for the operational RNA code for glycine appear conserved from bacteria to mammals. Images Fig. 1 PMID:7539919

  8. Mycobacterium abscessus WhiB7 regulates a species -specific repertoire of genes to confer extreme antibiotic resistance.

    PubMed

    Hurst-Hess, Kelley; Rudra, Paulami; Ghosh, Pallavi

    2017-09-05

    Mycobacterium abscessus causes acute and chronic broncho-pulmonary infection in patients with chronic lung damage, of which cystic fibrosis (CF) patients are particularly vulnerable. The major threat posed by this organism is its high intrinsic antibiotic resistance. A typical treatment regimen involves a 6-12 month long combination therapy of clarithromycin and amikacin, with cure rates below 50% and multiple side effects, especially due to amikacin. In the present work we show that M. abscessuswhiB7, a homologue of M. tuberculosis and M. smegmatis whiB7 with previously demonstrated effects on intrinsic antibiotic resistance, is strongly induced when exposed to clinically relevant antibiotics that target the ribosome - erythromycin, clarithromycin, amikacin, tetracycline and spectinomycin. Deletion of M. abscessuswhiB7 results in sensitivity to all of the above antibiotics. Further, we have defined and compared the whiB7 regulon of M. abscessus with the closely related (non-tuberculous mycobacterium) NTM, M. smegmatis to demonstrate the induction of species-specific repertoire of genes. Further we show that one such gene, eis2, is specifically induced in M. abscessus by whiB7, and contributes to its higher levels of intrinsic amikacin resistance. This species-specific pattern of gene induction could account for the differences in drug susceptibilities to other antibiotics and between different mycobacterial species. Copyright © 2017 American Society for Microbiology.

  9. General and species-specific impacts of a neonicotinoid insecticide on the ovary development and feeding of wild bumblebee queens.

    PubMed

    Baron, Gemma L; Raine, Nigel E; Brown, Mark J F

    2017-05-17

    Bumblebees are essential pollinators of crops and wild plants, but are in decline across the globe. Neonicotinoid pesticides have been implicated as a potential driver of these declines, but most of our evidence base comes from studies of a single species. There is an urgent need to understand whether such results can be generalized across a range of species. Here, we present results of a laboratory experiment testing the impacts of field-relevant doses (1.87-5.32 ppb) of the neonicotinoid thiamethoxam on spring-caught wild queens of four bumblebee species: Bombus terrestris, B. lucorum, B. pratorum and B. pascuorum. Two weeks of exposure to the higher concentration of thiamethoxam caused a reduction in feeding in two out of four species, suggesting species-specific anti-feedant, repellency or toxicity effects. The higher level of thiamethoxam exposure resulted in a reduction in the average length of terminal oocytes in queens of all four species. In addition to providing the first evidence for general effects of neonicotinoids on ovary development in multiple species of wild bumblebee queens, the discovery of species-specific effects on feeding has significant implications for current practices and policy for pesticide risk assessment and use. © 2017 The Authors.

  10. Species specificity and augmentation of responses to class II major histocompatibility complex molecules in human CD4 transgenic mice

    PubMed Central

    1992-01-01

    Murine T cell responses to human class II major histocompatibility complex (MHC) molecules were shown to be a minimum of 20-70-fold lower than responses to allogeneic molecules. Transgenic mice expressing slightly below normal (75-95%) or very high (250-380%) cell surface levels of human CD4 were utilized to determine whether this was due to a species-specific interaction between murine CD4 and class II molecules. Human CD4 was shown to function in signal transduction events in murine T cells based on the ability of anti-human CD4 antibody to synergize with suboptimal doses of anti-murine CD3 antibody in stimulating T cell proliferation. In mice expressing lower levels of human CD4, T cell responses to human class II molecules were enhanced up to threefold, whereas allogeneic responses were unaltered. In mice expressing high levels of human CD4, responses to human class II molecules were enhanced at least 10-fold, whereas allogeneic responses were between one and three times the level of normal responses. The relatively greater enhancement of the response to human class II molecules in both lines argues for a preferential interaction between human CD4 and human class II molecules. In mice expressing lower levels of human CD4, responses to human class II molecules were blocked by antibodies to CD4 of either species, indicating participation by both molecules. In mice expressing high levels of human CD4, responses to both human and murine class II molecules were almost completely blocked with anti-human CD4 antibody, whereas anti-murine CD4 antibody had no effect. However, anti-murine CD4 continued to synergize with anti-CD3 in stimulating T cell proliferation in these mice. Thus, overexpression of human CD4 selectively impaired the ability of murine CD4 to assist in the process of antigen recognition. The ability of human CD4 to support a strong allogeneic response under these conditions indicates that this molecule can interact with murine class II molecules to a

  11. Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

    PubMed Central

    2014-01-01

    Background Bacterial species coexist commonly in mixed communities, for instance those occurring in microbial infections of humans. Interspecies effects contribute to alterations in composition of communities with respect to species and thus, to the course and severity of infection. Therefore, knowledge concerning growth and viability of single species in medically-relevant mixed communities is of high interest to resolve complexity of interspecies dynamics and to support development of treatment strategies. In this study, a flow cytometric method was established to assess the species-specific viability in defined three-species mixed cultures. The method enables the characterization of viability of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus, which are relevant to lung infections of Cystic Fibrosis (CF) patients. The method combines fluorescence detection by antibody and lectin labeling with viability fluorescence staining using SYBR®Green I and propidium iodide. In addition, species-specific cell enumeration analysis using quantitative terminal restriction fragment length polymorphisms (qT-RFLP) was used to monitor the growth dynamics. Finally, to investigate the impact of substrate availability on growth and viability, concentrations of main substrates and metabolites released were determined. Results For each species, the time course of growth and viability during mixed culture cultivations was obtained by using qT-RFLP analysis in combination with flow cytometry. Comparison between mixed and pure cultures revealed for every species differences in growth properties, e.g. enhanced growth of P. aeruginosa in mixed culture. Differences were also observed for B. cepacia and S. aureus in the time course of viability, e.g. an early and drastic reduction of viability of S. aureus in mixed culture. Overall, P. aeruginosa clearly dominated the mixed culture with regard to obtained cell concentrations. Conclusions In combination with q

  12. An oyster species-specific miRNA scaffold42648_5080 modulates haemocyte migration by targeting integrin pathway.

    PubMed

    Chen, Hao; Wang, Hao; Jiang, Shuai; Xu, Jiachao; Wang, Lingling; Qiu, Limei; Song, Linsheng

    2016-10-01

    miRNAs are important gene regulators at post-transcriptional level and can modulate diverse biological processes, including immune response. Dozens of species-specific miRNAs have been identified in oyster Crassostrea gigas while their functions remain largely unknown. In the present study, an oyster species-specific miRNA scaffold42648_5080 was found responsive to LPS stimulation and might target a total of 31 oyster genes possibly involved in cell communication, cellular localization and cellular response to stimulus. Besides, in gain-of-function assay of scaffold42648_5080 in vivo, the phagocytosis (30.90% in miRNA group verse 23.20% in miRNA control group), apoptosis (3.10% in miRNA group verse 5.30% in miRNA control group) and migration rate (13.88% in miRNA group verse 21.03% in miRNA control group) of oyster haemocytes were found significantly altered after the injection of scaffold42648_5080 mimics. Among the target genes, integrin-linked kinase (CgILK) was considered crucial in cell migration and its interaction with scaffold42648_5080 was then verified both in vitro and in vivo. Consequently, a significant decrease of relative luciferase ratio was observed in CgILK 3'-UTR luciferase reporter assay after transfection of scaffold42648_5080 mimics (0.70-fold of that in blank group, p < 0.01). Meanwhile, when scaffold42648_5080 was overexpressed in vivo (5.41-fold of miRNA control group, p < 0.01), the expression of CgILK declined significantly to 0.25-fold of miRNA control group (p < 0.01). Comparatively, a significant decrease of the haemocyte migration rate (19.76% verse 34.82% in siEGFP control group, p < 0.01) was observed after knock-down of CgILK in vivo. The present study, as far as we know, for the first time revealed the immunomodulation role of an oyster species-specific miRNA, which might provide new insights into miRNA-mediated adaptation mechanism of oysters.

  13. Species-specific mutual regulation of p53 and miR-138 between human, rat and mouse

    PubMed Central

    Li, Jie; Xia, Wei; Su, Xueting; Qin, Xingliang; Chen, Ying; Li, Shaohua; Dong, Jie; Ding, Hongmei; Li, Hui; Huang, Aixue; Ge, Xingfeng; Hou, Lvbin; Wang, Chaonan; Sun, Leqiao; Bai, Chenjun; Shen, Xuelian; Fang, Tao; Liu, Yuanlin; Zhang, Yi; Zhang, Hongru; Zhang, Hongwen; Shao, Ningsheng

    2016-01-01

    In recent years, p53 was identified to regulate the expression of many miRNAs and was also regulated by miRNAs. In this paper, we found that miR-138 showed a pronounced increase after p53 activation in human non-small cell lung cancer (NSCLC) cells, which is mediated by p53 binding sites in the promoter region of its host gene, but this did not happen with rat and mouse cells. More interestingly, we found that p53 could be also regulated by miR-138 in mouse and rat cells, but not in the human NSCLC cells. Our results suggest the existence of species-specific differences of the regulations of miRNA against its targets and the regulations of miRNA itself by other proteins. PMID:27183959

  14. Nucleic acid spot hybridization based species-specific detection of Sclerotium rolfsii associated with collar rot disease of Amorphophallus paeoniifolius.

    PubMed

    Pravi, V; Jeeva, M L; Archana, P V

    2015-02-01

    Collar rot is one of the most destructive and prevalent disease of Amorphophallus paeoniifolius, resulting in heavy yield losses. The causative organism, Sclerotium rolfsii is a soil-borne polyphagous fungus characterized by prolific growth and ability to produce persistent sclerotia. The pathogen propagules surviving in soil and planting material are the major sources of inoculum. This study presents the suitability of DNA hybridization technique for species specific detection of S. rolfsii in soil and planting material. The detection limit of the probe was 10-15 pg of pure pathogen DNA. The developed probe was found to be highly specific and could be used for accurate identification of pathogen up to the species level. The protocol was standardized for detection of the pathogen in naturally infected field samples.

  15. Species-specific PCR to describe local-scale distributions of four cryptic species in the Penicillium chrysogenum complex☆

    PubMed Central

    Browne, Alexander G.P.; Fisher, Matthew C.; Henk, Daniel A.

    2013-01-01

    Penicillium chrysogenum is a ubiquitous airborne fungus detected in every sampled region of the Earth. Owing to its role in Alexander Fleming's serendipitous discovery of Penicillin in 1928, the fungus has generated widespread scientific interest; however its natural history is not well understood. Research has demonstrated speciation within P. chrysogenum, describing the existence of four cryptic species. To discriminate the four species, we developed protocols for species-specific diagnostic PCR directly from fungal conidia. 430 Penicillium isolates were collected to apply our rapid diagnostic tool and explore the distribution of these fungi across the London Underground rail transport system revealing significant differences between Underground lines. Phylogenetic analysis of multiple type isolates confirms that the ‘Fleming species’ should be named Penicillium rubens and that divergence of the four ‘Chrysogenum complex’ fungi occurred about 0.75 million yr ago. Finally, the formal naming of two new species, Penicillium floreyi and Penicillium chainii, is performed. PMID:24179477

  16. Take time to smell the frogs: vocal sac glands of reed frogs (Anura: Hyperoliidae) contain species-specific chemical cocktails

    PubMed Central

    Starnberger, Iris; Poth, Dennis; Peram, Pardha Saradhi; Schulz, Stefan; Vences, Miguel; Knudsen, Jette; Barej, Michael F; Rödel, Mark-Oliver; Walzl, Manfred; Hödl, Walter

    2013-01-01

    Males of all reed frog species (Anura: Hyperoliidae) have a prominent, often colourful, gular patch on their vocal sac, which is particularly conspicuous once the vocal sac is inflated. Although the presence, shape, and form of the gular patch are well-known diagnostic characters for these frogs, its function remains unknown. By integrating biochemical and histological methods, we found strong evidence that the gular patch is a gland producing volatile compounds, which might be emitted while calling. Volatile compounds were confirmed by gas chromatography–mass spectrometry in the gular glands in 11 species of the hyperoliid genera Afrixalus, Heterixalus, Hyperolius, and Phlyctimantis. Comparing the gular gland contents of 17 specimens of four sympatric Hyperolius species yielded a large variety of 65 compounds in species-specific combinations. We suggest that reed frogs might use a complex combination of at least acoustic and chemical signals in species recognition and mate choice. PMID:24277973

  17. Species-Specific Thiol-Disulfide Equilibrium Constant: A Tool To Characterize Redox Transitions of Biological Importance.

    PubMed

    Mirzahosseini, Arash; Somlyay, Máté; Noszál, Béla

    2015-08-13

    Microscopic redox equilibrium constants, a new species-specific type of physicochemical parameters, were introduced and determined to quantify thiol-disulfide equilibria of biological significance. The thiol-disulfide redox equilibria of glutathione with cysteamine, cysteine, and homocysteine were approached from both sides, and the equilibrium mixtures were analyzed by quantitative NMR methods to characterize the highly composite, co-dependent acid-base and redox equilibria. The directly obtained, pH-dependent, conditional constants were then decomposed by a new evaluation method, resulting in pH-independent, microscopic redox equilibrium constants for the first time. The 80 different, microscopic redox equilibrium constant values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.

  18. Species-specific production of microbial volatile organic compounds (MVOC) by airborne fungi from a compost facility.

    PubMed

    Fischer, G; Schwalbe, R; Möller, M; Ostrowski, R; Dott, W

    1999-08-01

    Thirteen airborne fungal species frequently isolated in composting plants were screened for microbial volatile organic compounds (MVOC), i.e., Aspergillus candidus, A. fumigatus, A. versicolor, Emericella nidulans, Paecilomyces variotii, Penicillium brevicompactum, Penicillium clavigerum, Penicillium crustosum, Penicillium cyclopium, Penicillium expansum, Penicillium glabrum, Penicillium verruculosum, and Tritirachium oryzae. Air samples from pure cultures were sorbed on Tenax GR and analyzed by thermal desorption in combination with GC/MS. Various hydrocarbons of different chemical groups and a large number of terpenes were identified. Some compounds such as 3-methyl-1-butanol and 1-octen-3-ol were produced by a number of species, whereas some volatiles were specific for single species. An inventory of microbial metabolites will allow identification of potential health hazards due to an exposure to fungal propagules and metabolites in the workplace. Moreover, species-specific volatiles may serve as marker compounds for the selective detection of fungal species in indoor domestic and working environments.

  19. Species-specific leaf volatile compounds of obligate Macaranga myrmecophytes and host-specific aggressiveness of symbiotic Crematogaster ants.

    PubMed

    Inui, Yoko; Itioka, Takao

    2007-11-01

    Macaranga myrmecophytes harbor species-specific Crematogaster ants that defend host trees from herbivores. We examined ant aggressive behaviors when artificially damaged leaf pieces from another tree were offered to four sympatric species of obligate Macaranga myrmecophytes. The ants showed aggressive behavior in response to leaf pieces regardless of the leaf species; however, aggressiveness was higher when conspecific leaf pieces were offered than when nonhost species were offered. Thus, ants can recognize leaf damage and distinguish among damaged leaf species. Chemical analyses of volatile compounds emitted from damaged leaves that may induce ant defense showed that the composition of the minor compounds differed among the four Macaranga species, although there were many compounds in common.

  20. Reciprocal controlled crosses between Pinus sylvestris and P. mugo verified by a species-specific cpDNA marker.

    PubMed

    Wachowiak, Witold; Lewandowski, Andrzej; Prus-Głowacki, Wiesław

    2005-01-01

    A species-specific marker of cpDNA (paternally inherited in pines) was used to verify the hybrid origin of seedlings from controlled reciprocal crosses between Pinus sylvestris and P. mugo. A very low degree of compatibility between those two species has been revealed. In the three consecutive years of experiments, no filled seeds were obtained in the combination with P. mugo as the seed parent. From P. sylvestris as the seed parent and P. mugo as the pollen donor, we succeeded to obtain four filled seeds (about 1 %), but only in one year. The seedling obtained from the seeds had cpDNA haplotypes specific to P. mugo, which proves their hybrid origin. This method enables verification of the result of controlled crosses. The importance of the results has been discussed in the aspect of postulated natural hybridisation in sympatric populations of the two species.

  1. Detection of all Chlamydophila and Chlamydia spp. of veterinary interest using species-specific real-time PCR assays.

    PubMed

    Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad

    2010-12-01

    The aim of the present study was to analyse the occurrence of chlamydiae in several mammalian host species. Clinical samples that previously tested positive in a Chlamydiaceae-specific real-time PCR were retested using six species-specific real-time PCR assays to identify the chlamydial species involved. Chlamydophila (Cp.) abortus was the agent most frequently found in cattle, sheep, horses, goats, and pigs. Detection in cattle of Cp. psittaci (11% of samples) and Chlamydia (C.) suis (9%), as well as Cp. psittaci in a goat sample was somewhat unexpected. DNA of two different chlamydiae was identified in 56 (12.7%) of 440 samples tested. Cp. felis was the predominant species found in cats, while in guinea pigs and rabbits only Cp. caviae was detected. Interestingly, the latter two pathogens were also identified in samples from dogs. The data show that mixed chlamydial infections are not rare and suggest an extended host range of individual species.

  2. Species-specific PCR to describe local-scale distributions of four cryptic species in the Penicillium chrysogenum complex.

    PubMed

    Browne, Alexander G P; Fisher, Matthew C; Henk, Daniel A

    2013-10-01

    Penicillium chrysogenum is a ubiquitous airborne fungus detected in every sampled region of the Earth. Owing to its role in Alexander Fleming's serendipitous discovery of Penicillin in 1928, the fungus has generated widespread scientific interest; however its natural history is not well understood. Research has demonstrated speciation within P. chrysogenum, describing the existence of four cryptic species. To discriminate the four species, we developed protocols for species-specific diagnostic PCR directly from fungal conidia. 430 Penicillium isolates were collected to apply our rapid diagnostic tool and explore the distribution of these fungi across the London Underground rail transport system revealing significant differences between Underground lines. Phylogenetic analysis of multiple type isolates confirms that the 'Fleming species' should be named Penicillium rubens and that divergence of the four 'Chrysogenum complex' fungi occurred about 0.75 million yr ago. Finally, the formal naming of two new species, Penicillium floreyi and Penicillium chainii, is performed.

  3. Detection and Identification of Gastrointestinal Lactobacillus Species by Using Denaturing Gradient Gel Electrophoresis and Species-Specific PCR Primers

    PubMed Central

    Walter, J.; Tannock, G. W.; Tilsala-Timisjarvi, A.; Rodtong, S.; Loach, D. M.; Munro, K.; Alatossava, T.

    2000-01-01

    Denaturing gradient gel electrophoresis (DGGE) of DNA fragments obtained by PCR amplification of the V2-V3 region of the 16S rRNA gene was used to detect the presence of Lactobacillus species in the stomach contents of mice. Lactobacillus isolates cultured from human and porcine gastrointestinal samples were identified to the species level by using a combination of DGGE and species-specific PCR primers that targeted 16S-23S rRNA intergenic spacer region or 16S rRNA gene sequences. The identifications obtained by this approach were confirmed by sequencing the V2-V3 region of the 16S rRNA gene and by a BLAST search of the GenBank database. PMID:10618239

  4. Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis

    PubMed Central

    2016-01-01

    Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus with other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, Staphylococcus epidermidis and Staphylococcus carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA contents of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set of between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidishas the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behaviour of these diverse staphylococcal strains. PMID:28348860

  5. Identification of Circular RNAs in Kiwifruit and Their Species-Specific Response to Bacterial Canker Pathogen Invasion

    PubMed Central

    Wang, Zupeng; Liu, Yifei; Li, Dawei; Li, Li; Zhang, Qiong; Wang, Shuaibin; Huang, Hongwen

    2017-01-01

    Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genus Actinidia under different situations using ribosomal RNA (rRNA) depleted RNA-Seq data. A total of 3,582 circRNAs were identified in Actinidia, of which 64.01, 21.44, and 14.55% were intergenic circRNAs, exonic circRNAs, and intronic circRNAs, respectively. Tissue-specific expression of circRNAs was observed in kiwifruit, and a species-specific response was detected when infected with Pseudomonas syringae pv. actinidiae (Psa), which is the causative agent of kiwifruit bacterial canker disease. Furthermore, we found that both exonic and intronic circRNAs were significantly positively correlated to parent protein-coding genes, and intronic circRNAs are a class of highly remarkable regulators the parent genes comparing to that of exonic circRNAs. Expression and weighted gene co-expression network analysis (WGCNA) identified a set of circRNAs that were closely associated with plant defense response. The findings of the presents study suggest that circRNAs exhibit tissue- and species-specific expression, as well as play an important role in plant immune response. PMID:28396678

  6. In vitro effects of metal pollution on Mediterranean sponges: species-specific inhibition of 2',5'-oligoadenylate synthetase.

    PubMed

    Saby, Emilie; Justesen, Just; Kelve, Merike; Uriz, Maria J

    2009-09-14

    Heavy metals are among the main pollutants of the Mediterranean coastal waters where they can harm sublittoral biota. Filter-feeder, long-living invertebrates that remain fixed to the rocky bottom, such as sponges, are good targets to metal contamination studies since they may be exposed to potential low levels of contamination for years. Several molecular and biochemical mechanisms are developed by sponges to counteract the effects of noxious metals. As a result, some of the normal cell functions can be altered. Here we show that the main heavy metals that can be found in marine sublittoral waters (i.e. copper, iron, zinc and manganese) may alter the immune system of sponges by inhibiting the activity of the sponge 2',5'-oligoadenylate synthetase (2-5A synthetase), which is an enzyme involved in the immune system of vertebrates. We selected the widespread Mediterranean sponges Geodia cydonium, Crella elegans and Chondrosia reniformis for the study. They exerted a high 2-5A synthetase activity and gave a unique profile of 2',5'-oligoadenylate product production. Several metals alter the 2-5A synthetase activity differently, in a species-specific manner. 2-5A synthetases from G. cydonium and C. elegans were inhibited by all the metal ions assayed. However, in C. reniformis, 2-5A synthetase was either activated or inhibited by the same ions depending on their final concentrations. Like in humans, metal contamination may have an effect on the OAS activity and thus it might alter the sponge immune system. However, since the effects are species-specific, 2-5A synthetase cannot be used as general biomarker of metal pollutions.

  7. Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells

    PubMed Central

    Cheng, Menglan; Zhang, Xuyuan; Yu, Haisheng; Du, Peishuang; Plumas, Joël; Chaperot, Laurance; Su, Lishan; Zhang, Liguo

    2015-01-01

    Dendritic cells (DCs) are sentinels of the immune system and comprise two distinct subsets: conventional DCs (cDCs) and plasmacytoid DCs (pDCs). Human pDCs are distinguished from mouse pDCs phenotypically and functionally. Basic helix-loop-helix protein E2-2 is defined as an essential transcription factor for mouse pDC development, cell fate maintenance and gene programe. It is unknown whether E2-2 regulation contributes to this species-specific difference. Here we investigated the function of E2-2 in human pDCs and screened human-specific genes regulated by E2-2. Reduced E2-2 expression in human pDC cell line GEN2.2 resulted in diminished IFN-α production in response to CpG but elevated antigen presentation capacity. Gene expression profiling showed that E2-2 silence down-regulated pDC signature genes but up-regulated cDC signature genes. Thirty human-specific genes regulated by E2-2 knockdown were identified. Among these genes, we confirmed that expression of Siglec-6 was inhibited by E2-2. Further more, Siglec-6 was expressed at a higher level on a human pDC subset with drastically lower expression of E2-2. Collectively, these results highlight that E2-2 modulates pDC function in a species-specific manner, which may provide insights for pDC development and functions. PMID:26182859

  8. Species specific and environment induced variation of δ13C and δ15N in alpine plants

    PubMed Central

    Yang, Yang; Siegwolf, Rolf T. W.; Körner, Christian

    2015-01-01

    Stable carbon and nitrogen isotope signals in plant tissues integrate plant-environment interactions over long periods. In this study, we hypothesized that humid alpine life conditions are narrowing the scope for significant deviations from common carbon, water and nitrogen relations as captured by stable isotope signals. We explored the variation in δ13C and δ15N in 32 plant species from tissue type to ecosystem scale across a suite of locations at c. Two thousand five hundred meter elevation in the Swiss Alps. Foliar δ13C and δ15N varied among species by about 3–4‰ and 7–8‰ respectively. However, there was no overall difference in means of δ13C and δ15N for species sampled in different plant communities or when bulk plant dry matter harvests of different plant communities were compared. δ13C was found to be highly species specific, so that the ranking among species was mostly maintained across 11 habitats. However, δ15N varied significantly from place to place in all species (a range of 2.7‰) except in Fabaceae (Trifolium alpinum) and Juncaceae (Luzula lutea). There was also a substantial variation among individuals of the same species collected next to each other. No difference was found in foliar δ15N of non-legumes, which were either collected next to or away from the most common legume, T. alpinum. δ15N data place Cyperaceae and Juncaceae, just like Fabaceae, in a low discrimination category, well separated from other families. Soil δ15N was higher than in plants and increased with soil depth. The results indicate a high functional diversity in alpine plants that is similar to that reported for low elevation plants. We conclude that the surprisingly high variation in δ13C and δ15N signals in the studied high elevation plants is largely species specific (genetic) and insensitive to obvious environmental cues. PMID:26097487

  9. MD-2 Residues Tyrosine 42, Arginine 69, Aspartic Acid 122, and Leucine 125 Provide Species Specificity for Lipid IVA*

    PubMed Central

    Meng, Jianmin; Drolet, Joshua R.; Monks, Brian G.; Golenbock, Douglas T.

    2010-01-01

    Lipopolysaccharide (LPS) activates the innate immune response through the Toll-like receptor 4 (TLR4)·MD-2 complex. A synthetic lipid A precursor, lipid IVA, induces an innate immune response in mice but not in humans. Both TLR4 and MD-2 are required for the agonist activity of lipid IVA in mice, with TLR4 interacting through specific surface charges at the dimerization interface. In this study, we used site-directed mutagenesis to identify the MD-2 residues that determine lipid IVA species specificity. A single mutation of murine MD-2 at the hydrophobic pocket entrance, E122K, substantially reduced the response to lipid IVA. Combining the murine MD-2 E122K with the murine TLR4 K367E/S386K/R434Q mutations completely abolished the response to lipid IVA, effectively converting the murine cellular response to a human-like response. In human cells, however, simultaneous mutations of K122E, K125L, Y41F, and R69G on human MD-2 were required to promote a response to lipid IVA. Combining the human MD-2 quadruple mutations with the human TLR4 E369K/Q436R mutations completely converted the human MD-2/human TLR4 receptor to a murine-like receptor. Because MD-2 residues 122 and 125 reside at the dimerization interface near the pocket entrance, surface charge differences here directly affect receptor dimerization. In comparison, residues 42 and 69 reside at the MD-2/TLR4 interaction surface opposite the dimerization interface. Surface charge differences there likely affect the binding angle and/or rigidity between MD-2 and TLR4, exerting an indirect influence on receptor dimerization and activation. Thus, surface charge differences at the two MD-2/TLR4 interfaces determine the species-specific activation of lipid IVA. PMID:20592019

  10. Applied genomics: data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA.

    PubMed

    Demas, Allison; Oberstaller, Jenna; DeBarry, Jeremy; Lucchi, Naomi W; Srinivasamoorthy, Ganesh; Sumari, Deborah; Kabanywanyi, Abdunoor M; Villegas, Leopoldo; Escalante, Ananias A; Kachur, S Patrick; Barnwell, John W; Peterson, David S; Udhayakumar, Venkatachalam; Kissinger, Jessica C

    2011-07-01

    Accurate and rapid diagnosis of malaria infections is crucial for implementing species-appropriate treatment and saving lives. Molecular diagnostic tools are the most accurate and sensitive method of detecting Plasmodium, differentiating between Plasmodium species, and detecting subclinical infections. Despite available whole-genome sequence data for Plasmodium falciparum and P. vivax, the majority of PCR-based methods still rely on the 18S rRNA gene targets. Historically, this gene has served as the best target for diagnostic assays. However, it is limited in its ability to detect mixed infections in multiplex assay platforms without the use of nested PCR. New diagnostic targets are needed. Ideal targets will be species specific, highly sensitive, and amenable to both single-step and multiplex PCRs. We have mined the genomes of P. falciparum and P. vivax to identify species-specific, repetitive sequences that serve as new PCR targets for the detection of malaria. We show that these targets (Pvr47 and Pfr364) exist in 14 to 41 copies and are more sensitive than 18S rRNA when utilized in a single-step PCR. Parasites are routinely detected at levels of 1 to 10 parasites/μl. The reaction can be multiplexed to detect both species in a single reaction. We have examined 7 P. falciparum strains and 91 P. falciparum clinical isolates from Tanzania and 10 P. vivax strains and 96 P. vivax clinical isolates from Venezuela, and we have verified a sensitivity and specificity of ∼100% for both targets compared with a nested 18S rRNA approach. We show that bioinformatics approaches can be successfully applied to identify novel diagnostic targets and improve molecular methods for pathogen detection. These novel targets provide a powerful alternative molecular diagnostic method for the detection of P. falciparum and P. vivax in conventional or multiplex PCR platforms.

  11. Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species.

    PubMed

    Singhal, Kopal; Khanna, Radhika; Mohanty, Sujata

    2017-06-01

    The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

  12. Species-specific detection of Lobaria pulmonaria (lichenized ascomycete) diaspores in litter samples trapped in snow cover.

    PubMed

    Walser, J C; Zoller, S; Büchler, U; Scheidegger, C

    2001-09-01

    The foliose lichen Lobaria pulmonaria has suffered a substantial decline in central and northern Europe during the twentieth century and is now considered to be critically endangered in many European lowland regions. Based on demographic studies, it has been proposed that under the present environmental conditions and forest management regimes, dispersal of diaspores and subsequent establishment of new thalli are insufficient to maintain the remnant small lowland populations. Chances of long-term survival may therefore be reduced. The data and analytical power of these demographic studies are limited. Since lichen diaspores show very few species-specific morphological characteristics, and are therefore almost indistinguishable, the accurate assessment of diaspore flux would be a fundamental first step in better understanding the life cycle of L. pulmonaria. Here we present a new molecular approach to investigate the dispersal of L. pulmonaria diaspores in its natural environment by specifically identifying small amounts of DNA in snow litter samples at varying distances from known sources. We used a species-specific polymerase chain reaction (PCR) primer pair to amplify the ribosomal internal transcribed spacer region (ITS rDNA) and a sensitive automated PCR product detection system using fluorescent labelled primers. We detected considerable amounts of naturally dispersed diaspores, deposited as far as 50 m away from the closest potential source. Diaspores were only found in the direction of the prevailing wind. Diaspore deposition varied from 1.2 diaspores per m(2) per day at 50 m distance from the source to 15 diaspores per m(2) per day at 1 m distance. The method described in this paper opens up perspectives for studies of population dynamics and dispersal ecology mainly in lichenized ascomycetes but also in other organisms with small, wind-dispersed diaspores.

  13. Development of Species-Specific Ah Receptor-Responsive Third Generation CALUX Cell Lines with Increased Sensitivity and Responsiveness

    PubMed Central

    Brennan, Jennifer C.; He, Guochun; Tsutsumi, Tomoaki; Zhao, Jing; Wirth, Ed; Fulton, Michael H.; Denison, Michael S.

    2016-01-01

    The Ah receptor (AhR)-responsive CALUX (chemically-activated luciferase expression) cell bioassay is commonly used for rapid screening of samples for the presence of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin), dioxin-like compounds, and AhR agonists/antagonists. By increasing the number of AhR DNA recognition sites (dioxin responsive elements), we previously generated a novel third generation (G3) recombinant AhR-responsive mouse CALUX cell line (H1L7.5c3) with significantly enhanced sensitivity and response to DLCs compared to existing AhR-CALUX cell bioassays. However, the elevated background luciferase activity of these cells and the absence of comparable G3 cell lines derived from other species have limited their utility for screening purposes. Here, we describe the development and characterization of species-specific G3 recombinant AhR-responsive CALUX cell lines (rat, human, and guinea pig) that exhibit significantly improved sensitivity and dramatically increased TCDD induction response. The low background luciferase activity, low minimal detection limit (0.1 pM TCDD) and enhanced induction response of the rat G3 cell line (H4L7.5c2) over the H1L7.5c3 mouse G3 cells, identifies them as a more optimal cell line for screening purposes. The utility of the new G3 CALUX cell lines were demonstrated by screening sediment extracts and a small chemical compound library for the presence of AhR agonists. The increased sensitivity and response of these new G3 CALUX cell lines will facilitate species-specific analysis of DLCs and AhR agonists in samples with low levels of contamination and/or in small sample volumes. PMID:26366531

  14. Species-Specific Activity of SIV Nef and HIV-1 Vpu in Overcoming Restriction by Tetherin/BST2

    PubMed Central

    Neidermyer, William; Rahmberg, Andrew; Mackey, John; Fofana, Ismael Ben; Johnson, Welkin E.; Westmoreland, Susan; Evans, David T.

    2009-01-01

    Tetherin, also known as BST2, CD317 or HM1.24, was recently identified as an interferon-inducible host–cell factor that interferes with the detachment of virus particles from infected cells. HIV-1 overcomes this restriction by expressing an accessory protein, Vpu, which counteracts tetherin. Since lentiviruses of the SIVsmm/mac/HIV-2 lineage do not have a vpu gene, this activity has likely been assumed by other viral gene products. We found that deletion of the SIVmac239 nef gene significantly impaired virus release in cells expressing rhesus macaque tetherin. Virus release could be restored by expressing Nef in trans. However, Nef was unable to facilitate virus release in the presence of human tetherin. Conversely, Vpu enhanced virus release in the presence of human tetherin, but not in the presence of rhesus tetherin. In accordance with the species-specificity of Nef in mediating virus release, SIV Nef downregulated cell-surface expression of rhesus tetherin, but did not downregulate human tetherin. The specificity of SIV Nef for rhesus tetherin mapped to four amino acids in the cytoplasmic domain of the molecule that are missing from human tetherin, whereas the specificity of Vpu for human tetherin mapped to amino acid differences in the transmembrane domain. Nef alleles of SIVsmm, HIV-2 and HIV-1 were also able to rescue virus release in the presence of both rhesus macaque and sooty mangabey tetherin, but were generally ineffective against human tetherin. Thus, the ability of Nef to antagonize tetherin from these Old World primates appears to be conserved among the primate lentiviruses. These results identify Nef as the viral gene product of SIV that opposes restriction by tetherin in rhesus macaques and sooty mangabeys, and reveal species-specificity in the activities of both Nef and Vpu in overcoming tetherin in their respective hosts. PMID:19436700

  15. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms

    PubMed Central

    Emmons-Bell, Maya; Durant, Fallon; Hammelman, Jennifer; Bessonov, Nicholas; Volpert, Vitaly; Morokuma, Junji; Pinet, Kaylinnette; Adams, Dany S.; Pietak, Alexis; Lobo, Daniel; Levin, Michael

    2015-01-01

    The shape of an animal body plan is constructed from protein components encoded by the genome. However, bioelectric networks composed of many cell types have their own intrinsic dynamics, and can drive distinct morphological outcomes during embryogenesis and regeneration. Planarian flatworms are a popular system for exploring body plan patterning due to their regenerative capacity, but despite considerable molecular information regarding stem cell differentiation and basic axial patterning, very little is known about how distinct head shapes are produced. Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina). We use morphometric analysis to quantify the ability of physiological network perturbations to induce different species-specific head shapes from the same genome. Moreover, we present a computational agent-based model of cell and physical dynamics during regeneration that quantitatively reproduces the observed shape changes. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain, the characteristic distribution of adult stem cells (neoblasts), and the bioelectric gradients of resting potential within the anterior tissues. Interestingly, the shape change is not permanent; after regeneration is complete, intact animals remodel back to G. dorotocephala-appropriate head shape within several weeks in a secondary phase of remodeling following initial complete regeneration. We present a conceptual model to guide future work to delineate the molecular mechanisms by which bioelectric networks stochastically select among a small set of discrete head morphologies. Taken together

  16. What if plant functional types conceal species-specific responses to environment? Study on arctic shrub communities.

    PubMed

    Saccone, Patrick; Hoikka, Kristiina; Virtanen, Risto

    2017-06-01

    Plant functional types (PFT) are increasingly used to outline biome-scale plant-environment relationship and predict global change effects on community structure. However, the potentials and limitations of the PFT approach have to be tested as they can be less sensitive than trait-based or species-level approaches. Here, we compare the responses of deciduous-evergreen shrub PFTs and species to gradual snow-related environmental conditions by also considering effects of aboveground architectural traits and neighboring shrubs. Five deciduous species and four evergreen dwarf shrub species were transplanted to be exposed to four levels of winter snow cover across mesotopographic gradients in northern Fennoscandian tundra. The survival and growth of individually tagged shoots were monitored over one year, and the change in cover of shrubs was monitored over four years. Evergreen species showed higher resistance to environmental severity and generally benefitted from higher abundance of neighboring shrubs. Deciduous species exhibited negligible to drastic responses to snow thickness and neighboring shrubs tended to have a negative effect on their performance and survival. Tall shoots of deciduous shrubs survived poorly under the thinnest snow cover. Overall, deciduous and evergreen PFTs showed modest differences in their performances along the gradient. Our results show that deciduous-evergreen leaf phenology categories predict shrub responses to changing environmental conditions only to a limited extent. Our findings highlight strong species-specific responses especially among deciduous shrubs, and a differential role of plant-plant interactions for shrubs. Our results emphasize that distribution patterns of arctic-alpine shrubs and shrub community responses to altered snow regimes depend on species-level plant functional attributes, species interactions and species-specific sensitivities to environmental severity. © 2017 by the Ecological Society of America.

  17. MD-2 residues tyrosine 42, arginine 69, aspartic acid 122, and leucine 125 provide species specificity for lipid IVA.

    PubMed

    Meng, Jianmin; Drolet, Joshua R; Monks, Brian G; Golenbock, Douglas T

    2010-09-03

    Lipopolysaccharide (LPS) activates the innate immune response through the Toll-like receptor 4 (TLR4).MD-2 complex. A synthetic lipid A precursor, lipid IV(A), induces an innate immune response in mice but not in humans. Both TLR4 and MD-2 are required for the agonist activity of lipid IV(A) in mice, with TLR4 interacting through specific surface charges at the dimerization interface. In this study, we used site-directed mutagenesis to identify the MD-2 residues that determine lipid IV(A) species specificity. A single mutation of murine MD-2 at the hydrophobic pocket entrance, E122K, substantially reduced the response to lipid IV(A). Combining the murine MD-2 E122K with the murine TLR4 K367E/S386K/R434Q mutations completely abolished the response to lipid IV(A), effectively converting the murine cellular response to a human-like response. In human cells, however, simultaneous mutations of K122E, K125L, Y41F, and R69G on human MD-2 were required to promote a response to lipid IV(A). Combining the human MD-2 quadruple mutations with the human TLR4 E369K/Q436R mutations completely converted the human MD-2/human TLR4 receptor to a murine-like receptor. Because MD-2 residues 122 and 125 reside at the dimerization interface near the pocket entrance, surface charge differences here directly affect receptor dimerization. In comparison, residues 42 and 69 reside at the MD-2/TLR4 interaction surface opposite the dimerization interface. Surface charge differences there likely affect the binding angle and/or rigidity between MD-2 and TLR4, exerting an indirect influence on receptor dimerization and activation. Thus, surface charge differences at the two MD-2/TLR4 interfaces determine the species-specific activation of lipid IV(A).

  18. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms.

    PubMed

    Emmons-Bell, Maya; Durant, Fallon; Hammelman, Jennifer; Bessonov, Nicholas; Volpert, Vitaly; Morokuma, Junji; Pinet, Kaylinnette; Adams, Dany S; Pietak, Alexis; Lobo, Daniel; Levin, Michael

    2015-11-24

    The shape of an animal body plan is constructed from protein components encoded by the genome. However, bioelectric networks composed of many cell types have their own intrinsic dynamics, and can drive distinct morphological outcomes during embryogenesis and regeneration. Planarian flatworms are a popular system for exploring body plan patterning due to their regenerative capacity, but despite considerable molecular information regarding stem cell differentiation and basic axial patterning, very little is known about how distinct head shapes are produced. Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina). We use morphometric analysis to quantify the ability of physiological network perturbations to induce different species-specific head shapes from the same genome. Moreover, we present a computational agent-based model of cell and physical dynamics during regeneration that quantitatively reproduces the observed shape changes. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain, the characteristic distribution of adult stem cells (neoblasts), and the bioelectric gradients of resting potential within the anterior tissues. Interestingly, the shape change is not permanent; after regeneration is complete, intact animals remodel back to G. dorotocephala-appropriate head shape within several weeks in a secondary phase of remodeling following initial complete regeneration. We present a conceptual model to guide future work to delineate the molecular mechanisms by which bioelectric networks stochastically select among a small set of discrete head morphologies. Taken together

  19. Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata).

    PubMed

    Prakhongcheep, Ornjira; Thapana, Watcharaporn; Suntronpong, Aorarat; Singchat, Worapong; Pattanatanang, Khampee; Phatcharakullawarawat, Rattanin; Muangmai, Narongrit; Peyachoknagul, Surin; Matsubara, Kazumi; Ezaz, Tariq; Srikulnath, Kornsorn

    2017-08-16

    Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species. The VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.

  20. Hippo pathway genes developed varied exon numbers and coevolved functional domains in metazoans for species specific growth control

    PubMed Central

    2013-01-01

    Background The Hippo pathway controls growth by mediating cell proliferation and apoptosis. Dysregulation of Hippo signaling causes abnormal proliferation in both healthy and cancerous cells. The Hippo pathway receives inputs from multiple developmental pathways and interacts with many tissue-specific transcription factors, but how genes in the pathway have evolved remains inadequately revealed. Results To explore the origin and evolution of Hippo pathway, we have extensively examined 16 Hippo pathway genes, including upstream regulators and downstream targets, in 24 organisms covering major metazoan phyla. From simple to complex organisms, these genes are varied in the length and number of exons but encode conserved domains with similar higher-order organization. The core of the pathway is more conserved than its upstream regulators and downstream targets. Several components, despite existing in the most basal metazoan sponges, cannot be convincingly identified in other species. Potential recombination breakpoints were identified in some genes. Coevolutionary analysis reveals that most functional domains in Hippo genes have coevolved with interacting functional domains in other genes. Conclusions The two essential upstream regulators cadherins fat and dachsous may have originated in the unicellular organism Monosiga brevicollis and evolved more significantly than the core of the pathway. Genes having varied numbers of exons in different species, recombination events, and the gain and loss of some genes indicate alternative splicing and species-specific evolution. Coevolution signals explain some species-specific loss of functional domains. These results significantly unveil the structure and evolution of the Hippo pathway in distant phyla and provide valuable clues for further examination of Hippo signaling. PMID:23547742

  1. Coagulase-negative Staphylococcus species in bulk milk: Prevalence, distribution, and associated subgroup- and species-specific risk factors.

    PubMed

    De Visscher, A; Piepers, S; Haesebrouck, F; Supré, K; De Vliegher, S

    2017-01-01

    Coagulase-negative staphylococci (CNS) have become the main pathogens causing bovine mastitis in recent years. A huge variation in species distribution among herds has been observed in several studies, emphasizing the need to identify subgroup- and species-specific herd-level factors to improve our understanding of the differences in ecological and epidemiological nature between species. The use of bulk milk samples enables the inclusion of a large(r) number of herds needed to identify herd-level risk factors and increases the likelihood of recovering enough isolates per species needed for conducting subgroup- and, eventually, species-specific analyses at the same time. This study aimed to describe the prevalence and distribution of CNS species in bulk milk samples and to identify associated subgroup- and species-specific herd-level factors. Ninety percent of all bulk milk samples yielded CNS. Staphylococcus equorum was the predominant species, followed by Staphylococcus haemolyticus and Staphylococcus epidermidis. A seasonal effect was observed for several CNS species. Bulk milk samples from herds with a loose-pack or a tiestall housing system were more likely to yield CNS species compared with herds with a freestall barn, except for S. epidermidis, Staphylococcus simulans, and Staphylococcus cohnii. In September, herds in which udders were clipped had lower odds of yielding Staphylococcus chromogenes, S. simulans, and Staphylococcus xylosus, the CNS species assumed to be most relevant for udder health, in their bulk milk than herds in which udder clipping was not practiced. Bulk milk of herds participating in a monthly veterinary udder health-monitoring program was more likely to yield these 3 CNS species. Herds always receiving their milk quality premium or predisinfecting teats before attachment of the milking cluster had lower odds of having S. equorum in their bulk milk. Herds not using a single dry cotton or paper towel for each cow during premilking udder

  2. Impact of trace metal concentrations on coccolithophore growth and morphology: species-specific responses in past and present ocean

    NASA Astrophysics Data System (ADS)

    Faucher, Giulia; Hoffmann, Linn; Bach, Lennart Thomas; Bottini, Cinzia; Erba, Elisabetta; Riebesell, Ulf

    2017-04-01

    The Cretaceous witnessed intervals of profound perturbation named "Oceanic Anoxic Events (OAEs)" characterized by volcanic injection of large amounts of CO2, ocean anoxia, eutrophication, and introduction of biologically relevant metals. Some of these extreme events were characterized by size reduction and/or morphological changes of a number of nannofossil species. To detect the cause/s of such changes in the fossil record is challenging. Evidence of a correspondence between intervals of high trace metals concentrations and nannofossil dwarfism may be suggestive for a negative effect of these elements on nannoplankton biocalcification process. In order to verify the hypothesis that anomalously high quantities of essential and/or toxic metals were the cause of coccolith dwarfism, we explored the toxicities of a mixture of trace metals on four living coccolithophores species, namely Emiliania huxleyi, Gephyrocapsa oceanica, Pleurochrysis carterae and Coccolithus pelagicus. The trace metals tested were chosen based upon concentration peaks identified in the geological record and upon known trace metal interaction with living coccolithophores algae. Our results demonstrate a species-specific response to trace metal enrichment in living coccolithophores: E. huxleyi, G. oceanica and C. pelagicus showed a decrease in their growth rate with progressively and exponentially increased trace metal concentrations, while P. carterae is unresponsive to trace metal content. Furthermore, E. huxleyi, G. oceanica and C. pelagicus evidenced a decrease in the cell diameter. Smaller coccoliths were detected in E. huxleyi and C. pelagicus, while coccolith of G. oceanica showed a decrease in size only at the highest trace metal concentrations tested. P. carterae size was unresponsive for changing trace metal concentration. Our results on living coccolithophore algae, demonstrate that elevated trace metal concentrations not only affect growth but also coccolith size and/or weight and that

  3. Effect of silver nanoparticles on Mediterranean sea urchin embryonal development is species specific and depends on moment of first exposure.

    PubMed

    Burić, Petra; Jakšić, Željko; Štajner, Lara; Dutour Sikirić, Maja; Jurašin, Darija; Cascio, Claudia; Calzolai, Luigi; Lyons, Daniel Mark

    2015-10-01

    With the ever growing use of nanoparticles in a broad range of industrial and consumer applications there is increasing likelihood that such nanoparticles will enter the aquatic environment and be transported through freshwater systems, eventually reaching estuarine or marine waters. Due to silver's known antimicrobial properties and widespread use of silver nanoparticles (AgNP), their environmental fate and impact is therefore of particular concern. In this context we have investigated the species-specific effects of low concentrations of 60 nm AgNP on embryonal development in Mediterranean sea urchins Arbacia lixula, Paracentrotus lividus and Sphaerechinus granularis. The sensitivity of urchin embryos was tested by exposing embryos to nanoparticle concentrations in the 1-100 μg L(-1) range, with times of exposure varying from 30 min to 24 h (1 h-48 h for S. granularis) post-fertilisation which corresponded with fertilized egg, 4 cell, blastula and gastrula development phases. The most sensitive species to AgNP was A. lixula with significant modulation of embryonal development at the lowest AgNP concentrations of 1-10 μg L(-1) with high numbers of malformed embryos or arrested development. The greatest impact on development was noted for those embryos first exposed to nanoparticles at 6 and 24 h post fertilisation. For P. lividus, similar effects were noted at higher concentrations of 50 μg L(-1) and 100 μg L(-1) for all times of first exposure. The S. granularis embryos indicated a moderate AgNP impact, and significant developmental abnormalities were recorded in the concentration range of 10-50 μg L(-1). As later post-fertilisation exposure times to AgNP caused greater developmental changes in spite of a shorter total exposure time led us to postulate on additional mechanisms of AgNP toxicity. The results herein indicate that toxic effects of AgNP are species-specific. The moment at which embryos first encounter AgNP is also shown to be

  4. Inflammation of the Orbit

    MedlinePlus

    ... Cavernous Sinus Thrombosis Inflammation of the Orbit Orbital Cellulitis Preseptal Cellulitis Tumors of the Orbit Any or all of ... Cavernous Sinus Thrombosis Inflammation of the Orbit Orbital Cellulitis Preseptal Cellulitis Tumors of the Orbit NOTE: This ...

  5. FGF23 and inflammation

    PubMed Central

    Sharaf El Din, Usama A A; Salem, Mona M; Abdulazim, Dina O

    2017-01-01

    Systemic inflammation is a recognized feature in chronic kidney disease (CKD). The role of systemic inflammation in the pathogenesis of vascular calcification was recently settled. FGF23 was recently accused as a direct stimulus of systemic inflammation. This finding explains the strong association of FGF23 to vascular calcification and increased mortality among CKD. PMID:28101453

  6. THE ANTIGENIC COMPLEX OF STREPTOCOCCUS HAEMOLYTICUS : III. CHEMICAL AND IMMUNOLOGICAL PROPERTIES OF THE SPECIES-SPECIFIC SUBSTANCE.

    PubMed

    Lancefield, R C

    1928-02-29

    1. The chemical and immunological characteristics of the species-specific substance (C) of Streptococcus haemolyticus are considered. (a) It seems to be a carbohydrate because considerably purified preparations of C resisted prolonged tryptic and peptic digestion and were negative for the ordinary protein color tests but gave positive Molisch reactions to the limit of the precipitin titer. One such "purified" lot, however, had 4.2 per cent nitrogen and only 28 per cent reducing sugars on hydrolysis. Whether the nitrogen was due to impurities or was combined in the C substance itself, as is true of the Type I pneumococcus specific polysaccharide, cannot be stated without more material. (b) The C substance forms precipitates with antibacterial sera prepared against heterologous, as well as against homologous hemolytic streptococci. These precipitates are typical discs like those formed by type-specific carbohydrates of other species of bacteria. C does not precipitate antinucleoprotein sera. (c) While there is only slight direct evidence that the C substance is not antigenic, there is considerable indirect proof that this is the case. It probably is a haptene in the sense of Landsteiner. 2. A discussion is included of the chemical and immunological relationships of all the serologically active substances so far identified in extracts of the hemolytic streptococcus.

  7. Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.

    PubMed

    Wang, Lan; Ren, Shifang; Zhu, Haiyan; Zhang, Dongmei; Hao, Yuqing; Ruan, Yuanyuan; Zhou, Lei; Lee, Chiayu; Qiu, Lin; Yun, Xiaojing; Xie, Jianhui

    2012-08-01

    CLEC-2 was first identified by sequence similarity to C-type lectin-like molecules with immune functions and has been reported as a receptor for the platelet-aggregating snake venom toxin rhodocytin and the endogenous sialoglycoprotein podoplanin. Recent researches indicate that CLEC-2-deficient mice were lethal at the embryonic stage associated with disorganized and blood-filled lymphatic vessels and severe edema. In view of a necessary role of CLEC-2 in the individual development, it is of interest to investigate its phylogenetic homology and highly conserved functional regions. In this work, we reported that CLEC-2 from different species holds with an extraordinary conservation by sequence alignment and phylogenetic tree analysis. The functional structures including N-linked oligosaccharide sites and ligand-binding domain implement a structural and functional conservation in a variety of species. The glycosylation sites (N120 and N134) are necessary for the surface expression CLEC-2. CLEC-2 from different species possesses the binding activity of mouse podoplanin. Nevertheless, the expression of CLEC-2 is regulated with a species-specific manner. The alternative splicing of pre-mRNA, a regulatory mechanism of gene expression, and the binding sites on promoter for several key transcription factors vary between different species. Therefore, CLEC-2 shares high sequence homology and functional identity. However the transcript expression might be tightly regulated by different mechanisms in evolution.

  8. The use of real-time PCR and species-specific primers for the identification and monitoring of Paecilomyces lilacinus.

    PubMed

    Atkins, Simon D; Clark, Ian M; Pande, Sonal; Hirsch, Penny R; Kerry, Brian R

    2005-01-01

    The Paecilomyces lilacinus is the most widely tested fungus for the control of root-knot and cyst nematodes. The fungus has also been implicated in a number of human and animal infections, difficulties in diagnosis often result in misdiagnosis or delays in identification leading to a delay in treatment. Here, we report the development of species-specific primers for the identification of P. lilacinus based on sequence information from the ITS gene, and their use in identifying P. lilacinus isolates, including clinical isolates of the fungus. The primer set generated a single PCR fragment of 130 bp in length that was specific to P. lilacinus and was also used to detect the presence of P. lilacinus from soil, roots and nematode eggs. Real-time PCR primers and a TaqMan probe were also developed and provided quantitative data on the population size of the fungus in two field sites. PCR, bait and culture methods were combined to investigate the presence and abundance of the fungus from two field sites in the United Kingdom where potato cyst nematode populations were naturally declining, and results demonstrated the importance of using a combination of methods to investigate population size and activity of fungi.

  9. Immunoreactivity between venoms and commercial antiserums in four Chinese snakes and venom identification by species-specific antibody.

    PubMed

    Gao, Jian-Fang; Wang, Jin; Qu, Yan-Fu; Ma, Xiao-Mei; Ji, Xiang

    2013-01-31

    We studied the immunoreactivity between venoms and commercial antiserums in four Chinese venomous snakes, Bungarus multicinctus, Naja atra, Deinagkistrodon acutus and Gloydius brevicaudus. Venoms from the four snakes shared common antigenic components, and most venom components expressed antigenicity in the immunological reaction between venoms and antiserums. Antiserums cross-reacted with heterologous venoms. Homologous venom and antiserum expressed the highest reaction activity in all cross-reactions. Species-specific antibodies (SSAbs) were obtained from four antiserums by immunoaffinity chromatography: the whole antiserum against each species was gradually passed through a medium system coated with heterologous venoms, and the cross-reacting components in antiserum were immunoabsorbed by the common antigens in heterologous venoms; the unbound components (i.e., SSAbs) were collected, and passed through Hitrap G protein column and concentrated. The SSAbs were found to have high specificity by western blot and enzyme-linked immunosorbent assay (ELISA). A 6-well ELISA strip coated with SSAbs was used to assign a venom sample and blood and urine samples from the envenomed rats to a given snake species. Our detections could differentiate positive and negative samples, and identify venoms of a snake species in about 35 min. The ELISA strips developed in this study are clinically useful in rapid and reliable identification of venoms from the above four snake species.

  10. Method- and species-specific detection probabilities of fish occupancy in Arctic lakes: Implications for design and management

    USGS Publications Warehouse

    Haynes, Trevor B.; Rosenberger, Amanda E.; Lindberg, Mark S.; Whitman, Matthew; Schmutz, Joel A.

    2013-01-01

    Studies examining species occurrence often fail to account for false absences in field sampling. We investigate detection probabilities of five gear types for six fish species in a sample of lakes on the North Slope, Alaska. We used an occupancy modeling approach to provide estimates of detection probabilities for each method. Variation in gear- and species-specific detection probability was considerable. For example, detection probabilities for the fyke net ranged from 0.82 (SE = 0.05) for least cisco (Coregonus sardinella) to 0.04 (SE = 0.01) for slimy sculpin (Cottus cognatus). Detection probabilities were also affected by site-specific variables such as depth of the lake, year, day of sampling, and lake connection to a stream. With the exception of the dip net and shore minnow traps, each gear type provided the highest detection probability of at least one species. Results suggest that a multimethod approach may be most effective when attempting to sample the entire fish community of Arctic lakes. Detection probability estimates will be useful for designing optimal fish sampling and monitoring protocols in Arctic lakes.

  11. Embryo-induced transcriptome changes in bovine endometrium reveal species-specific and common molecular markers of uterine receptivity.

    PubMed

    Bauersachs, Stefan; Ulbrich, Susanne E; Gross, Karin; Schmidt, Susanne E M; Meyer, Heinrich H D; Wenigerkind, Hendrik; Vermehren, Margarete; Sinowatz, Fred; Blum, Helmut; Wolf, Eckhard

    2006-08-01

    The endometrium plays a central role among the reproductive tissues in the context of early embryo-maternal communication and pregnancy. This study investigated transcriptome profiles of endometrium samples from day 18 pregnant vs non-pregnant heifers to get insight into the molecular mechanisms involved in conditioning the endometrium for embryo attachment and implantation. Using a combination of subtracted cDNA libraries and cDNA array hybridisation, 109 mRNAs with at least twofold higher abundance in endometrium of pregnant animals and 70 mRNAs with higher levels in the control group were identified. Among the mRNAs with higher abundance in pregnant animals, at least 41 are already described as induced by interferons. In addition, transcript levels of many new candidate genes involved in the regulation of transcription, cell adhesion, modulation of the maternal immune system and endometrial remodelling were found to be increased. The different expression level was confirmed with real-time PCR for nine genes. Localisation of mRNA expression in the endometrium was shown by in situ hybridisation for AGRN, LGALS3BP, LGALS9, USP18, PARP12 and BST2. A comparison with similar studies in humans, mice, and revealed species-specific and common molecular markers of uterine receptivity.

  12. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute.

    PubMed

    Islam, Md Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

    2015-01-01

    MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other cr