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

  1. The role of the arachidonic acid cascade in the species-specific X-ray-induced inflammation of the rabbit eye

    SciTech Connect

    Bito, L.Z.; Klein, E.M.

    1982-05-01

    To identify the mediator(s) of the apparently species-specific X-ray-induced inflammation of the rabbit eye, inhibitors of the synthesis and/or release of known or putative mediators of ocular inflammation were administered prior to irradiation. The X-ray-induced ocular inflammation, particularly the rise in intraocular pressure, was found to be inhibited by intravenous pretreatment of rabbits with flurbiprofen, indomethacin, or imidazole (1, 10, and 100 mg/kg i.v., respectively), or by combined intravitreal and topical administration of flurbiprofen. Systemic, intravitreal, and/or topical pretreatment with prednisolone or disodium cromoglycate or the retrobulbar injection of ethyl alcohol or capsaicin failed to block the inflammatory response, whereas vitamin E apparently exerted some protective effect. These findings show that the X-ray-induced inflammation of the rabbit eye is mediated, at least in part, by prostaglandins (PGs) and/or related autacoids. In addition, these results suggest that the unique sensitivity of the rabbit eye to X-ray-induced inflammation is due either to the presence in this species of a unique or uniquely effective triggering mechanism for the release of PG precursors or to the greater sensitivity of this species to the ocular inflammatory effects of PGs. Thus the rabbit eye may provide a unique model for studying some aspects of arachidonic acid release or ocular PG effects, but extreme caution must be exercised in generalizing such findings to other species.

  2. X-ray-Induced Changes in the Expression of Inflammation-Related Genes in Human Peripheral Blood

    PubMed Central

    Wang, Ping; Guo, Fei; Han, Lin; Wang, Xi’ai; Li, Jie; Guo, Yan; LÜ, Yumin

    2014-01-01

    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. PMID:25350114

  3. 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.

  4. 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.

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

    PubMed

    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

  6. 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.

  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. 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

  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. Innovations in X-ray-induced electron emission spectroscopy (XIEES)

    SciTech Connect

    Pogrebitsky, K. Ju. Sharkov, M. D.

    2010-06-15

    Currently, a pressing need has arisen for controlling the local atomic and electron structure of materials irrespective of their aggregate state. Efficient approaches to the studies of short-range order are based on phenomena accompanied by interference of secondary electrons excited by primary X-ray radiation. The set of such approaches are commonly referred to as the X-ray absorption fine structure (XAFS) methods. In reality, the XAFS methods are based on the use of synchrotron radiation and applied to structural studies in two modes of measurements, transmission analysis and recording of secondary effects. Only two such effects-specifically, the X-ray fluorescence an d X-ray-induced electron emission effect-are commonly discussed. Access to synchrotron accelerators is problematic for most researchers, so a demand is created for designing laboratory systems that make direct access possible. Since the power of laboratory systems is much lower than that of synchrotrons, it is essential to use much more efficient detectors of secondary electrons. In addition, it is of interest to analyze energy characteristics with a high spatial resolution. Channel multipliers and multichannel boards are incapable of providing such a possibility. For this reason, an improved electron detector has been developed to analyze the photoemission effect in an accelerating field.

  12. Kinetic Modeling of the X-ray-induced Damage to a Metalloprotein

    PubMed Central

    Davis, Katherine M.; Kosheleva, Irina; Henning, Robert W.; Seidler, Gerald T.; Pushkar, Yulia

    2013-01-01

    It is well known that biological samples undergo x-ray-induced degradation. One of the fastest occurring x-ray-induced processes involves redox modifications (reduction or oxidation) of redox-active cofactors in proteins. Here we analyze room temperature data on the photoreduction of Mn ions in the oxygen evolving complex (OEC) of photosystem II, one of the most radiation damage sensitive proteins and a key constituent of natural photosynthesis in plants, green algae and cyanobacteria. Time-resolved x-ray emission spectroscopy with wavelength-dispersive detection was used to collect data on the progression of x-ray-induced damage. A kinetic model was developed to fit experimental results, and the rate constant for the reduction of OEC MnIII/IV ions by solvated electrons was determined. From this model, the possible kinetics of x-ray-induced damage at variety of experimental conditions, such as different rates of dose deposition as well as different excitation wavelengths, can be inferred. We observed a trend of increasing dosage threshold prior to the onset of x-ray-induced damage with increasing rates of damage deposition. This trend suggests that experimentation with higher rates of dose deposition is beneficial for measurements of biological samples sensitive to radiation damage, particularly at pink beam and x-ray FEL sources. PMID:23815809

  13. Retinoid protection against x-ray-induced chromatid damage in human peripheral blood lymphocytes.

    PubMed Central

    Sanford, K K; Parshad, R; Price, F M; Tarone, R E; Kraemer, K H

    1992-01-01

    Oral administration of isotretinoin (13-cis retinoic acid) was shown previously (Kraemer, K. H., J. J. DiGiovanna, A. N. Moshell, R. E. Tarone, and G. L. Peck. 1988. N. Engl. J. Med. 318:1633-1637) to reduce the frequency of skin cancers in xeroderma pigmentosum (XP) patients. The mechanism of protection was unclear. In the present study, x-ray-induced chromatid damage in PHA-stimulated blood lymphocytes from five XP patients receiving isotretinoin was approximately half that in blood samples from the same patients before or subsequent to treatment. The x-ray-induced chromatid damage in blood lymphocytes from a normal control was reduced significantly by cocultivation with blood or plasma from an XP patient receiving isotretinoin or by addition of 10(-6) M isotretinoin to cultures 1 h before x-irradiation. A similar reduction in x-ray-induced chromatid damage was reported previously by adding to the culture medium, mannitol, a scavenger of the free hydroxyl radical, or catalase, which decomposes hydrogen peroxide; both of these products are generated during ionizing radiation. The present observations suggest that isotretinoin acts as a scavenger of such radiation products, thereby providing protection against x-ray-induced chromatid damage. PMID:1430230

  14. 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.

  15. Are there x-ray induced signature mutations in human cells?

    SciTech Connect

    Nelson, S.L.; Giver, C.R.; Grosovsky, A.J.

    1994-12-31

    Investigations of mutational spectra generally have two primary objectives: identification of mutagen specific hallmark mutations, and insight into mutagenic mechanisms. In order to address these two crucial issues we have examined the spectrum of 116 x-ray induced, and 78 spontaneous, HPRT{sup -} mutants derived from the human B lymphoblastoid cell line TK6. Multiplex PCR analysis demonstrated that the overall representation of large deletions was not significantly different in the 2 spectra, although highly significant differences were observed for specific deletion types. Total gene deletions represented 41/78 (.53) of x-ray induced, but only 7/43 (.16) of spontaneous, deletions (p < .0001). In contrast, 5{prime} terminal deletions were significantly more common among spontaneous (17/43, .40) than x-ray induced (13/78, .17) large deletions (p=.0079). Chromosomal scale investigation of x-ray induced and spontaneous hprt total deletion mutants was also performed using cytogenetic examination, and X-linked PCR probes. The types of point mutations induced by x-ray exposure were very diverse, including all classes of transitions and transversions, tandem base substitutions, frameshifts, and a deletion/insertion compound mutation. Compared to spontaneous data, radiation induced point mutations exhibited a significantly reduced number of transitions, and an increased representation of small deletions. Small deletions were uniformly surrounded by direct sequence repeats. The distribution of x-ray induced point mutations was characterized by a cluster of 8 mutants within a 30 base region of exon 8. Thirteen HPRT{sup -} point mutants exhibited aberrant splicing, 4 of which were attributable to coding sequence alterations within exons 4 and 8. These results suggest that it may be possible to identify hallmark mutations associated with x-ray exposure of human cells.

  16. Pump-probe spectrometer for measuring x-ray induced strain.

    PubMed

    Loether, A; Adams, B W; DiCharia, A; Gao, Y; Henning, R; Walko, D A; DeCamp, M F

    2016-05-01

    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. We present a proof-of-concept experiment which directly measures x-ray induced crystalline lattice strain. PMID:27128053

  17. 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.

  18. 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.

  19. 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.

  20. Constraining X-ray-Induced Photoevaporation of Protoplanetary Disks Orbiting Low-Mass Stars

    NASA Astrophysics Data System (ADS)

    Punzi, Kristina M.; Kastner, Joel H.; Rodriguez, David; Principe, David A.; Vican, Laura

    2016-01-01

    Low-mass, pre-main sequence stars possess intense high-energy radiation fields as a result of their strong stellar magnetic activity. This stellar UV and X-ray radiation may have a profound impact on the lifetimes of protoplanetary disks. We aim to constrain the X-ray-induced photoevaporation rates of protoplanetary disks orbiting low-mass stars by analyzing serendipitous XMM-Newton and Chandra X-ray observations of candidate nearby (D < 100 pc), young (age < 100 Myr) M stars identified in the GALEX Nearby Young-Star Survey (GALNYSS).

  1. 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

  2. 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.

  3. X-ray-induced chromosome aberrations in Down lymphocytes: an explanation of their increased sensitivity

    SciTech Connect

    Preston, R.J.

    1981-01-01

    Unstimulated lymphocytes from individuals with Down Syndrome (trisomy 21) are more sensitive to the induction of dicentric and ring aberrations by X rays than normal lymphocytes. Several explanations involving the more rapid rejoining of X-ray--induced lesions in Down cells have been offered. It is shown here that the repair of the DNA damage converted into chromosome aberrations is more rapid in Down cells than normal cells. This more rapid repair results in a higher probability of producing chromosomes aberrations, and hence higher aberration frequencies in Down than normal cells.

  4. X-ray-induced chromosome aberrations in Down lymphocytes: an explanation of their increased sensitivity

    SciTech Connect

    Preston, R.J.

    1981-01-01

    Unstimulated lymphocytes from individuals with Down Syndrome (trisomy 21) are more sensitive to the induction of dicentric and ring aberrations by X rays than normal lymphocytes. Several explanations involving the more rapid rejoining of X-ray-induced lesions in Down cells have been offered. It is shown here that the repair of the DNA damage converted into chromosome aberrations is more rapid in Down cells than normal cells. This more rapid repair results in a higher probability of producing chromosome aberrations, and hence higher aberration frequencies in Down than normal cells.

  5. Roles of NAD+, PARP-1, and Sirtuins in Cell Death, Ischemic Brain Injury, and Synchrotron Radiation X-Ray-Induced Tissue Injury

    PubMed Central

    2013-01-01

    NAD+ plays crucial roles in a variety of biological processes including energy metabolism, aging, and calcium homeostasis. Multiple studies have also shown that NAD+ administration can profoundly decrease oxidative cell death and ischemic brain injury. A number of recent studies have further indicated that NAD+ administration can decrease ischemic brain damage, traumatic brain damage and synchrotron radiation X-ray-induced tissue injury by such mechanisms as inhibiting inflammation, decreasing autophagy, and reducing DNA damage. Our latest study that applies nano-particles as a NAD+ carrier has also provided first direct evidence demonstrating a key role of NAD+ depletion in oxidative stress-induced ATP depletion. Poly(ADP-ribose) polymerase-1 (PARP-1) and sirtuins are key NAD+-consuming enzymes that mediate multiple biological processes. Recent studies have provided new information regarding PARP-1 and sirtuins in cell death, ischemic brain damage and synchrotron radiation X-ray-induced tissue damage. These findings have collectively supported the hypothesis that NAD+ metabolism, PARP-1 and sirtuins play fundamental roles in oxidative stress-induced cell death, ischemic brain injury, and radiation injury. The findings have also supported “the Central Regulatory Network Hypothesis”, which proposes that a fundamental network that consists of ATP, NAD+ and Ca2+ as its key components is the essential network regulating various biological processes. PMID:24386592

  6. X-ray induced stellar mass loss near active galactic nuclei

    NASA Technical Reports Server (NTRS)

    Voit, G. Mark; Shull, J. Michael

    1988-01-01

    The effects of UV and X-ray radiation on stars in active galactic nuclei (AGN) are critically evaluated. Mass loss rates in X-ray-induced winds are evaluated for realistic red giant models, and the effects of the ablation of stellar envelopes by radiation pressure are considered. The importance of X-ray-induced mass loss in the standard quasar model is evaluated and whether it can provide a source of accretion fuel or emission-line clouds is discussed. It is concluded that thermal winds driven by X-ray heating are a minor total supply of mass to AGN, but that thermal plus line-driven winds and stellar ablation may increase the mass loss and improve the chances for supplying a fraction of the necessary mass supply to the central object. It is speculated that when steady winds are inefficient, complex time-dependent processes due to X-ray energy injection deep into a stellar atmosphere could still release significant mass from stars.

  7. 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.

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    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 Mg2+ 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.

  11. X-ray Induced Luminescence Spectroscopy of Samarium Doped Barium Sulfate Prepared by Sintering Method

    NASA Astrophysics Data System (ADS)

    Kumeda, T.; Maeda, K.; Shirano, Y.; Fujiwara, K.; Sakai, K.; Ikari, T.

    2015-06-01

    X-ray induced luminescence (XL) properties of phosphor materials made of samarium doped barium sulfate have been investigated. The samples were prepared by sintering method heated at 900-1250 °C for 3 hours in air from the mixture of BaSO4 and Sm2O3. The concentration of Sm were prepared from 0.01-6 at.%. In as-prepared sample, the Sm3+ was detected by photoluminescence (PL). The PL intensity is maximum about 2 at.% with Sm, and then starts decreasing. The PL intensity showed concentration quenching. The XL observed Sm2+ and Sm3+ ions. The XL was shown from the sample sintered up to 1200 °C. The XL intensity increased with Sm concentration up to 1 at.%. The intensity was almost constant larger than 1 at.% Sm. These concentration dependences is different since the X-ray energy absorbed to the host material at once, and the energy transferred to both Sm3+ and Sm2+ ions. Sm doped BaSO4 is found a host for XL phosphor materials.

  12. 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.

  13. 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)

  14. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples

    PubMed Central

    George, Graham N.; Pickering, Ingrid J.; Pushie, M. Jake; Nienaber, Kurt; Hackett, Mark J.; Ascone, Isabella; Hedman, Britt; Hodgson, Keith O.; Aitken, Jade B.; Levina, Aviva; Glover, Christopher; Lay, Peter A.

    2012-01-01

    As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts. PMID:23093745

  15. X-ray induced dimerization of cinnamic acid: Time-resolved inelastic X-ray scattering study

    PubMed Central

    Inkinen, Juho; Niskanen, Johannes; Talka, Tuomas; Sahle, Christoph J.; Müller, Harald; Khriachtchev, Leonid; Hashemi, Javad; Akbari, Ali; Hakala, Mikko; Huotari, Simo

    2015-01-01

    A classic example of solid-state topochemical reactions is the ultraviolet-light induced photodimerization of α-trans-cinnamic acid (CA). Here, we report the first observation of an X-ray-induced dimerization of CA and monitor it in situ using nonresonant inelastic X-ray scattering spectroscopy (NRIXS). The time-evolution of the carbon core-electron excitation spectra shows the effects of two X-ray induced reactions: dimerization on a short time-scale and disintegration on a long time-scale. We used spectrum simulations of CA and its dimerization product, α-truxillic acid (TA), to gain insight into the dimerization effects. From the time-resolved spectra, we extracted component spectra and time-dependent weights corresponding to CA and TA. The results suggest that the X-ray induced dimerization proceeds homogeneously in contrast to the dimerization induced by ultraviolet light. We also utilized the ability of NRIXS for direct tomography with chemical-bond contrast to image the spatial progress of the reactions in the sample crystal. Our work paves the way for other time-resolved studies on chemical reactions using inelastic X-ray scattering. PMID:26568420

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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 × 1010 cm-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. 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. PMID:26702498

  20. X-ray-induced P-selectin localization to the lumen of tumor blood vessels.

    PubMed

    Hallahan, D E; Staba-Hogan, M J; Virudachalam, S; Kolchinsky, A

    1998-11-15

    P-selectin is a cell adhesion molecule that is sequestered in Weibel-Palade storage reservoirs within the vascular endothelium and alpha granules in platelets. P-selectin is rapidly translocated to the vascular lumen after tissue injury to initiate the adhesion and activation of platelets and leukocytes. We studied the histological pattern of P-selectin expression in irradiated tumor blood vessels. We observed that P-selectin was localized within the endothelium of tumor vessels prior to treatment. At 1-6 h following irradiation, P-selectin was mobilized to the lumen of blood vessels. To determine whether radiation-induced vascular lumen localization of P-selectin was tumor type specific or species specific, we studied tumors in rats, C3H mice, C57BL6 mice, and nude mice. P-selectin localization to the vascular lumen was present in all tumors and all species studied. Irradiated intracranial gliomas showed P-selectin localization to the vascular lumen within 1 h, whereas blood vessels in normal brain showed no P-selectin staining in the endothelium and no localization to the irradiated vascular lumen. Radiation-induced P-selectin localization to the vascular lumen increased in time-dependent manner, until 24 h after irradiation. P-selectin in platelets may account for the time-dependent increase in staining within the vascular lumen after irradiation. We therefore used immunohistochemistry for platelet antigen GP-IIIa to differentiate between endothelial and platelet localization of P-selectin. We found that GP-IIIa staining was not present at 1 h after irradiation, but it increased at 6 and 24 h. P-selectin localization to the vascular lumen at 6-24 h was, in part, associated with platelet aggregation. These findings indicate that radiation-induced P-selectin staining in the vascular lumen of neoplasms is associated with aggregation of platelets. Radiation-induced localization of P-selectin to the vascular lumen is specific to the microvasculature of malignant

  1. 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.

  2. 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).

  3. Persistence of X-ray-induced chromosomal rearrangements in long-term cultures of human diploid fibroblasts

    SciTech Connect

    Kano, Y.; Little, J.B.

    1984-09-01

    As part of a long-term study of mechanisms of human cell neoplastic transformation, the authors have examined the change in the frequencies of X-ray-induced chromosome rearrangements in density-inhibited human foreskin fibroblasts as a function of subculture time. In nonproliferating cells, the frequency of chromosomal aberrations declined within 24 to 48 hr but still remained at a relatively high level up to 43 days after irradiation. Aberrations disappeared rapidly, however, when the cells were allowed to proliferate, indicating that these lesions are lethal to dividing cells. The frequency of induced translocations, as determined by analysis of G-banded karyotypes, was dose dependent and remained stable up to 20 mean population doublings after irradiation. When subculture of density-inhibited cultures was delayed for 4 hr after irradiation (confluent holding), the frequency of chromosomal aberrations in the first mitosis declined, whereas the translocation frequencies at later passage were elevated as compared with cells subcultured immediately. This correlates with the reported increase in the frequency of transformation under similar conditions. These findings support the hypothesis that chromosomal rearrangements induced by DNA damage may be involved in the initiation of cancer.

  4. 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.

  5. X-ray induced fluorescence measurement of segregation in a DyI3-Hg metal-halide lamp.

    SciTech Connect

    Nimalasuriya , T.; Curry, J. J.; Sansonetti, C. J.; Ridderhof, E. J.; Shastri, S. D.; Filkweert, A. J.; Stoffels, W. W.; Haverlag, M.; van der Mullen, J. J.; Eindhoven Univ. of Technology; NIST

    2007-05-07

    Segregation of elemental Dy in a DyI{sub 3}-Hg metal-halide high-intensity discharge lamp has been observed with x-ray induced fluorescence. Significant radial and axial Dy segregation are seen, with the axial segregation characterized by a Fischer parameter value of {lambda} = 0.215 {+-} 0.002 mm{sup -1}. This is within 7% of the value ({lambda} = 0.20 {+-} 0.01 mm{sup -1}) obtained by Flikweert et al based on laser absorption by neutral Dy atoms. Elemental I is seen to exhibit considerably less axial and radial segregation. Some aspects of the observed radial segregation are compatible with a simplified fluid picture describing two main transition regions in the radial coordinate. The first transition occurs in the region where DyI{sub 3} molecules are in equilibrium with neutral Dy atoms. The second transition occurs where neutral Dy atoms are in equilibrium with ionized Dy. These measurements are part of a larger study on segregation in metal-halide lamps under a variety of conditions.

  6. 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.

  7. 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.

  8. 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

  9. Rejoining of x-ray induced chromosome breaks in human cells and its relationship to cellular repair

    SciTech Connect

    Cornforth, M.N.

    1985-01-01

    A method was developed to improve the resolution for measuring breaks produced in interphase chromosomes by X-rays following the induction of premature chromosome condensation (PCC). It is based on the principle of 5-BrdU incorporation into the DNA of HeLa mitotic cells, which act as inducers of PCC when they are fused to diploid human fibroblasts. After a modified Fluorescence Plus Giemsa (FPG) protocol, the PCC stain intensely, while the mitotic inducer chromosomes stain faintly. The dose response for density inhibited (G/sub 0/) human cells was linear from 10.9 to 600 rad, with a slope of 0.06 breaks per cell per rad. Upon incubation at 37/sup 0/C, half of the breaks disappeared in 2 hours. Following a dose of 600 rad the initial rate of break rejoining mirrored the rate of increase in survival from post-irradiation incubation, due to the repair of potentially lethal damage (PLD). The X-ray induced PCC rejoining characteristics from two ataxia telangiectasia (A-T) cell lines were compared to profiles obtained with normal cells. Both normal and A-T cells apparently sustained the same initial level of radiation damage, and both cell types rejoined breaks at the same rate. However, while normal cells eventually rejoined all but about 5% of the breaks produced by 600 rad, the A-T lines were left with 5-6 times the level of residual damage. These experiments demonstrate that progression of cells into S phase is not a necessary condition for the measured frequency of chromosome fragments observed in X-irradiated A-T cells.

  10. MCI extraction from Turkish galls played protective roles against X-ray-induced damage in AHH-1 cells

    PubMed Central

    Yang, Jianhua; Zhou, Yan; Liu, Huibin; Wang, Jianhua; Hu, Junping

    2015-01-01

    Objective: To investigate the protective effects of MCI extract from Turkish galls against apoptosis induced by X-ray radiation in the AHH-1. Methods: The cells were divided into: control group; X-ray radiation group; MCI group, in which the confluent cells were preincubated with 5 μg/ml MCI for 2 h followed by radiation. For the radiation, cells preincubated with MCI were exposed to X-ray beams with a dose of 8 Gy in total. Cell viability, apoptosis and intracellular alteration of redox were monitored by MTT and flow cytometry. Results: Compared with radiation group, the number of cells arrested at the G0/G1 phase was significantly reduced in MCI group (P < 0.05). X-ray radiation induces remarkable apoptosis in AHH-1, which was reversed by MCI. Compared with the radiation group, the generation of intracellular reactive oxygen species (ROS) was abrogated by pre-incubation with MCI (P < 0.05). In addition, the up-regulation of procaspase-3 induced by radiation was reversed by MCI. Radiation could induce up-regulation of Bax and down-regulation of Bcl-2; however, it is reversed completely after administration of MCI. Further, the enhanced expression of ERK and JNK induced by radiation was reversed by MCI. Conclusions: MCI extract from Turkish galls played protective effects on the X-ray induced damage through enhancing the scavenging activity of ROS, decreasing Bax/Bcl-2 ratio and the down-regulating the activity of procaspase-3, as well as modulating the mitogen-activated protein kinase (MAPK) signaling pathways. PMID:26339380

  11. 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.

  12. 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.

  13. 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.

  14. Inflammation: Species-specific TLR signalling -- insight into human disease.

    PubMed

    Perkins, Darren J; Vogel, Stefanie N

    2016-04-01

    The selective utilization of IRAK kinases, which are thought to be recruited to MyD88 to form the ‘Myddosome’, has been shown to differ substantially in mouse and human cells. This finding has important implications for the development of therapeutics for inflammatory and autoimmune disorders associated with Toll-like receptors. PMID:27006311

  15. Evidence for an indirect effect of radiation on mammalian chromosomes. III. UV- and x-ray-induced sister chromatid exchanges in heterokaryons

    SciTech Connect

    Graves, J.A.; Kellow, G.N.

    1983-04-01

    The hypothesis that chromosomes may be damaged indirectly by radiation was examined by assaying sister chromatid exchange, (SCE) frequency in heterokaryons between irradiated and unirradiated mouse and Chinese hamster cells. One cell line was UV or x irradiated, then fused to unirradiated BrdU-labeled cells of the other line; SCEs in the unirradiated set were scored in heterokaryons. A dose-dependent increase was consistently observed; the magnitude of which suggested that 25% of UV-induced and up to 60% of x-ray-induced SCEs are indirectly induced. Medium transfer experiments, cell mixing, and fusion with irradiated chick erythrocyte ghosts suggested that unirradiated chromosomes in heterokaryons are damaged by a stable, nondiffusible cytoplasmic component contributed by the irradiated cell.

  16. Species-specific beaked whale echolocation signals.

    PubMed

    Baumann-Pickering, Simone; McDonald, Mark A; Simonis, Anne E; Solsona Berga, Alba; Merkens, Karlina P B; Oleson, Erin M; Roch, Marie A; Wiggins, Sean M; Rankin, Shannon; Yack, Tina M; Hildebrand, John A

    2013-09-01

    Beaked whale echolocation signals are mostly frequency-modulated (FM) upsweep pulses and appear to be species specific. Evolutionary processes of niche separation may have driven differentiation of beaked whale signals used for spatial orientation and foraging. FM pulses of eight species of beaked whales were identified, as well as five distinct pulse types of unknown species, but presumed to be from beaked whales. Current evidence suggests these five distinct but unidentified FM pulse types are also species-specific and are each produced by a separate species. There may be a relationship between adult body length and center frequency with smaller whales producing higher frequency signals. This could be due to anatomical and physiological restraints or it could be an evolutionary adaption for detection of smaller prey for smaller whales with higher resolution using higher frequencies. The disadvantage of higher frequencies is a shorter detection range. Whales echolocating with the highest frequencies, or broadband, likely lower source level signals also use a higher repetition rate, which might compensate for the shorter detection range. Habitat modeling with acoustic detections should give further insights into how niches and prey may have shaped species-specific FM pulse types. PMID:23967959

  17. 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.

  18. Continuous-time photon-stimulated desorption spectroscopy studies on soft x-ray-induced reactions of CF3Br adsorbed on Si(111)-7×7.

    PubMed

    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(3)Br molecules adsorbed on Si(111)-7×7 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(3)Br-covered surfaces show the production of surface SiF species, while those from the high-CF(3)Br-covered surfaces depict the formation of surface SiF, SiF(2), and SiF(3) species. The photolysis cross section of the submonolayer CF(3)Br-covered surface is determined as ∼4.3×10(-18) cm(2). A comparison with the results on CF(3)Cl/Si(111)-7×7 surface is discussed. PMID:22047260

  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

    PubMed Central

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

    2013-01-01

    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. PMID:24311579

  20. The rate of X-ray-induced DNA double-strand break repair in the embryonic mouse brain is unaffected by exposure to 50 Hz magnetic fields

    PubMed Central

    Woodbine, Lisa; Haines, Jackie; Coster, Margaret; Barazzuol, Lara; Ainsbury, Elizabeth; Sienkiewicz, Zenon; Jeggo, Penny

    2015-01-01

    Abstract Purpose: Following in utero exposure to low dose radiation (10–200 mGy), we recently observed a linear induction of DNA double-strand breaks (DSB) and activation of apoptosis in the embryonic neuronal stem/progenitor cell compartment. No significant induction of DSB or apoptosis was observed following exposure to magnetic fields (MF). In the present study, we exploited this in vivo system to examine whether exposure to MF before and after exposure to 100 mGy X-rays impacts upon DSB repair rates. Materials and methods: 53BP1 foci were quantified following combined exposure to radiation and MF in the embryonic neuronal stem/progenitor cell compartment. Embryos were exposed in utero to 50 Hz MF at 300 μT for 3 h before and up to 9 h after exposure to 100 mGy X-rays. Controls included embryos exposed to MF or X-rays alone plus sham exposures. Results: Exposure to MF before and after 100 mGy X-rays did not impact upon the rate of DSB repair in the embryonic neuronal stem cell compartment compared to repair rates following radiation exposure alone. Conclusions: We conclude that in this sensitive system MF do not exert any significant level of DNA damage and do not impede the repair of X-ray induced damage. PMID:25786477

  1. X-ray-induced photoconductivity in YBa{sub 2}Cu{sub 3}O{sub 6} between 70 and 300 K

    SciTech Connect

    Jimenez de Castro, M.; Alvarez Rivas, J.L.

    1996-04-01

    The x-ray-induced photoconductivity in bulk ceramic samples of YBa{sub 2}Cu{sub 3}O{sub 6+{ital x}}, with {ital x}{approx_equal}0, at temperatures between 70 and 300 K has been studied. In addition to a prompt current, which occurs at the beginning of the irradiation, the photocurrent exhibits a saturation growth stage up to values quite larger than the prompt. The amplitude of the saturating stage depends on dose and dose rate. The photocurrent level also increases with the irradiation temperature, but the fractional change in electric carriers decreases as the irradiation temperature increases. It has been found that after irradiation the samples show a persistent photoconductivity (PPC). The isothermal decay curves at the irradiation temperature of the PPC show that its thermal stability increases for an increase of either the irradiation dose or the irradiation temperature. Above 200 K the thermal stability decreases and the sample completely recovers after several hours at room temperature. The possible relation between this PPC and the well known PPC induced by laser illumination in thin films of this material is discussed. {copyright} {ital 1996 The American Physical Society.}

  2. 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.

  3. X-ray induced Sm3+ to Sm2+ conversion in fluorophosphate and fluoroaluminate glasses for the monitoring of high-doses in microbeam radiation therapy

    NASA Astrophysics Data System (ADS)

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

    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 Sm3+ to the divalent form Sm2+. Both types of glasses show similar conversion rates and may be used as a linear sensor up to ˜150 Gy and as a nonlinear sensor up to ˜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 Tg while annealing at TA < Tg enhances the Sm conversion. This enhancement is explained by a thermally stimulated relaxation of host glass ionic matrix surrounding x-ray induced Sm2+ ions. In addition, some of the Sm3+-doped glasses were codoped with Eu2+-ions but the results show that there is no marked improvement in the conversion efficiency by the introduction of Eu2+.

  4. 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.

  5. X-ray-induced specific-locus mutations in the ad-3 region of two-component heterokaryons of Neurospora crassa. X. Heterozygous effects of multilocus deletion mutations of genotype ad-3A or ad-3B.

    PubMed

    de Serres, F J; Overton, L K; Sadler, B M

    1992-05-01

    Previous studies on X-ray-induced irreparable adenine-3 mutations (designated [ad-3]IR), induced in heterokaryon 12 of Neurospora crassa, demonstrated that they were not recessive and exhibited heterozygous effects in terms of markedly reduced linear growth rates (de Serres, 1965). Complementation tests with a series of tester strains carrying multilocus deletion mutations in the ad-3 and immediately adjacent genetic regions demonstrated that X-ray-induced irreparable mutations map, in the main part, as a series of overlapping multilocus deletion mutations that extend both proximally and distally into the immediately adjacent genetic regions, as well as into the 'X' region (a region of unknown, but essential function) between ad-3A and ad-3B (de Serres, 1968, 1989). Further studies (de Serres and Miller, 1988) have shown that the heterozygous effects of multilocus deletion mutations in the ad-3 region can be modified genetically and biochemically. In the present paper, the heterozygous effects of X-ray-induced multilocus deletion mutations of genotype ad-3A or ad-3B, induced in heterokaryon 12 (Webber and de Serres, 1965; de Serres, 1988, 1989), have been determined. These data show that 57.7% (15/26) of X-ray-induced multilocus deletion mutations covering the ad-3A locus have heterozygous effects, in terms of reduced linear growth rates, in forced dikaryons with a gene/point mutant at the ad-3B locus and 80.0% (20/25) in forced dikaryons with a multilocus deletion mutation covering the ad-3B locus. In addition, 35.1% (20/57) of X-ray-induced multilocus deletion mutations covering the ad-3B locus have heterozygous effects in forced dikaryons with a gene/point mutant at the ad-3A locus, and 100.0% (35/35) in forced dikaryons with a multilocus deletion mutation covering the ad-3A locus. These results demonstrate that the dominant or recessive characteristics of X-ray-induced specific-locus mutations resulting from multilocus deletion mutations are allele specific

  6. Continuous-time core-level photon-stimulated desorption spectroscopy for monitoring soft x-ray-induced reactions of molecules adsorbed on a single-crystal surface

    SciTech Connect

    Chou, L.-C.; Wen, C.-R.

    2006-05-15

    Continuous-time core-level photon-stimulated desorption (PSD) spectroscopy was proposed for monitoring the soft x-ray-induced reactions of molecules adsorbed on a single-crystal surface. Monochromatic synchrotron radiation was used as a soft x-ray light source in the photon-induced reactions of CF{sub 3}Cl adsorbed on a Si(111)-7x7 surface at 30 K and also as a probe for studying the produced fluorination states of the bonding surface Si atom in the positive-ion PSD spectroscopy. The F{sup +} PSD spectrum was obtained by monitoring the F{sup +} signal as a function of incident photon energy near the Si(2p) edge (98-110 eV). Sequential F{sup +} PSD spectra were measured as a function of photon exposure at four adsorbate coverages (the first dose=0.3x10{sup 15} molecules/cm{sup 2}, the second dose=0.8x10{sup 15} molecules/cm{sup 2}, the third dose=2.2x10{sup 15} molecules/cm{sup 2}, and the fourth dose=3.2x10{sup 15} molecules/cm{sup 2}). For the first and second CF{sub 3}Cl-dosed surfaces, the sequential F{sup +} PSD spectra show the variation of their shapes with photon exposure and indicate the formation of surface SiF species. The sequential F{sup +} PSD spectra for the third and fourth CF{sub 3}Cl-dosed surfaces also show the variation of their shapes with photon exposure and depict the production of surface SiF and SiF{sub 3} species.

  7. 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. PMID:26627648

  8. Organ- and species-specific biological activity of rosmarinic acid.

    PubMed

    Iswandana, R; Pham, B T; van Haaften, W T; Luangmonkong, T; Oosterhuis, D; Mutsaers, H A M; Olinga, P

    2016-04-01

    Rosmarinic acid (RA), a compound found in several plant species, has beneficial properties, including anti-inflammatory and antibacterial effects. We investigated the toxicity, anti-inflammatory, and antifibrotic effects of RA using precision-cut liver slices (PCLS) and precision-cut intestinal slices (PCIS) prepared from human, mouse, and rat tissue. PCLS and PCIS were cultured up to 48h in the absence or presence of RA. Gene expression of the inflammatory markers: IL-6, IL-8/CXCL1/KC, and IL-1β, as well as the fibrosis markers: pro-collagen 1a1, heat shock protein 47, α-smooth muscle actin, fibronectin (Fn2) and plasminogen activator inhibitor-1 (PAI-1) were evaluated by qPCR. RA was only toxic in murine PCIS. RA failed to mitigate the inflammatory response in most models, while it clearly reduced IL-6 and CXCL1/KC gene expression in murine PCIS at non-toxic concentrations. With regard to fibrosis, RA decreased the gene levels of Fn2 and PAI-1 in murine PCLS, and Fn2 in murine PCIS. Yet, no effect was observed on the gene expression of fibrosis markers in human and rat PCIS. In conclusion, we observed clear organ- and species-specific effects of RA. RA had little influence on inflammation. However, our study further establishes RA as a potential candidate for the treatment of liver fibrosis. PMID:26804033

  9. Repair of Radiation-Induced Damage in Escherichia coli II. Effect of rec and uvr Mutations on Radiosensitivity, and Repair of X-Ray-Induced Single-Strand Breaks in Deoxyribonucleic Acid1

    PubMed Central

    Kapp, Daniel S.; Smith, Kendric C.

    1970-01-01

    Strains of Escherichia coli K-12 mutant in the genes controlling excision repair (uvr) and genetic recombination (rec) have been studied with reference to their radiosensitivity and their ability to repair X-ray-induced single-strand breaks in deoxyribonucleic acid (DNA). Mutations in the rec genes appreciably increase the radiosensitivity of E. coli K-12, whereas uvr mutations produce little if any increase in radiosensitivity. For a given dose of X-rays, the yield of single-strand breaks has been shown by alkaline sucrose gradient studies to be largely independent of the presence of rec or uvr mutations. The rec+ cells (including those carrying the uvrB5 mutation) could efficiently rejoin X-ray-induced single-strand breaks in DNA, whereas recA56 mutants could not repair these breaks to any great extent. The recB21 and recC22 mutants showed some indication of repair capacity. From these studies, it is concluded that a correlation exists between the inability to repair single-strand breaks and the radiosensitivity of the rec mutants of E. coli K-12. This suggests that unrepaired single-strand breaks may be lethal lesions in E. coli. PMID:4912530

  10. Species-specific polyamines from diatoms control silica morphology

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

    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.

  11. 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.

  12. 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+}.

  13. Species-specific accumulation of interspersed sequences in genus Saccharum.

    PubMed

    Nakayama, Shigeki

    2004-12-01

    The genus Saccharum consists of two wild and four cultivated species. Novel interspersed sequences were isolated from cultivated sugar cane S. officinarum. These sequences were accumulated in all four cultivated species and their wild ancestral species S. robustum, but were not detected in the other wild species S. spontaneum and the relative Erianthus arundinaceus. The species-specific accumulation of interspersed sequences would correlate to the domestication of sugar canes. PMID:15729004

  14. 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

  15. 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. PMID:24256192

  16. 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

  17. 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.

  18. 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. PMID:27130543

  19. 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. PMID:25404531

  20. 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. PMID:25872445

  1. Corynebacterium endocarditis species-specific risk factors and outcomes

    PubMed Central

    Belmares, Jaime; Detterline, Stephanie; Pak, Janet B; Parada, Jorge P

    2007-01-01

    Background Corynebacterium species are recognized as uncommon agents of endocarditis, but little is known regarding species-specific risk factors and outcomes in Corynebacterium endocarditis. Methods Case report and Medline search of English language journals for cases of Corynebacterium endocarditis. Inclusion criteria required that cases be identified as endocarditis, having persistent Corynebacterium bacteremia, murmurs described by the authors as identifying the affected valve, or vegetations found by echocardiography or in surgical or autopsy specimens. Cases also required patient-specific information on risk factors and outcomes (age, gender, prior prosthetic valve, other prior nosocomial risk factors (infected valve, involvement of native versus prosthetic valve, need for valve replacement, and death) to be included in the analysis. Publications of Corynebacterium endocarditis which reported aggregate data were excluded. Univariate analysis was conducted with chi-square and t-tests, as appropriate, with p = 0.05 considered significant. Results 129 cases of Corynebacterium endocarditis involving nine species met inclusion criteria. Corynebacterium endocarditis typically infects the left heart of adult males and nearly one third of patients have underlying valvular disease. One quarter of patients required valve replacement and one half of patients died. Toxigenic C. diphtheriae is associated with pediatric infections (p < 0.001). Only C. amycolatum has a predilection for women (p = 0.024), while C. pseudodiphtheriticum infections are most frequent in men (p = 0.023). C. striatum, C. jeikeium and C. hemolyticum are associated with nosocomial risk factors (p < 0.001, 0.028, and 0.024, respectively). No species was found to have a predilection for any particular heart valve. C. pseudodiphtheriticum is associated with a previous prosthetic valve replacement (p = 0.004). C. jeikeium infections are more likely to require valve replacement (p = 0.026). Infections

  2. Species-Specific Identification of Human Adenoviruses in Sewage.

    PubMed

    Wieczorek, Magdalena; Krzysztoszek, Arleta; Witek, Agnieszka

    2015-01-01

    Human adenovirus (HAdV) diversity in sewage was assessed by species-specific molecular methods. Samples of raw sewage were collected in 14 sewage disposal systems from January to December 2011, in Poland. HAdVs were detected in 92.1% of the analysed sewage samples and was significantly higher at cities of over 100 000 inhabitants. HAdV DNA was detected in sewage during all seasons. The most abundant species identified were HAdV-F (average 89.6%) and -A (average 19.6%), which are associated with intestine infections. Adenoviruses from B species were not detected. The result of the present study demonstrate that human adenoviruses are consistently present in sewage in Poland, demonstrating the importance of an adequate treatment before the disposal in the environment. Multiple HAdV species identified in raw sewage provide new information about HAdV circulation in the Polish population. PMID:26094312

  3. 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

  4. Fimbriae and determination of host species specificity of Bordetella bronchiseptica.

    PubMed Central

    Burns, E H; Norman, J M; Hatcher, M D; Bemis, D A

    1993-01-01

    A monoclonal antibody, designated CF8 and prepared against fimbrial protein enrichments of Bordetella bronchiseptica 110H, was determined by immunogold electron microscopy to bind to some but not all fimbrial filaments on intact bacterial cells. Comparison of the reactivity of this antibody with that of monoclonal antibody BPF2, which is specific for Bordetella pertussis serotype 2 fimbriae, indicated that CF8 recognizes an epitope similar to that recognized by BPF2. By Western blot (immunoblot), it was determined that monoclonal antibody CF8 does not react with proteins denatured by treatment with sodium dodecyl sulfate and beta-mercaptoethanol and by boiling for 5 min but that it does recognize fimbrial proteins in their native, nondenatured state. This antibody was used to compare fimbriae between strains of B. bronchiseptica isolated from different species. Strains from pigs, dogs, guinea pigs, and four other species were compared by an enzyme immunoassay. Strains isolated from pigs were found to express significantly more CF8-reactive and B. pertussis serotype 2 cross-reactive fimbriae than strains isolated from guinea pigs. Strains from dogs were more variable in reactivity than those from pigs or guinea pigs. The reactivity with antifimbrial monoclonal antibody CF8 did not correlate with enzyme electromorphotype but did correlate with the host species, suggesting a role for fimbriae in the determination of host species specificity of B. bronchiseptica. Images PMID:8102377

  5. 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.

  6. 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. PMID:24771948

  7. 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. PMID:15123173

  8. 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

  9. [The species-specific feeding of rabbits in pet husbandry].

    PubMed

    Kamphues, J

    2001-03-01

    To meet nutrient demands as well as the species specific requirements of an animal it is absolutely necessary to know its nutrition physiology (KAMPHUES et al. 1999). Characteristics of the nutrition physiology of rabbits include the anatomy of the intestinal tract (i.e. the teeth, the size of gut as well as the small intestine and colon), the special ingesting behaviour (selection, intensity of gnawing and chewing) and digestive processes within the intestinal tract (digestion by own as well as by microbial enzymes, processes of separation (producing soft faeces) and the excretion of digested or undigested nutrients (excretion via faeces or kidneys, quality of faeces). In feeding pet rabbits it has to be recommended, that these species do not need concentrates, but ingredients with higher crude fiber contents due to their origin and their intestinal tract. Therefore these herbivorous species should be fed with hay, straw or vegetables and not with concentrates exclusively. If these components are not offered (an usual feeding practice in rabbits kept as companion animals), other products rich in crude fibre have to be fed. The offer of a pressed diet in cube form with long fibrous ingredients would be a possibility to upgrade a ration poor in crude fibre. To meet the gnawing requirement of the rabbits this cubes should be pressed intensively. Furthermore it is advisable to exchange ingredients of the mixed feed with a high energy content (i.e. sunflower seeds, nuts) for ingredients of lower energy density (i.e. oat hulls, pelleted ground hay). Finally calcium oversupply has to be avoided because higher calcium intake may result in urolithiasis (calcium stones/concrements). PMID:11314470

  10. [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

  11. 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

    2016-01-01

    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. PMID:26830914

  12. Species-Specific Associations Between Soil-Transmitted Helminths and Micronutrients in Vietnamese Schoolchildren.

    PubMed

    de Gier, Brechje; Nga, Tran Thuy; Winichagoon, Pattanee; Dijkhuizen, Marjoleine A; Khan, Nguyen Cong; van de Bor, Margot; Ponce, Maiza Campos; Polman, Katja; Wieringa, Frank T

    2016-07-01

    Soil-transmitted helminth (STH) infections and micronutrient deficiencies are closely related and often coexist among low-income populations. We studied the association between infections with specific STH species and micronutrient status in rural Vietnamese schoolchildren. Children (N = 510) aged 6-9 years were recruited from two primary schools. STH infections were determined in stool samples. Hemoglobin, ferritin, retinol, and zinc were measured in blood samples, as well as C-reactive protein to control for inflammation. Iodine excretion was measured in urine. Associations of single and multiple infections with Ascaris lumbricoides, Trichuris trichiura, and hookworm with micronutrient status (hemoglobin, plasma ferritin, retinol, zinc, and urinary iodine) were estimated by multiple regression analysis. Ascaris infections showed a specific and intensity-dependent negative association with vitamin A. Trichuris and hookworm infections were associated with lower hemoglobin concentration, but not with plasma ferritin. Trichuris-infected children had zinc deficiency less often than uninfected children. In conclusion, our study shows species-specific associations between STH infections and micronutrient status in children. The different life cycles of STH species might have specific effects on the absorption or loss of specific micronutrients. Tailor-made combinations of deworming and nutritional interventions may be needed to improve child health and nutrition. PMID:27246448

  13. A Novel Gene Family Controls Species-Specific Morphological Traits in Hydra

    PubMed Central

    Khalturin, Konstantin; Anton-Erxleben, Friederike; Sassmann, Sylvia; Wittlieb, Jörg; Hemmrich, Georg; Bosch, Thomas C. G

    2008-01-01

    Understanding the molecular events that underlie the evolution of morphological diversity is a major challenge in biology. Here, to identify genes whose expression correlates with species-specific morphologies, we compared transcriptomes of two closely related Hydra species. We find that species-specific differences in tentacle formation correlate with expression of a taxonomically restricted gene encoding a small secreted protein. We show that gain of function induces changes in morphology that mirror the phenotypic differences observed between species. These results suggest that “novel” genes may be involved in the generation of species-specific morphological traits. PMID:19018660

  14. 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

  15. 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. PMID:25444936

  16. 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. PMID:20962883

  17. 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.

  18. 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. ...

  19. 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…

  20. 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.

  1. 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

  2. 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

  3. [Orbital inflammation].

    PubMed

    Mouriaux, F; Coffin-Pichonnet, S; Robert, P-Y; Abad, S; Martin-Silva, N

    2014-12-01

    Orbital inflammation is a generic term encompassing inflammatory pathologies affecting all structures within the orbit : anterior (involvement up to the posterior aspect of the globe), diffuse (involvement of intra- and/or extraconal fat), apical (involvement of the posterior orbit), myositis (involvement of only the extraocular muscles), dacryoadenitis (involvement of the lacrimal gland). We distinguish between specific inflammation and non-specific inflammation, commonly referred to as idiopathic inflammation. Specific orbital inflammation corresponds to a secondary localization of a "generalized" disease (systemic or auto-immune). Idiopathic orbital inflammation corresponds to uniquely orbital inflammation without generalized disease, and thus an unknown etiology. At the top of the differential diagnosis for specific or idiopathic orbital inflammation are malignant tumors, represented most commonly in the adult by lympho-proliferative syndromes and metastases. Treatment of specific orbital inflammation begins with treatment of the underlying disease. For idiopathic orbital inflammation, treatment (most often corticosteroids) is indicated above all in cases of visual loss due to optic neuropathy, in the presence of pain or oculomotor palsy. PMID:25455557

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

    PubMed

    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

  5. 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

  6. Preparation of species-specific murine monoclonal antibodies against the yeast phase of Paracoccidioides brasiliensis.

    PubMed Central

    Figueroa, J I; Hamilton, A J; Bartholomew, M A; Harada, T; Fenelon, L; Hay, R J

    1990-01-01

    A panel of four murine monoclonal antibodies showing species specificity for the yeast phase of the pathogenic dimorphic fungus Paracoccidioides brasiliensis was produced by using a modification of the standard monoclonal antibody technology. This involved the use of the immunosuppressive drug cyclophosphamide to suppress the immune response of test animals to fungi showing cross-reactivity, i.e., to Histoplasma capsulatum. One monoclonal antibody, P4, which had a high titer by enzyme-linked immunosorbent assay, was shown to recognize a linear antigenic epitope of P. brasiliensis at a molecular size of 70,000 to 75,000 daltons by Western blot (immunoblot) analysis. The potential use of these monoclonal antibodies, which are the first species-specific probes to P. brasiliensis that have been produced, in the field of serodiagnosis is discussed. Images PMID:2394802

  7. 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.

  8. Species-specific ultrastructure of neuronal lipofuscin in hippocampus and neocortex of subhuman mammals and humans.

    PubMed

    Boellaard, J W; Schlote, W; Hofer, W

    2004-01-01

    Lipofuscin represents an integral part of neurons and glial cells in mammals and in submammalian species. It is a special lysosomal organelle, takes part of cellular metabolism, and is a structural expression of catabolic pathways. Species-specific differences of lipofuscin indicate metabolic differences of the relevant neurons. The authors have studied the ultrastructure of neuronal lipofuscin in the hippocampus and cerebral neocortex of dogs, horses, cows, elephants, rats, mice, apes, and humans to answer the question of species-specific differences of this organelle. Paraffin sections of formalin-fixed material were investigated by hematoxylin-eosin and PAS staining, by fluorescence microscopy for autofluorescence, with a laser scanning confocal microscope and by electron microscopy. In the animals studied and in humans the lipofuscin displayed, in addition to the general trilaminar substructure, species-specific appearances. No differences were found in the lipofuscin structure between neocortical and hippocampal neurons of the separate animal species. In contrast, in humans, neurons of the hippocampus showed a particular lipofuscin structure, not only different from the neocortical one, but also with differences between CA1 and CA3/4 sectors. Interestingly, in apes a transitional situation was found with slight differences between neocortical and hippocampal lipofuscin, especially in the rhesus monkey. This peculiarity was corroborated by the distribution of special pentilaminar linear structures in the lipofuscin pigment in all animals, only sparsely in the rhesus monkey and not in humans. The results indicate that lipofuscin ultrastructure of neocortical and hippocampal neurons is species specific and that lipofuscin in the human hippocampal neurons displays structures characteristic of man differing from the neocortical neuronal lipofuscin. The neuronal lipofuscin of apes, especially of the rhesus monkey displays structures in between humans and lower

  9. [Analysis of species specific acoustic signals in the mesencephalic, diencephalic, and neostriatal structures of the brain].

    PubMed

    Shliafer, T P; Aleksandrova, Zh G

    1979-10-01

    In chronic experiments, the neuronal activity in structures of the auditory analyzer was studied during perception of species-specific signals in the chicken. The majority of the neostriatum cells responded to territorial vocalizations of the rooster and to squeaking of the chicken; in the midbrain structures the maximal responses occurred to signals of distress and alarm. The greatest number of cells responded most obviously to the cardinal component of the chicken vocalization spectrum. PMID:510592

  10. Femtosecond X-ray-induced fragmentation of fullerenes

    NASA Astrophysics Data System (ADS)

    Berrah, N.; Murphy, B.; Xiong, H.; Fang, L.; Osipov, T.; Kukk, E.; Guehr, M.; Feifel, R.; Petrovic, V. S.; Ferguson, K. R.; Bozek, J. D.; Bostedt, C.; Frasinski, L. J.; Bucksbaum, P. H.; Castagna, J. C.

    2016-02-01

    A new class of femtosecond, intense, short - wavelength lasers - the free-electron laser - has opened up new opportunities to investigate the structure and dynamics in many scientific areas. These new lasers, whose performance keeps increasing, enable the understanding of physical and chemical changes at an atomic spatial scale and on the time scale of atomic motion which is essential for a broad range of scientific fields. We describe here the interaction of fullerenes in the multiphoton regime with the Linac Coherent Light Source (LCLS) X-ray free-electron laser at SLAC National Laboratory. In particular, we report on new data regarding the ionization of Ho3N@C80 molecules and compare the results with our prior C60 investigation of radiation damage induced by the LCLS pulses. We also discuss briefly the potential impact of newly available instrumentation to physical and chemical sciences when they are coupled with FELs as well as theoretical calculations and modeling.

  11. X-ray induced damage observations in ZERODUR mirrors

    SciTech Connect

    Takacs, P.Z.; Furenlid, K.; Furenlid, L.

    1997-07-01

    Catastrophic damage has been observed in some ZERODUR mirrors used as first mirrors in two beam lines at the National Synchrotron Light Source (NSLS). Despite the high reflectivity of the coatings used on these mirrors, a significant flux of high energy photons penetrates below the coating and is absorbed in the substrate. Although model calculations indicate that the local temperature does not increase significantly, the authors suspect that over long time periods the absorbed flux produces structural changes in the material, leading to a build-up of surface stress, gross figure changes, and growth of fractures. These changes are probably related to the nature of the two-phase glass-ceramic composition of the ZERODUR material. Metal mirrors and single-phase materials do not exhibit such catastrophic damage under similar exposure conditions.

  12. Recoil splitting of x-ray-induced optical fluorescence

    SciTech Connect

    Gavrilyuk, S.; Aagren, H.; Gel'mukhanov, F.; Sun, Y.-P.; Levin, S.

    2010-03-15

    We show that the anisotropy of the recoil velocity distribution of x-ray-ionized atoms or molecules leads to observable splittings in subsequent optical fluorescence or absorption when the polarization vector of the x rays is parallel to the momentum of the fluorescent photons. The order of the magnitude of the recoil-induced splitting is about 10 {mu}eV, which can be observed using Fourier or laser-absorption spectroscopic techniques.

  13. Hard-X-Ray-Induced Multistep Ultrafast Dissociation

    NASA Astrophysics Data System (ADS)

    Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

    2016-05-01

    Creation of deep core holes with very short (τ ≤1 fs ) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1 s →σ* excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon.

  14. Hard-X-Ray-Induced Multistep Ultrafast Dissociation.

    PubMed

    Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

    2016-05-27

    Creation of deep core holes with very short (τ≤1  fs) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1s→σ^{*} excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon. PMID:27284654

  15. X-ray-induced persistent photoconductivity in vanadium dioxide

    SciTech Connect

    Dietze, S. H.; Marsh, M. J.; Wang, Siming; Ramírez, J. -G.; Cai, Z. -H.; Mohanty, J. R.; Schuller, Ivan K.; Shpyrko, O. G.

    2014-10-08

    The resistivity of vanadium dioxide (VO2) decreased by over one order of magnitude upon localized illumination with x rays at room temperature. Despite this reduction, the structure remained in the monoclinic phase and had no signature of the high-temperature tetragonal phase that is usually associated with the lower resistance. Once illumination ceased, relaxation to the insulating state took tens of hours near room temperature. However, a full recovery of the insulating state was achieved within minutes by thermal cycling. We show that this behavior is consistent with random local-potential fluctuations and random distribution of discrete recombination sites used to model residual photoconductivity.

  16. 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.

  17. Lipophosphoglycan and secreted acid phosphatase of Leishmania tropica share species-specific epitopes.

    PubMed

    Jaffe, C L; Perez, L; Schnur, L F

    1990-06-01

    Several species-specific monoclonal antibodies (T11, T13-T15) which only react with Leishmania tropica, recognize phosphorlated carbohydrate epitopes on lipophosphoglycan and the structurally related molecule, phosphoglycan, which is shed by promastigotes into spent culture medium. During immunoaffinity isolation of [32P]orthophosphate-labeled phosphoglycan on monoclonal antibody T15 conjugated to Sepharose 4B, a high-Mr component (approx. 200,000) was co-purified. The latter material is metabolically labeled with [35S]methionine and [3H]glucosamine. This glycoprotein was separated from phosphoglycan by chromatography on lentil lectin resin. The glycoprotein exhibited a L-tatrate-sensitive acid phosphatase activity, typical of secreted acid phosphatase (EC 3.1.3.2) from Leishmania. Monospecific antibodies to Leishmania donovani-secreted acid phosphatase selectively precipitated the L. tropica enzyme from immunoaffinity purified mixtures of the two antigens, and monoclonal antibodies to lipophosphoglycan precipitate the pure enzyme. Species-specific monoclonal antibodies to L. major lipophosphoglycan also recognized both L. tropica antigens. Treatment of the acid phosphatase with periodate or phosphodiesterase I abolished binding by the monoclonal antibodies to the pure enzyme. These results demonstrate that the two major secreted glycoconjugates of Leishmania tropica, the lipophosphoglycan and the acid phosphatase, share species-specific phosphorylated carbohydrate epitope(s). PMID:1697935

  18. 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.

  19. 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. PMID:21619939

  20. 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. PMID:24392838

  1. 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...

  2. Species-specific alternative splicing leads to unique expression of sno-lncRNAs

    PubMed Central

    2014-01-01

    Background Intron-derived long noncoding RNAs with snoRNA ends (sno-lncRNAs) are highly expressed from the imprinted Prader-Willi syndrome (PWS) region on human chromosome 15. However, sno-lncRNAs from other regions of the human genome or from other genomes have not yet been documented. Results By exploring non-polyadenylated transcriptomes from human, rhesus and mouse, we have systematically annotated sno-lncRNAs expressed in all three species. In total, using available data from a limited set of cell lines, 19 sno-lncRNAs have been identified with tissue- and species-specific expression patterns. Although primary sequence analysis revealed that snoRNAs themselves are conserved from human to mouse, sno-lncRNAs are not. PWS region sno-lncRNAs are highly expressed in human and rhesus monkey, but are undetectable in mouse. Importantly, the absence of PWS region sno-lncRNAs in mouse suggested a possible reason why current mouse models fail to fully recapitulate pathological features of human PWS. In addition, a RPL13A region sno-lncRNA was specifically revealed in mouse embryonic stem cells, and its snoRNA ends were reported to influence lipid metabolism. Interestingly, the RPL13A region sno-lncRNA is barely detectable in human. We further demonstrated that the formation of sno-lncRNAs is often associated with alternative splicing of exons within their parent genes, and species-specific alternative splicing leads to unique expression pattern of sno-lncRNAs in different animals. Conclusions Comparative transcriptomes of non-polyadenylated RNAs among human, rhesus and mouse revealed that the expression of sno-lncRNAs is species-specific and that their processing is closely linked to alternative splicing of their parent genes. This study thus further demonstrates a complex regulatory network of coding and noncoding parts of the mammalian genome. PMID:24734784

  3. Functional characterization of chicken TLR5 reveals species-specific recognition of flagellin.

    PubMed

    Keestra, A Marijke; de Zoete, Marcel R; van Aubel, Rémon A M H; van Putten, Jos P M

    2008-03-01

    Mammalian Toll-like receptor 5 (TLR5) senses flagellin of several bacterial species and activates the innate immune system. The avian TLR repertoire exhibits considerable functional diversity compared to mammalian TLRs and evidence of a functional TLR5 in the avian species is lacking. In the present study we cloned and successfully expressed chicken TLR5 (chTLR5) in HeLa cells, as indicated by laser confocal microscopy. Infection of chTLR5 transfected cells with Salmonella enterica serovar Enteritidis activated NF-kappaB in a dose- and flagellin-dependent fashion. Similar NF-kappaB activation was observed with recombinant bacterial flagellin. Targeted mutagenesis of the proline residue at position 737 in the chTLR5-TIR domain was detrimental to chTLR5 function, confirming that the observed effects were conferred via chTLR5 and the MyD88 signaling pathway. Comparison of human, mouse and chicken TLR5 activation by flagellin of S. enterica serovar Typhimurium revealed that chTLR5 consistently yielded stronger responses than human but not mouse TLR5. This species-specific reactivity was not observed with flagellin of serovar Enteritidis. The species-specific TLR5 response was nullified after targeted mutagenesis of a single amino acid (Q89A) in serovar Typhimurium flagellin, while L415A and N100A substitutions had no effect. These results show that chickens express a functional TLR5 albeit with different flagellin sensing qualities compared to human TLR5. The finding that single amino acid substitutions in bacterial flagellin can alter the species-specific TLR5 response may influence the host range and susceptibility of infection. PMID:17964652

  4. Effect of species-specific sound stimulation on the development and hatching of broiler chicks.

    PubMed

    Tong, Q; McGonnell, I M; Romanini, C E B; Bergoug, H; Roulston, N; Exadaktylos, V; Berckmans, D; Bahr, C; Guinebretière, M; Eterradossi, N; Garain, P; Demmers, T

    2015-04-01

    1. Previous research has reported that chicken embryos develop a functionary auditory system during incubation and that prenatal sound may play an important role in embryo development and alter the hatch time. In this study the effects of prenatal auditory stimulation on hatch process, hatch performance, the development of embryo and blood parameters were investigated. 2. Four batches of Ross 308 broiler breeder eggs were incubated either in control or in sound-stimulated groups. The sound-stimulated embryos were exposed to a discontinuous sound of species-specific calls by means of a speaker at 72 dB for 16 h a day: maternal calls from d 10 to d 19 of incubation time and embryo/chick calls from d 19 until hatching. The species-specific sound was excluded from the control group. 3. The onset of hatch was delayed in the sound-stimulated group compared to the controls. This was also supported by comparison of the exact hatching time of individual focal chicks within the two groups. However, the sound-stimulated embryos had a lower hatchability than the control group, mainly due to significantly increased numbers of late deaths. 4. The embryos exhibited a similar growth pattern between the sound-stimulated group and the control group. Although sound exposure decreased body weight at d 16, no consistent effect of sound on body weight at incubation stage was observed. Species-specific sound stimulation also had no impact on chick quality, blood values and plasma corticosterone concentrations during hatch. PMID:25559058

  5. Restriction fragment length polymorphism species-specific patterns in the identification of white truffles.

    PubMed

    Bertini, L; Potenza, L; Zambonelli, A; Amicucci, A; Stocchi, V

    1998-07-15

    A molecular method for the identification of ectomycorrhizae belonging to five species of white truffle is described. The polymerase chain reaction (PCR) and universal primers were used to amplify internal transcribed spacers and 5.8S rDNA, target sequences present in a high number of copies. The amplified products were digested with restriction enzymes in order to detect interspecific polymorphisms. Species-specific restriction fragment length polymorphism patterns were determined for all five species. The use of PCR in conjunction with restriction enzymes provides a sensitive and efficient tool for use in distinguishing ectomycorrhizal species and monitoring inoculated seedlings or field mycorrhizal populations. PMID:9682488

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

    PubMed

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

    2016-09-01

    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. PMID:27289191

  7. 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. PMID:25567925

  8. 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

  9. 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. PMID:21332639

  10. 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

  11. 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. PMID:25899252

  12. 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

  13. 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

    2014-01-01

    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. PMID:24938705

  14. Serotonin modulates responses to species-specific vocalizations in the inferior colliculus.

    PubMed

    Hurley, Laura M; Pollak, George D

    2005-06-01

    Neuromodulators such as serotonin are capable of altering the neural processing of stimuli across many sensory modalities. In the inferior colliculus, a major midbrain auditory gateway, serotonin alters the way that individual neurons respond to simple tone bursts and linear frequency modulated sweeps. The effects of serotonin are complex, and vary among neurons. How serotonin transforms the responses to spectrotemporally complex sounds of the type normally heard in natural settings has been poorly examined. To explore this issue further, the effects of iontophoretically applied serotonin on the responses of individual inferior colliculus neurons to a variety of recorded species-specific vocalizations were examined. These experiments were performed in the Mexican free-tailed bat, a species that uses a rich repertoire of vocalizations for the purposes of communication as well as echolocation. Serotonin frequently changed the number of recorded calls that were capable of evoking a response from individual neurons, sometimes increasing (15% of serotonin-responsive neurons), but usually decreasing (62% of serotonin-responsive neurons), this number. A functional consequence of these serotonin-evoked changes would be to change the population response to species-specific vocalizations. PMID:15830241

  15. Antigenic cross-reactivity and species-specific identification of Pseudocerastes persicus fieldi snake venom.

    PubMed

    Ibrahim, Nihal M; El-Kady, Ebtsam M

    2016-09-01

    In the present study, we recognized progressively high immunological cross-reactivity between Pseudocerastes persicus fieldi (Pf) venom and six other medically important Egyptian snake venoms belonging to families Viperidae and Elapidae. Antibodies with a range of bonding strengths were shown to be involved in such cross-reactivity. Two strategies have been tried to access specificity; (i) using affinity purified species-specific anti-Pf antivenom antibodies, (ii) conducting the assay in the presence of ammonium thiocyanate (NH4SCN). The discrimination power of the prepared species-specific antivenom was demonstrated by its ability to detect Pf venom over a range of Pf concentrations (2.5 ng-2.5 μg) in a variety of body fluids. The assay could distinguish circulating Pf antigens from other viper antigens in the whole blood of experimentally envenomed mice. What seems promising in our work is the use of the chaotrope, NH4SCN, which renders the reaction medium more favorable for the specific homologous antigen-antibody interactions, primarily via preventing lower avid antibodies to share and, to a bit lesser extent, by decreasing non-specific absorbance signals frequently encountered with ELISA assays. The ELISA described herein may be useful for clinicians for identification of snake bites inflicted by Pf snake species. Balancing between specificity and sensitivity has to be considered for best results. PMID:27319296

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

    PubMed

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

    2013-11-01

    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

  17. 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. PMID:19194502

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

    PubMed

    Balas, Benjamin; Stevenson, Kate

    2013-08-01

    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

  19. 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

  20. Detection of Mycobacterium avium subsp. paratuberculosis in Infected Tissues by New Species-Specific Immunohistological Procedures

    PubMed Central

    Coetsier, Christophe; Havaux, Xavier; Mattelard, Francois; Sadatte, Sanaa; Cormont, Francoise; Buergelt, Klaus; Limbourg, Bernard; Latinne, Dominique; Bazin, Herve; Denef, Jean-Francois; Cocito, Carlo

    1998-01-01

    We have previously described the cloning and sequencing of a gene portion coding for the terminal part of a 34-kDa protein of Mycobacterium avium subsp. paratuberculosis, the etiological agent of Johne’s disease (P. Gilot, M. De Kesel, L. Machtelinckx, M. Coene, and C. Cocito, J. Bacteriol. 175:4930–4935, 1993). The recombinant polypeptide (a362) carries species-specific B-cell epitopes which do not cross-react with other mycobacterial pathogens (M. De Kesel, P. Gilot, M.-C. Misonne, M. Coene, and C. Cocito, J. Clin. Microbiol. 31:947–954, 1993). The present work describes the preparation of polyclonal and monoclonal antibodies directed against a362 and the use of these immunoglobulins for histopathological diagnosis of Johne’s disease. The new immunohistological procedures herewith detailed proved to be able to identify M. avium subsp. paratuberculosis antigens in the intestinal tissues and lymph nodes of cattle affected by either the paucibacillary or pluribacillary form of the disease. They yielded negative responses not only with healthy animals but also with those affected by tuberculosis (Mycobacterium bovis). Both immunohistological procedures proved to be as sensitive as or more sensitive than Ziehl-Neelsen staining and, in addition, to be endowed with species specificity. PMID:9665946

  1. 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

  2. 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. PMID:26107496

  3. 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

  4. 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

  5. Species-specific ontogenetic diet shifts among Neotropical Crenicichla: using stable isotopes and tissue stoichiometry.

    PubMed

    Burress, E D; Duarte, A; Serra, W S; Gangloff, M M; Siefferman, L

    2013-06-01

    Ontogenetic diet shifts were compared among five sympatric pike cichlids Crenicichla in a subtropical South American stream using stable C and N isotopes and tissue stoichiometry (C:N). Within species, stable N isotopes were positively related to body size while C:N showed negative relationships. Stable C isotopes, however, were not related to body size in any species. By modelling the switch to piscivory using gut content-isotope-body size relationships, diet shifts were shown to be species-specific with regard to both rate and degree of piscivory. Compared to other piscivorous lineages, Crenicichla appear to be unusually small-bodied (based on maximum body size). Because of their diversity, abundance and dynamic size-structured functional roles, Crenicichla may exert broad and complex predation pressures on the aquatic community. PMID:23731144

  6. Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above-belowground herbivore interactions.

    PubMed

    Huang, Wei; Siemann, Evan; Xiao, Li; Yang, Xuefang; Ding, Jianqing

    2014-01-01

    Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of the tallow tree specialist beetle Bikasha collaris and multiple heterospecific aboveground species interact to determine herbivore performance. Conspecific aboveground adults facilitate belowground larvae, but other aboveground damage inhibits larvae or has no effect. Belowground larvae increase conspecific adult feeding, but decrease heterospecific aboveground insect feeding and abundance. Chemical analyses and experiments with plant populations varying in phenolics show that all these positive and negative effects on insects are closely related to root and shoot tannin concentrations. Our results show that specific plant herbivore responses allow herbivore facilitation and inhibition to co-occur, likely shaping diverse aboveground and belowground communities. Considering species-specific responses of plants is critical for teasing apart inter- and intraspecific interactions in aboveground and belowground compartments. PMID:25241651

  7. Identification of Brugia malayi in vectors with a species-specific DNA probe.

    PubMed

    Sim, B K; Mak, J W; Cheong, W H; Sutanto, I; Kurniawan, L; Marwoto, H A; Franke, E; Campell, J R; Wirth, D F; Piessens, W F

    1986-05-01

    We evaluated the potential value of a cloned sequence of genomic DNA of Brugia malayi as a species-specific probe. Clone pBm 15 reacted with all stages of 8 different geographic isolates of B. malayi and cross-hybridized with microfilariae of B. timori. It did not hybridize with Wuchereria bancrofti or with B. pahangi, W. kalimantani, Dirofilaria repens, Breinlia booliati or Cardiofilaria species, animal filariids that can be sympatric with B. malayi. P32-labeled clone pBm 15 correctly identified mosquitoes infected even with 1 infective larva of B. malayi. This specific DNA probe should be an invaluable tool to monitor control programs of Brugian filariasis. PMID:3518507

  8. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

    PubMed

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-04-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition. PMID:25854683

  9. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    PubMed Central

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-01-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition. PMID:25854683

  10. 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

  11. LINE-1 distribution in six rodent genomes follow a species-specific pattern.

    PubMed

    Vieira-da-Silva, A; Adega, F; Guedes-Pinto, H; Chaves, R

    2016-03-01

    L1 distribution in mammal's genomes is yet a huge riddle. However, these repetitive sequences were already found in all chromosomic regions, and in general, they seem to be nonrandomly distributed in the genome. It also seems that after insertion and when they are not deleterious, they are always involved in dynamic processes occurring on that particular chromosomic region. Furthermore, it seems that large-scale genome rearrangements and L1 activity and accumulation are somehow interconnected. In the present study, we analysed L1 genomic distribution in Tatera gambiana (Muridae, Gerbillinae), Acomys sp. (Muridae, Deomyinae), Cricetomys sp. (Nesomyidae, Cricetomyinae), Microtus arvalis (Cricetidae, Arvicolinae), Phodopus roborovskii and P. sungorus (Cricetidae, Cricetinae). All the species studied here seems to exhibit a species-specific pattern.Possible mechanisms, and processes involved in L1 distribution and preferential accumulation in certain regions are di scussed. PMID:27019429

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

    PubMed

    Jordt, Sven-Eric; Julius, David

    2002-02-01

    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. PMID:11853675

  13. 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

  14. 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

  15. 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. PMID:26590597

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

    PubMed Central

    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

    2012-01-01

    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. PMID:21993395

  17. Species-specificity of growth-promoting effects of prolactin during rat embryogenesis

    PubMed Central

    KARABULUT, AHMET KAGAN; PRATTEN, MARGARET K.

    1998-01-01

    In the early stages of embryonic development, many growth-promoting molecules must be provided by the maternal system. The molecules involved in growth processes may be either hormones or growth factors, or molecules that interact with such factors. The pregnancy related hormone, prolactin (PRL, MW 23 kDa) has been implicated in the control of embryonic growth. The growth-promoting potential of PRL and its species-specificity was investigated by culturing 9.5 d rat embryos in vitro for 48 h in depleted serum in the presence and absence of PRL from 3 different species. The growth-supporting capacity of the serum was reduced by removal of low molecular weight molecules by prolonged filtration of the serum using filters with a molecular weight exclusion of 30 kDa. This method provided a ‘semidefined’ medium (retenate) in which embryonic growth and development was significantly reduced, demonstrating that the low molecular weight fraction of serum may contain some growth-promoting factors. Addition of PRL (0.4–25.6 ng/ml) from different species (human, sheep and rat) to retenate significantly improved embryonic growth and development, suggesting that the developing embryo may utilise PRL. Amongst PRLs, rat PRL was found to be active at much lower concentrations than either of the other molecules, and human PRL had more effect in low concentrations than sheep PRL suggesting a species-specificity for this hormone. It may be that the PRL receptors of the rat embryos have greater affinity for the rat hormone as different responses for hormones from different species have been shown. These findings suggest that embryos may be able to utilise maternally derived PRL during organogenesis. PMID:9568556

  18. Species-specific fibroblasts required for triggering invasiveness of partially transformed oral keratinocytes.

    PubMed

    Costea, Daniela Elena; Kulasekara, Keerthi; Neppelberg, Evelyn; Johannessen, Anne Christine; Vintermyr, Olav Karsten

    2006-06-01

    This study tests the hypothesis that invasion of partially transformed keratinocytes is initiated by diffusible, proinvasive signals provided by species-specific fibroblasts. In vitro organotypic cultures of neoplastic human oral mucosa were constructed by growing a partially transformed, nontumorigenic keratinocytic cell line isolated from a dysplastic human oral lesion (DOK-ECACC94122104) on top of various types of connective tissue equivalents. Cultured tissues were analyzed by histomorphometry (depth and area of invasion: Dinv, Ainv) and immunohistochemistry. Presence of human fibroblasts in the matrix induced a local invasion of DOK (Dinv = 95.6 +/- 7.1 microm, Ainv = 45.8 +/- 3.5%). Minimal invasion (P < 0.05) was observed when DOK grew on simple collagen matrix (Dinv = 14.1 +/- 2.1 microm, Ainv = 3.7 +/- 0.8%) or matrices containing fibroblasts from mouse (Dinv = 11.5 +/- 4.0 microm, Ainv = 4.3 +/- 1.0%) or rat (Dinv = 15.6 +/- 1.2 microm, Ainv = 6.1 +/- 0.5%). In these cultures, local invasion could be induced by the presence of human fibroblasts in a bottom layer of the collagen matrix (P < 0.05) or by conditioned medium from organotypic cultures of DOK on human fibroblast-containing matrix (P < 0.05) but not by conditioned medium from human fibroblast monocultures (P > 0.05). Deposition of human collagen IV was observed at epithelial-matrix interface only when DOK behaved invasively. In conclusion, invasion of partially transformed oral keratinocytes was triggered by keratinocyte-induced fibroblast-derived diffusible factor(s) in a species-specific manner and associated with de novo synthesis of collagen IV. PMID:16723704

  19. 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

  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. 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

  2. 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

  3. Development of species-specific primers for detection of Streptococcus mutans in mixed bacterial samples

    PubMed Central

    Chen, Zhou; Saxena, Deepak; Caufield, Page W.; Ge, Yao; Wang, Minqi; Li, Yihong

    2009-01-01

    Streptococcus mutans is the major microbial pathogen associated with dental caries in children. The objectives of this study were to design and evaluate species-specific primers for the identification of S. mutans. Validation of the best primer set, Sm479F/R, was performed using 7 S. mutans reference strains, 48 ATCC non-S. mutans strains, 92 S. mutans clinical isolates, DNA samples of S. mutans-S. sobrinus or S. mutans-S. sanguinis, and mixed bacterial DNA of saliva samples from 33 18-month-old children. All of the S. mutans samples tested positive, and no PCR products were amplified from members of the other streptococci or non-streptococci strains examined. The lowest detection level for PCR was 10−2 nanograms of S. mutans DNA (approximately 4.6 × 103 copies) in the test samples. The results of our study suggest that the Sm479F/R primer pair is highly specific and sensitive for identification of S. mutans in either purified or mixed DNA samples. PMID:17521362

  4. 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. PMID:25822715

  5. Leishmania-sand fly interactions controlling species-specific vector competence.

    PubMed

    Sacks, D L

    2001-04-01

    Leishmaniasis is caused by a wide range of parasites that are transmitted by an even wider range of sand fly vectors. The phlebotomine vectors of Leishmaniasis are in some cases only permissive to the complete development of the species of Leishmania that they transmit in nature. The parasite-sand fly interactions that control this specificity are related to differences in the ability of the parasite to inhibit or to resist killing by proteolytic enzymes released into the mid-gut soon after blood feeding, and/or to maintain infection in the mid-gut during excretion of the digested blood meal. In each case, surface expressed or released phosphoglycan-containing molecules appear to promote parasite survival. The evidence that the surface lipophosphoglycan (LPG) mediates promastigote attachment to the mid-gut epithelium so as to prevent their loss during blood-meal excretion is especially strong based on the comparison of development in sand flies using LPG-deficient mutants. LPG displays interspecies polymorphisms in their phosphoglycan domains that in most cases can fully account for species-specific vector competence. PMID:11298643

  6. Comparative in-silico genome analysis of Leishmania (Leishmania) donovani: A step towards its species specificity

    PubMed Central

    S., Satheesh Kumar; R.K., Gokulasuriyan; Ghosh, Monidipa

    2014-01-01

    Comparative genome analysis of recently sequenced Leishmania (L.) donovani was unexplored so far. The present study deals with the complete scanning of L. (L.) donovani genome revealing its interspecies variations. 60 distinctly present genes in L. (L.) donovani were identified when the whole genome was compared with Leishmania (L.) infantum. Similarly 72, 159, and 265 species specific genes were identified in L. (L.) donovani when compared to Leishmania (L.) major, Leishmania (L.) mexicana and Leishmania (Viannia) braziliensis respectively. The cross comparison of L. (L.) donovani in parallel with the other sequenced species of leishmanial led to the identification of 55 genes which are highly specific and expressed exclusively in L. (L.) donovani. We found mainly the discrepancies of surface proteins such as amastins, proteases, and peptidases. Also 415 repeat containing proteins in L. (L.) donovani and their differential distribution in other leishmanial species were identified which might have a potential role during pathogenesis. The genes identified can be evaluated as drug targets for anti-leishmanial treatment, exploring the scope for extensive future investigations. PMID:25606461

  7. Development of a Species-Specific Probe for Pythium insidiosum and the Diagnosis of Pythiosis

    PubMed Central

    Schurko, Andrew M.; Mendoza, Leonel; de Cock, Arthur W. A. M.; Bedard, James E. J.; Klassen, Glen R.

    2004-01-01

    Pythium insidiosum, the only species in the genus that infects mammals, is the etiological agent of pythiosis, a granulomatous disease characterized by cutaneous and subcutaneous lesions and vascular diseases. Accurate diagnosis of pythiosis and identification of its causal agent are often inconsistent with current immunological diagnostic methods. A species-specific DNA probe was constructed by using a 530-bp HinfI fragment from the ribosomal DNA intergenic spacer of P. insidiosum. When the probe was incubated with dot blots of genomic DNA from 104 Pythium species, it hybridized only to the DNA of P. insidiosum and P. destruens—two species that have been considered conspecific. The probe also hybridized to DNA from 22 P. insidiosum isolates in this study, regardless of their geographic origin or animal host. When tested against genomic DNA from other pathogenic organisms (Aspergillus fumigatus, Basidiobolus ranarum, Conidiobolus coronatus, Lagenidium giganteum, Paracoccidioides brasiliensis, and Prototheca wickerhamii), no cross-hybridization of the probe was detected. The specificity of the probe to hybridize to genomic DNA from all isolates of P. insidiosum and not cross-react with DNA from other Pythium species or pathogens that cause symptoms similar to pythiosis in their hosts makes it a powerful tool for the accurate diagnosis of pythiosis. In addition, the probe has the potential for pathological and environmental diagnostic applications. PMID:15184412

  8. Differences in environmental stress response among yeasts is consistent with species-specific lifestyles

    PubMed Central

    Brion, Christian; Pflieger, David; Souali-Crespo, Sirine; Friedrich, Anne; Schacherer, Joseph

    2016-01-01

    Defining how organisms respond to environmental change has always been an important step toward understanding their adaptive capacity and physiology. Variation in transcription during stress has been widely described in model species, especially in the yeast Saccharomyces cerevisiae, which helped to shape general rules regarding how cells cope with environmental constraints, as well as to decipher the functions of many genes. Comparison of the environmental stress response (ESR) across species is essential to obtaining better insight into the common and species-specific features of stress defense. In this context, we explored the transcriptional landscape of the yeast Lachancea kluyveri (formerly Saccharomyces kluyveri) in response to diverse stresses, using RNA sequencing. We investigated variation in gene expression and observed a link between genetic plasticity and environmental sensitivity. We identified the ESR genes in this species and compared them to those already found in S. cerevisiae. We observed common features between the two species, as well as divergence in the regulatory networks involved. Of interest, some changes were related to differences in species lifestyle. Thus we were able to decipher how adaptation to stress has evolved among different yeast species. Finally, by analyzing patterns of coexpression, we were able to propose potential biological functions for 42% of genes and also annotate 301 genes for which no function could be assigned by homology. This large data set allowed for the characterization of the evolution of gene regulation and provides an efficient tool for assessing gene function. PMID:27009200

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

    PubMed

    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; Weiss, Mitchell J

    2014-03-20

    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

  10. Stability and Species Specificity of Renal VEGF-A Splicing Patterns in Kidney Disease.

    PubMed

    Turner, R J; Eikmans, M; Bajema, I M; Bruijn, J A; Baelde, H J

    2016-01-01

    Vascular endothelial growth factor A (VEGF-A) is essential for maintaining the glomerular filtration barrier. Absolute renal levels of VEGF-A change in patients with diabetic nephropathy and inflammatory kidney diseases, but whether changes in the renal splicing patterns of VEGF-A play a role remains unclear. In this study, we investigated mRNA splicing patterns of pro-angiogenic isoforms of VEGF-A in glomeruli and whole kidney samples from human patients with kidney disease and from mouse models of kidney disease. Kidney biopsies were obtained from patients with acute rejection following kidney transplantation, patients with diabetic nephropathy, and control subjects. In addition, kidney samples were obtained from mice with lupus nephritis, mice with diabetes mellitus, and control mice. The relative expression of each VEGF-A splice variant was measured using RT-PCR followed by quantitative fragment analysis. The pattern of renal VEGF-A splice variants was unchanged in diabetic nephropathy and lupus nephritis and was stable throughout disease progression in acute transplant rejection and diabetic nephropathy; these results suggest renal VEGF-A splicing stability during kidney disease. The splicing patterns were species-specific; in the control human kidney samples, VEGF-A 121 was the dominant isoform, whereas VEGF-A 164 was the dominant isoform measured in the mouse kidney samples. PMID:27598902

  11. Cytotaxonomy of the subgenus Artibeus (Phyllostomidae, Chiroptera) by characterization of species-specific markers.

    PubMed

    Pinto, Marcela Maria Pereira de Lemos; Calixto, Merilane da Silva; de Souza, Maria José; de Araújo, Ana Paloma Tavares; Langguth, Alfredo; Santos, Neide

    2012-01-01

    The genus Artibeus represents a highly diverse group of bats from the Neotropical region, with four large species occurring in Brazil. In this paper, a comparative cytogenetic study was carried out on the species Artibeus obscurus Schinz, 1821, Artibeus fimbriatus Gray, 1838, Artibeus lituratus Olfers, 1818 and Artibeus planirostris Spix, 1823 that live sympatrically in the northeast of Brazil, through C-banding, silver staining and DNA-specific fluorochromes (CMA3 and DAPI). All the species had karyotypes with 2n=30,XX and 2n=31,XY1Y2, and FN=56. C-banding showed constitutive heterochromatin (CH) blocks in the pericentromeric regions of all the chromosomes and small CH blocks at the terminal region of pairs 5, 6, and 7 for all species. Notably, our C-banding data revealed species-specific autosomic CH blocks for each taxon, as well as different heterochromatic constitution of Y2 chromosomes of Artibeus planirostris. Ag-NORs were observed in the short arms of chromosomes 5, 6 and 7 in all species. The sequential staining AgNO3/CMA3/DA/DAPI indicated a positive association of CH with Ag-NORs and positive CMA3 signals, thus reflecting GC-richness in these regions in Artibeus obscurus and Artibeus fimbriatus. In this work it was possible to identify interespecific divergences in the Brazilian large Artibeus species using C-banding it was possible provided a suitable tool in the cytotaxonomic differentiation of this genus. PMID:24260649

  12. Species-specific recognition of the carrier insect by dauer larvae of the nematode Caenorhabditis japonica.

    PubMed

    Okumura, Etsuko; Tanaka, Ryusei; Yoshiga, Toyoshi

    2013-02-15

    Host recognition is crucial during the phoretic stage of nematodes because it facilitates their association with hosts. However, limited information is available on the direct cues used for host recognition and host specificity in nematodes. Caenorhabditis japonica forms an intimate association with the burrower bug Parastrachia japonensis. Caenorhabditis japonica dauer larvae (DL), the phoretic stage of the nematode, are mainly found on adult P. japonensis females but no other species. To understand the mechanisms of species-specific and female carrier-biased ectophoresy in C. japonica, we investigated whether C. japonica DL could recognize their hosts using nematode loading and chemoattraction experiments. During the loading experiments, up to 300 C. japonica DL embarked on male and female P. japonensis, whereas none or very few utilized the other shield bugs Erthesina fullo and Macroscytus japonensis or the terrestrial isopod Armadillidium vulgare. In the chemoattraction experiments, hexane extracts containing the body surface components of nymphs and both adult P. japonensis sexes attracted C. japonica DL, whereas those of other shield bugs did not. Parastrachia japonensis extracts also arrested the dispersal of C. japonica DL released at a site where hexane extracts were spotted on an agar plate; i.e. >50% of DL remained at the site even 60 min after nematode inoculation whereas M. japonensis extracts or hexane alone did not have the same effect. These results suggest that C. japonica DL recognize their host species using direct chemical attractants from their specific host to maintain their association. PMID:23077159

  13. Acoustic communication in crocodilians: information encoding and species specificity of juvenile calls.

    PubMed

    Vergne, Amélie L; Aubin, Thierry; Martin, Samuel; Mathevon, Nicolas

    2012-11-01

    In the Crocodylia order, all species are known for their ability to produce sounds in several communication contexts. Though recent experimental studies have brought evidence of the important biological role of young crocodilian calls, especially at hatching time, the juvenile vocal repertoire still needs to be clarified in order to describe thoroughly the crocodilian acoustic communication channel. The goal of this study is to investigate the acoustic features (structure and information coding) in the contact call of juveniles from three different species (Nile crocodile Crocodylus niloticus, Black caiman, Melanosuchus niger and Spectacled caiman, Caiman crocodilus). We have shown that even though substantial structural differences exist between the calls of different species, they do not seem relevant for crocodilians. Indeed, juveniles and adults from the species studied use a similar and non-species-specific way of encoding information, which relies on frequency modulation parameters. Interestingly, using conditioning experiments, we demonstrated that this tolerance in responses to signals of different acoustic structures was unlikely to be related to a lack of discriminatory abilities. This result reinforced the idea that crocodilians have developed adaptations to use sounds efficiently for communication needs. PMID:22820991

  14. 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. PMID:26163486

  15. Children’s neural response to contrast-negated faces is species-specific

    PubMed Central

    Balas, Benjamin; Stevenson, Kate

    2013-01-01

    Face recognition abilities develop dramatically during the first year of life, but comparatively little is known about the nature of face-specific perceptual development in early childhood. Face-specific effects of image appearance on recognition, including face inversion and contrast negation, are a useful means of understanding the functional properties of face perception developmentally. Here, we examined the generality of the impact of contrast-negation on face perception in early childhood using event-related potentials (ERPs). Specifically, we recorded continuous EEG while adult participants and children between the ages of 4–6 years old viewed human and non-human primate faces presented either in positive or negative contrast. We examined both the P100 and N170 components to determine whether or not sensitivity to contrast polarity was evident in face-sensitive components in early childhood, and also whether or not that sensitivity was specific to species category. We find evidence of a species-specific effect of contrast negation at the N170, suggesting that by early childhood some aspects of face-specific processing have been restricted to a relatively narrow class of face stimuli. However, this effect is of opposite sign relative to adults, suggesting that there is continued maturation of face-specific processing during childhood. PMID:24309247

  16. Reactivity of monoclonal antibodies to species-specific antigens of Entamoeba histolytica.

    PubMed

    Tachibana, H; Kobayashi, S; Nagakura, K; Kaneda, Y; Takeuchi, T

    1991-01-01

    Twenty monoclonal antibodies were produced against trophozoites of Entamoeba histolytica strains HK-9 and HM-1: IMSS. When reactivity to various enteric protozoa was examined by an indirect fluorescence antibody test, 15 of the monoclonal antibodies were strongly reactive with E. histolytica trophozoites. Species-specific antigens recognized by these monoclonal antibodies were located on the plasma membrane, nucleus, cytoplasm, and cytoskeletal structures of the trophozoites. Two of the remaining five monoclonals reacted strongly with trophozoites of the E. histolytica-like Laredo strain. The determinant antigen was located in the cytoplasm. The three remaining monoclonal antibodies were found to recognize cross-reactive antigens between E. histolytica and E. histolytica-like Laredo, E. hartmanni, E. coli, Dientamoeba fragilis, Giardia lamblia, and Trichomonas hominis. These three antibodies were also reactive with T. vaginalis and mammalian cells such as HeLa cells. Thus, the combined use of monoclonal antibodies seems capable of distinguishing E. histolytica and/or E. histolytica-like Laredo from other enteric protozoa. PMID:1724012

  17. A safety assessment of coumarin taking into account species-specificity of toxicokinetics.

    PubMed

    Felter, S P; Vassallo, J D; Carlton, B D; Daston, G P

    2006-04-01

    Coumarin (1,2-benzopyrone) is a naturally occurring fragrant compound found in a variety of plants and spices. Exposure to the general public is through the diet and from its use as a perfume raw material in personal care products. High doses of coumarin by the oral route are known to be associated with liver toxicity in rodents. Chronic oral bioassays conducted in the 1990s reported liver tumors in rats and mice and lung tumors in mice, raising concerns regarding the safety of coumarin. Since then, an extensive body of research has focused on understanding the etiology of these tumors. The data support a conclusion that coumarin is not DNA-reactive and that the induction of tumors at high doses in rodents is attributed to cytotoxicity and regenerative hyperplasia. The species-specific target organ toxicity is shown to be related to the pharmacokinetics of coumarin metabolism, with data showing rats to be particularly susceptible to liver effects and mice to be particularly susceptible to lung effects. A quantitative human health risk assessment that integrates both cancer and non-cancer effects is presented, confirming the safety of coumarin exposure from natural dietary sources as well as from its use as a perfume in personal care products. PMID:16203076

  18. Behavioral relevance of species-specific vasotocin anatomy in gregarious finches

    PubMed Central

    Kelly, Aubrey M.; Goodson, James L.

    2013-01-01

    Despite substantial species differences in the vasotocin/vasopressin (VT/VP) circuitry of the medial bed nucleus of the stria terminalis (BSTm) and lateral septum (LS; a primary projection target of BSTm VT/VP cells), functional consequences of this variation are poorly known. Previous experiments in the highly gregarious zebra finch (Estrildidae: Taeniopygia guttata) demonstrate that BSTm VT neurons promote gregariousness in a male-specific manner and reduce anxiety in both sexes. However, in contrast to the zebra finch, the less gregarious Angolan blue waxbill (Estrildidae: Uraeginthus angolensis) exhibits fewer VT-immunoreactive cells in the BSTm as well as differences in receptor distribution across the LS subnuclei, suggesting that knockdown of VT production in the BSTm would produce behavioral effects in Angolan blue waxbills that are distinct from zebra finches. Thus, we here quantified social contact, gregariousness (i.e., preference for the larger of two groups), and anxiety-like behavior following bilateral antisense knockdown of VT production in the BSTm of male and female Angolan blue waxbills. We find that BSTm VT neurons promote social contact, but not gregariousness (as in male zebra finches), and that antisense effects on social contact are significantly stronger in male waxbills than in females. Knockdown of BSTm VT production has no effect on anxiety-like behavior. These data provide novel evidence that species differences in the VT/VP circuitry arising in the BSTm are accompanied by species-specific effects on affiliation behaviors. PMID:24381536

  19. Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus.

    PubMed

    Aleti, Gajender; Lehner, Sylvia; Bacher, Markus; Compant, Stéphane; Nikolic, Branislav; Plesko, Maja; Schuhmacher, Rainer; Sessitsch, Angela; Brader, Günter

    2016-09-01

    Cyclic lipopeptides (cLP) and especially surfactins produced by Bacillus spp. trigger biofilm formation and root colonization and are crucial for biocontrol activity and systemic resistance in plants. Bacillus atrophaeus 176s isolated from the moss Tortella tortuosa produces the cLP fengycins, iturins and surfactins, possesses antifungal activities and can protect tomato, lettuce and sugar beet against Rhizoctonia solani infection. In B. atrophaeus we identified for the first time the variant surfactin C, which differs from surfactin A produced by B. subtilis and B. amyloliquefaciens by an isoleucine instead of a leucine at position 7 of the lipopeptide backbone. The analysis of the complete surfactin gene clusters revealed that the dissimilarity is encoded in the adenylation domain of srfC and show that surfactin variations are distributed in a species-specific manner in bacilli. We demonstrate that the surfactin A and C with subtle structural differences have varying signal strengths on biofilm formation and root colonization and act specifically on the respective producing strain. This became evident as biofilm formation and root colonization but not swarming motility in surfactin biosynthesis mutants was restored differentially in the presence of exogenously supplemented cognate and non-cognate surfactin variants. PMID:27306252

  20. 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

  1. 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

    2012-03-01

    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. PMID:22324365

  2. 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

  3. 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

  4. Species-specific alternative splicing generates a catalytically inactive form of human hormone-sensitive lipase.

    PubMed

    Laurell, H; Grober, J; Vindis, C; Lacombe, T; Dauzats, M; Holm, C; Langin, D

    1997-11-15

    Hormone-sensitive lipase (HSL) catalyses the rate-limiting step of adipose tissue lipolysis. The enzyme is also expressed in steroidogenic tissues, mammary gland, muscle tissues and macrophages. A novel HSL mRNA termed hHSL-S, 228 bp shorter than the full-length HSL mRNA, was detected in human adipocytes. hHSL-S mRNA results from the in-frame skipping of exon 6, which encodes the serine residue of the catalytic triad. The corresponding 80 kDa protein was identified in human adipocytes after immunoprecipitation. The truncated protein expressed in COS cells showed neither lipase nor esterase activity but was phosphorylated by cAMP-dependent protein kinase. hHSL-S mRNA was found in all human tissues expressing HSL, except brown adipose tissue from newborns. It represented approx. 20% of total HSL transcripts in human subcutaneous adipocytes. No alternative splicing was detected in other mammals. Human and mouse three-exon HSL minigenes transfected into primate and rodent cell lines reproduced the splicing pattern of the endogenous HSL genes. Analysis of hybrid human/mouse minigenes transfected into human cell lines showed that cis-acting elements responsible for the skipping of human exon 6 were restricted to a 247 bp region including exon 6 and the first 19 nt of intron 6. Moreover, divergence in exonic splicing elements between mouse and human was shown to be critical for the species-specific alternative splicing. PMID:9359844

  5. 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. PMID:17362333

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

    PubMed

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

    2011-01-01

    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. PMID:21341214

  7. 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. PMID:27190163

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

    PubMed

    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

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

    PubMed

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

    2016-01-01

    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

  10. 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

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

    PubMed

    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

  12. PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species.

    PubMed Central

    Ersek, T; Schoelz, J E; English, J T

    1994-01-01

    We used PCR to differentiate species in the genus Phytophthora, which contains a group of devastating plant pathogenic fungi. We focused on Phytophthora parasitica, a species that can infect solanaceous plants such as tomato, and on Phytophthora citrophthora, which is primarily a citrus pathogen. Oligonucleotide primers were derived from sequences of a 1,300-bp P. parasitica-specific DNA segment and of an 800-bp P. citrophthora-specific segment. Under optimal conditions, the primers developed for P. parasitica specifically amplified a 1,000-bp sequence of DNA from isolates of P. parasitica. Primers for P. citrophthora similarly and specifically amplified a 650-bp sequence of DNA from isolates of P. citrophthora. Detectable amplification of these specific DNA sequences required picogram quantities of chromosomal DNA. Neither pair of primers amplified these sequences with DNAs from other species of Phytophthora or from the related genus Pythium. DNAs from P. parasitica and P. citrophthora growing in infected tomato stem tissue were amplified as distinctly as DNAs from axenic cultures of each fungal species. This is the first report on PCR-driven amplification with Phytophthora species-specific primers. Images PMID:8074533

  13. Species-specific optical genosensors for the detection of mycotoxigenic Fusarium fungi in food samples.

    PubMed

    Peltomaa, Riikka; Vaghini, Silvia; Patiño, Belén; Benito-Peña, Elena; Moreno-Bondi, María C

    2016-09-01

    Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label. The developed genosensors had detection limits of 1.8 pM and 3.0 pM for F. proliferatum and F. verticillioides, respectively, using synthetic DNA targets. Furthermore, the biosensors were used to analyze natural fungal contamination of commercial maize samples. After amplification of the genomic DNA the sensors detected the presence of the fungi, in accordance with previous results obtained with PCR. No cross-reactivity between F. verticillioides and F. proliferatum, or other fungi species tested, was observed. The developed biosensors can provide a valuable tool to evaluate the potential for mycotoxin contamination in conditions where detection of mycotoxins directly is challenging. PMID:27543032

  14. 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. PMID:26456330

  15. 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. PMID:25307691

  16. 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. PMID:26829069

  17. Rapid Identification of Candida Species with Species-Specific DNA Probes

    PubMed Central

    Elie, Cheryl M.; Lott, Timothy J.; Reiss, Errol; Morrison, Christine J.

    1998-01-01

    Rapid identification of Candida species has become more important because of an increase in infections caused by species other than Candida albicans, including species innately resistant to azole antifungal drugs. We previously developed a PCR assay with an enzyme immunoassay (EIA) format to detect amplicons from the five most common Candida species by using universal fungal primers and species-specific probes directed to the ITS2 region of the gene for rRNA. We designed probes to detect seven additional Candida species (C. guilliermondii, C. kefyr, C. lambica, C. lusitaniae, C. pelliculosa, C. rugosa, and C. zeylanoides) included in the API 20C sugar assimilation panel, five probes for species not identified by API 20C (C. haemulonii, C. norvegica, C. norvegensis, C. utilis, and C. viswanathii), and a probe for the newly described species C. dubliniensis, creating a panel of 18 Candida species probes. The PCR-EIA correctly identified multiple strains of each species tested, including five identified as C. albicans by the currently available API 20C database but determined to be C. dubliniensis by genotypic and nonroutine phenotypic characteristics. Species identification time was reduced from a mean of 3.5 days by conventional identification methods to 7 h by the PCR-EIA. This method is simple, rapid, and feasible for identifying Candida species in clinical laboratories that utilize molecular identification techniques and provides a novel method to differentiate the new species, C. dubliniensis, from C. albicans. PMID:9774576

  18. Species-specific signals for the splicing of a short Drosophila intron in vitro.

    PubMed Central

    Guo, M; Lo, P C; Mount, S M

    1993-01-01

    The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species. Images PMID:8423778

  19. 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

  20. 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

  1. 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

  2. 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. PMID:22697906

  3. 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. PMID:25008269

  4. Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA

    PubMed Central

    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. PMID:26761677

  5. 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. PMID:23274850

  6. Host cell species-specific effect of cyclosporine A on simian immunodeficiency virus replication

    PubMed Central

    2012-01-01

    Background An understanding of host cell factors that affect viral replication contributes to elucidation of the mechanism for determination of viral tropism. Cyclophilin A (CypA), a peptidyl-prolyl cis-trans isomerase (PPIase), is a host factor essential for efficient replication of human immunodeficiency virus type 1 (HIV-1) in human cells. However, the role of cyclophilins in simian immunodeficiency virus (SIV) replication has not been determined. In the present study, we examined the effect of cyclosporine A (CsA), a PPIase inhibitor, on SIV replication. Results SIV replication in human CEM-SS T cells was not inhibited but rather enhanced by treatment with CsA, which inhibited HIV-1 replication. CsA treatment of target human cells enhanced an early step of SIV replication. CypA overexpression enhanced the early phase of HIV-1 but not SIV replication, while CypA knock-down resulted in suppression of HIV-1 but not SIV replication in CEM-SS cells, partially explaining different sensitivities of HIV-1 and SIV replication to CsA treatment. In contrast, CsA treatment inhibited SIV replication in macaque T cells; CsA treatment of either virus producer or target cells resulted in suppression of SIV replication. SIV infection was enhanced by CypA overexpression in macaque target cells. Conclusions CsA treatment enhanced SIV replication in human T cells but abrogated SIV replication in macaque T cells, implying a host cell species-specific effect of CsA on SIV replication. Further analyses indicated a positive effect of CypA on SIV infection into macaque but not into human T cells. These results suggest possible contribution of CypA to the determination of SIV tropism. PMID:22225545

  7. 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

  8. 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

  9. 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. PMID:26302433

  10. 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

  11. 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

  12. 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

  13. 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. PMID:26804654

  14. 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. PMID:25827840

  15. Species Specific Differences of CD1d Oligomer Loading In Vitro

    PubMed Central

    Paletta, Daniel; Fichtner, Alina Suzann; Starick, Lisa; Porcelli, Steven A.; Savage, Paul B.; Herrmann, Thomas

    2015-01-01

    CD1d molecules are MHC class I-like molecules that present glycolipids to iNKT cells. The highly conserved interaction between CD1d:α-Galactosylceramide (αGC) complexes and the iNKT TCR not only defines this population of αβ T cells but can also be used for its direct identification. Therefore, CD1d oligomers are a widely used tool for iNKT cell related investigations. To this end, the lipid chains of the antigen have to be inserted into the hydrophobic pockets of the CD1d binding cleft, often with help of surfactants. In this study, we investigated the influence of different surfactants (Triton X-100, Tween 20, Tyloxapol) on in vitro loading of CD1d molecules derived from four different species (human, mouse, rat and cotton rat) with αGC and derivatives carrying modifications of the acyl-chain (DB01-1, PBS44) and a 6-acetamido-6-deoxy-addition at the galactosyl head group (PBS57). We also compared rat CD1d dimers with tetramers and staining of an iNKT TCR transductant was used as readout for loading efficacy. The results underlined the importance of CD1d loading efficacy for proper analysis of iNKT TCR binding and demonstrated the necessity to adjust loading conditions for each oligomer/glycolipid combination. The efficient usage of surfactants as a tool for CD1d loading was revealed to be species-specific and depending on the origin of the CD1d producing cells. Additional variation of surfactant-dependent loading efficacy between tested glycolipids was influenced by the acyl-chain length and the modification of the galactosyl head group with PBS57 showing the least dependence on surfactants and the lowest degree of species-dependent differences. PMID:26599805

  16. Assessment of Anopheles salivary antigens as individual exposure biomarkers to species-specific malaria vector bites

    PubMed Central

    2012-01-01

    Background Malaria transmission occurs during the blood feeding of infected anopheline mosquitoes concomitant with a saliva injection into the vertebrate host. In sub-Saharan Africa, most malaria transmission is due to Anopheles funestus s.s and to Anopheles gambiae s.l. (mainly Anopheles gambiae s.s. and Anopheles arabiensis). Several studies have demonstrated that the immune response against salivary antigens could be used to evaluate individual exposure to mosquito bites. The aim of this study was to assess the use of secreted salivary proteins as specific biomarkers of exposure to An. gambiae and/or An. funestus bites. Methods For this purpose, salivary gland proteins 6 (SG6) and 5′nucleotidases (5′nuc) from An. gambiae (gSG6 and g-5′nuc) and An. funestus (fSG6 and f-5′nuc) were selected and produced in recombinant form. The specificity of the IgG response against these salivary proteins was tested using an ELISA with sera from individuals living in three Senegalese villages (NDiop, n = 50; Dielmo, n = 38; and Diama, n = 46) that had been exposed to distinct densities and proportions of the Anopheles species. Individuals who had not been exposed to these tropical mosquitoes were used as controls (Marseille, n = 45). Results The IgG responses against SG6 recombinant proteins from these two Anopheles species and against g-5′nucleotidase from An. gambiae, were significantly higher in Senegalese individuals compared with controls who were not exposed to specific Anopheles species. Conversely, an association was observed between the level of An. funestus exposure and the serological immune response levels against the f-5′nucleotidase protein. Conclusion This study revealed an Anopheles salivary antigenic protein that could be considered to be a promising antigenic marker to distinguish malaria vector exposure at the species level. The epidemiological interest of such species-specific antigenic markers is discussed. PMID:23276246

  17. 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.

  18. Species-specific polymerase chain reaction primer sets for the diagnosis of Tenacibaculum maritimum infection.

    PubMed

    Avendaño-Herrera, Rubén; Magariños, Beatriz; Toranzo, Alicia E; Beaz, Roxana; Romalde, Jesús L

    2004-11-23

    In this study the specificity and sensitivity of 2 primer pairs, MAR1-MAR2 and Mar1-Mar2, for the detection of Tenacibaculum maritimum were evaluated in parallel using 79 T. maritimum strains isolated from different fish species, as well as 53 representatives of related and unrelated bacterial species. Both primer pairs were species-specific for T. maritimum, since no amplification products were obtained from chromosomal DNA of the non-T. maritimum bacteria tested. However, whereas MAR1-MAR2 identified all the T. maritimum strains studied, producing a unique and clear PCR band of the expected 1088 bp length, the Marl-Mar2 primer pair failed to amplify the 400 bp specific band in 3 sole isolates. To verify if these strains belonged to T. maritimum species, 2 endonucleases (PvuI and SacII) were selected as the most adequate enzymes to confirm the specificity of the MAR1-MAR2 amplified fragment. The digestion patterns obtained with both endonucleases supported the assignation of all the strains to T. maritimum. The sensitivity of both PCR detection methods was also different, showing a reduction of sensitivity in at least one order of magnitude of the Marl-Mar2 primer pair in comparison with MAR1-MAR2. When the MAR-MAR2 PCR protocol was applied to different seeded turbot tissues, the detection limit was 10(2) to 10(4) T. maritimum cells per reaction. In addition, a nested PCR protocol for detection of this pathogens based on MAR1-MAR2 was developed, which increased the sensitivity by approximately 2 orders of magnitude, ranging from 1 to 250 T. maritimum cells per reaction depending on the tissue employed. The tissues that allowed the most easy detection of T. maritimum were the skin and mucus. Based on the findings reported here, we propose the nested PCR protocol as the most adequate for an accurate detection of T. maritimum in diagnostic pathology as well as in epidemiological studies of gliding bacterial disease of marine fish. PMID:15648833

  19. 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

  20. Neural crest-mediated bone resorption is a determinant of species-specific jaw length.

    PubMed

    Ealba, Erin L; Jheon, Andrew H; Hall, Jane; Curantz, Camille; Butcher, Kristin D; Schneider, Richard A

    2015-12-01

    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

  1. Examining the Species-Specificity of Rhesus Macaque Cytomegalovirus (RhCMV) in Cynomolgus Macaques

    PubMed Central

    Perciani, Catia T.; Russell, Justen N. Hoffman; Chan, Jacqueline K.; Janes, Michelle; Antony, Joseph M.; Pilon, Richard; Sandstrom, Paul; Willer, David O.; MacDonald, Kelly S.

    2015-01-01

    Cytomegalovirus (CMV) is a highly species-specific virus that has co-evolved with its host over millions of years and thus restricting cross-species infection. To examine the extent to which host restriction may prevent cross-species research between closely related non-human primates, we evaluated experimental infection of cynomolgus macaques with a recombinant rhesus macaque-derived CMV (RhCMV-eGFP). Twelve cynomolgus macaques were randomly allocated to three groups: one experimental group (RhCMV-eGFP) and two control groups (UV-inactivated RhCMV-eGFP or media alone). The animals were given two subcutaneous inoculations at week 0 and week 8, and a subset of animals received an intravenous inoculation at week 23. No overt clinical or haematological changes were observed and PBMCs isolated from RhCMV-eGFP inoculated animals had comparable eGFP- and IE-1-specific cellular responses to the control animals. Following inoculation with RhCMV-eGFP, we were unable to detect evidence of infection in any blood or tissue samples up to 4 years post-inoculation, using sensitive viral co-culture, qPCR, and Western blot assays. Co-culture of urine and saliva samples demonstrated the presence of endogenous cynomolgus CMV (CyCMV) cytopathic effect, however no concomitant eGFP expression was observed. The absence of detectable RhCMV-eGFP suggests that the CyCMV-seropositive cynomolgus macaques were not productively infected with RhCMV-eGFP under these inoculation conditions. In a continued effort to develop CMV as a viral vector for an HIV/SIV vaccine, these studies demonstrate that CMV is highly restricted to its host species and can be highly affected by laboratory cell culture. Consideration of the differences between lab-adapted and primary viruses with respect to species range and cell tropism should be a priority in evaluating CMV as vaccine vector for HIV or other pathogens at the preclinical development stage. PMID:25822981

  2. 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

  3. 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

  4. Validation of a TaqMan diagnostic assay for the systematic development of Phytophthora genus and species specific markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. Species Specificity of the Putative Male Antennal Aphrodisiac Pheromone in Leptopilina heterotoma, Leptopilina boulardi, and Leptopilina victoriae

    PubMed Central

    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. PMID:26839881

  7. 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. PMID:26839881

  8. Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses.

    PubMed

    Oberste, M Steven; Maher, Kaija; Williams, Alford J; Dybdahl-Sissoko, Naomi; Brown, Betty A; Gookin, Michelle S; Peñaranda, Silvia; Mishrik, Nada; Uddin, Moyez; Pallansch, Mark A

    2006-01-01

    The 65 serotypes of human enteroviruses are classified into four species, Human enterovirus (HEV) A to D, based largely on phylogenetic relationships in multiple genome regions. The 3'-non-translated region of enteroviruses is highly conserved within a species but highly divergent between species. From this information, species-specific RT-PCR primers were developed that can be used to rapidly screen collections of enterovirus isolates to identify species of interest. The four primer pairs were 100 % specific when tested against enterovirus prototype strains and panels of isolates of known serotype (a total of 193 isolates). For evaluation in a typical application, the species-specific primers were used to screen 186 previously uncharacterized non-polio enterovirus isolates. The HEV-B primers amplified 68.3 % of isolates, while the HEV-A and HEV-C primers accounted for 9.7 and 11.3 % of isolates, respectively; no isolates were amplified with the HEV-D primers. Twelve isolates (6.5 %) were amplified by more than one primer set and eight isolates (4.3 %) were not amplified by any of the four primer pairs. Serotypes were identified by partial sequencing of the VP1 capsid gene, and in every case sequencing confirmed that the species-specific PCR result was correct; the isolates that were amplified by more than one species-specific primer pair were mixtures of two (11 isolates) or three (one isolate) species of viruses. The eight isolates that were not amplified by the species-specific primers comprised four new serotypes (EV76, EV89, EV90 and EV91) that appear to be unique members of HEV-A based on VP1, 3D and 3'-non-translated region sequences. PMID:16361424

  9. Rapid and reliable identification of Staphylococcus equorum by a species-specific PCR assay targeting the sodA gene.

    PubMed

    Blaiotta, Giuseppe; Ercolini, Danilo; Mauriello, Gianluigi; Salzano, Giovanni; Villani, Francesco

    2004-11-01

    Rapid and reliable identification of Staphylococcus (S.) equorum was achieved by species-specific PCR assays. A set of primers targeting the manganese-dependent superoxide dismutase (sodA) gene of S. equorum was designed. Species-specificity of the primer set was evaluated by using a total of 112 strains (including 27 reference strains of the DSM collection), representing 26 different species of the genus Staphylococcus, 3 species of the genus Kocuria, and different strains of Macrococcus caseolyticus. By using primers SdAEqF and SdAEqR the expected PCR fragment was obtained only when DNA from S. equorum strains was used as template. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. equorum strains. PMID:15612627

  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. Development of species-specific hybridization probes for marine luminous bacteria by using in vitro DNA amplification

    SciTech Connect

    Wimpee, C.F.; Nadeau, T.L.; Nealson, K.H. )

    1991-05-01

    By using two highly conserved regions of the luxA gene as primers, polymerase chain reaction amplification methods were used to prepare species-specific probes against the luciferase gene from four major groups of marine luminous bacteria. Laboratory studies with test strains indicated that three of the four probes cross-reacted with themselves and with one or more of the other species at low stringencies but were specific for members of their own species at high stringencies. The fourth probe, generated from Vibrio harveyi DNA, a cross-reacted with DNAs from two closely related species, V. orientalis and V. vulnificus. When nonluminous cultures were tested with the species-specific probes, no false-positive results were observed, even at low stringencies. Two field isolates were correctly identified as Photobacterium phosphoreum by using the species-specific hybridization probes at high stringency. A mixed probe (four different hybridization probes) used at low stringency gave positive results with all of the luminous bacteria tested, including the terrestrial species Xenorhabdus luminescens, and the taxonomically distinct marine bacterial species Shewanella hanedai; minimal cross-hybridization with these species was seen at higher stringencies.

  12. DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India.

    PubMed

    Rebijith, K B; Asokan, R; Kumar, N K Krishna; Srikumar, K K; Ramamurthy, V V; Bhat, P Shivarama

    2012-10-01

    Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed <1% intraspecific divergence for all four species examined, whereas the interspecific distances ranged from 7 to 13%. This study showed that the DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any. PMID:23068182

  13. Molecular identification of prey in the stomach contents of Harp Seals (Pagophilus groenlandicus) using species-specific oligonucleotides.

    PubMed

    Marshall, H D; Hart, K A; Yaskowiak, E S; Stenson, G B; McKinnon, D; Perry, E A

    2010-01-01

    All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey-species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA with species-specific primers, we developed a DNA-based method that complements HPA and provides an alternative means to detect prey from stomach contents of Harp Seals (Pagophilus groenlandicus). The target size that could be reliably amplified was determined using a digestion time-series of Atlantic Cod (Gadus morhua) tissue in simulated seal stomachs. Various target lengths were trialed using general teleost primers; amplicons of approximately 800 bp or less were consistently obtained. Prey species-specific PCR primers for Atlantic Cod, Arctic Cod (Boreogadus saida) and Capelin (Mallotus villosus) were designed and tested with DNA from the stomach contents of 31 Harp Seals. Amplicons were obtained for all three species-specific primer sets. Amplification results compared with HPA revealed: (i) Atlantic Cod hard parts were found in five stomachs where no Atlantic Cod DNA amplified, suggesting that Atlantic Cod may be over-represented in the estimated diet, (ii) amplification of Arctic Cod DNA occurred for 17 stomachs, including all 12 stomachs with, and five stomachs without, Arctic Cod hard parts, and (iii) Capelin DNA amplified for four of five stomachs with Capelin hard parts and for one stomach without Capelin hard parts. We conclude that PCR amplification of specific prey DNA provides a viable means to complement Harp Seal diet analysis by HPA, but suggest that valuable information for quantitative diet analysis rests in a quantitative PCR approach. PMID:21565007

  14. 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. PMID:23352902

  15. 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. PMID:23298914

  16. 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

  17. 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

  18. 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

  19. 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. PMID:26079260

  20. 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.

  1. Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma

    PubMed Central

    Grossman, Iris; Ilani, Tal; Fleishman, Sarel Jacob; Fass, Deborah

    2016-01-01

    The secreted disulfide catalyst Quiescin sulfhydryl oxidase-1 (QSOX1) affects extracellular matrix organization and is overexpressed in various adenocarcinomas and associated stroma. Inhibition of extracellular human QSOX1 by a monoclonal antibody decreased tumor cell migration in a cell co-culture model and hence may have therapeutic potential. However, the species specificity of the QSOX1 monoclonal antibody has been a setback in assessing its utility as an anti-metastatic agent in vivo, a common problem in the antibody therapy industry. We therefore used structurally guided engineering to expand the antibody species specificity, improving its affinity toward mouse QSOX1 by at least four orders of magnitude. A crystal structure of the re-engineered variant, complexed with its mouse antigen, revealed that the antibody accomplishes dual-species targeting through altered contacts between its heavy and light chains, plus replacement of bulky aromatics by flexible side chains and versatile water-bridged polar interactions. In parallel, we produced a surrogate antibody targeting mouse QSOX1 that exhibits a new QSOX1 inhibition mode. This set of three QSOX1 inhibitory antibodies is compatible with various mouse models for pre-clinical trials and biotechnological applications. In this study we provide insights into structural blocks to cross-reactivity and set up guideposts for successful antibody design and re-engineering. PMID:26819240

  2. 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

  3. Immunohistochemical study of androgenic gland hormone: localization in the male reproductive system and species specificity in the terrestrial isopods.

    PubMed

    Hasegawa, Yuriko; Okuno, Atsuro; Nagasawa, Hiromichi

    2002-02-01

    Androgenic gland hormone (AGH) is responsible for male sexual differentiation in crustaceans. AGH of the terrestrial isopod, Armadillidium vulgare, is a heterodimetric glycoprotein. To determine the distribution of AGH in the male reproductive system, an immunohistochemical study was carried out using antibodies raised against different components of the proAGH molecule of A. vulgare, for example, the whole molecule of recombinant proAGH expressed in Escherichia coli (E. coli-rAGH), the N-terminal nonapeptide of the B chain, and the N-terminal octapeptide of the A chain. The androgenic gland (AG) showed strong immunoreactivity to all three of these antibodies, while the testis, the seminal vesicle, and the vas deferens did not show immunostaining. To examine the species specificity of AGH, the male reproductive systems in nine species of Oniscidea were examined immunohistochemically with antibody raised against E. coli-rAGH. A positive reaction was observed in the AGs of species belonging to the Armadillidiidae, Porcellionidae, and Scyphacidae families. Immunoreactivity was strongest in A. vulgare and was stronger in Armadillidiidae than in Porcellionidae or in Scyphacidae. These results suggest that structural similarity of AGH may exist among some terrestrial isopods, although AGH seems to harbor a relatively high degree of species specificity. PMID:11884067

  4. A mesocarp-and species-specific cDNA clone from oil palm encodes for sesquiterpene synthase.

    PubMed

    Shah; Cha

    2000-05-29

    The differential display method was used to isolate cDNAs corresponding to transcripts that accumulate during the period of lipid synthesis, 12-20 weeks after anthesis (WAA) in the mesocarp of two oil palms, Elaeis oleifera and Elaeis guineensis, Tenera. DNA-free total RNA from mesocarp and kernel of E. guineensis, Tenera and E. oleifera (15 WAA) were used to obtain differential gene expression patterns between these tissues from the two species. In this report, we describe the isolation and characterization of a specific cDNA clone, MO1 (434 bp) which was shown to be mesocarp-specific as well as species-specific for E. oleifera Sequencing of this fragment showed homology to the enzyme sesquiterpene synthase. Its longer cDNA clone, pMO1 (1072 bp), isolated from a 15-week E. oleifera mesocarp cDNA library confirmed that it encodes for sesquiterpene synthase. The complete sequence of 1976 bp was obtained using 5'RACE method. Northern hybridization showed that MO1 and pMO1 mRNA transcripts are highly expressed only in the mesocarp of E. oleifera from 5 to 20 WAA. No expression was detected in the kernel (12-17 WAA) and vegetative tissues of both species nor in the mesocarp of E. guineensis. This is the first communication to document on the isolation and characterisation of a mesocarp-and species-specific cDNA clone from oil palm. PMID:10729614

  5. Species-specific multiplex PCR for the diagnosis of Brucella ovis, Actinobacillus seminis, and Histophilus somni infection in rams

    PubMed Central

    2013-01-01

    Background Infectious ovine epididymitis results in substantial economic losses worldwide due to reproductive failure and culling of breeders. The most common causative agents of these infections are Brucella ovis, Actinobacillus seminis, and Histophilus somni. The aim of this study was to develop a multiplex PCR assay for simultaneous detection of Brucella ovis, Actinobacillus seminis, and Histophilus somni with species-specific primers applied to biological samples for molecular diagnosis of these infections. Results The multiplex assay was capable of detecting B. ovis, A. seminis, and H. somni DNA simultaneously from genomic bacterial DNA samples and pool of semen samples from experimentally infected rams. The method was highly specific since it did not amplify DNA from other bacterial species that can potentially cause epididymitis in rams as well as species phylogenetically related to B. ovis. All negative control samples were negative in PCR multiplex assay. Urine can be used as an alternative to semen samples. Conclusions The species-specific multiplex PCR assay developed in this study can be successfully used for the detection of three of the most common bacterial causes of ovine epididymitis. PMID:23514236

  6. Comprehensive RNAi-based screening of human and mouse TLR pathways identifies species-specific preferences in signaling protein use.

    PubMed

    Sun, Jing; Li, Ning; Oh, Kyu-Seon; Dutta, Bhaskar; Vayttaden, Sharat J; Lin, Bin; Ebert, Thomas S; De Nardo, Dominic; Davis, Joie; Bagirzadeh, Rustam; Lounsbury, Nicolas W; Pasare, Chandrashekhar; Latz, Eicke; Hornung, Veit; Fraser, Iain D C

    2016-01-01

    Toll-like receptors (TLRs) are a major class of pattern recognition receptors, which mediate the responses of innate immune cells to microbial stimuli. To systematically determine the roles of proteins in canonical TLR signaling pathways, we conducted an RNA interference (RNAi)-based screen in human and mouse macrophages. We observed a pattern of conserved signaling module dependencies across species, but found notable species-specific requirements at the level of individual proteins. Among these, we identified unexpected differences in the involvement of members of the interleukin-1 receptor-associated kinase (IRAK) family between the human and mouse TLR pathways. Whereas TLR signaling in mouse macrophages depended primarily on IRAK4 and IRAK2, with little or no role for IRAK1, TLR signaling and proinflammatory cytokine production in human macrophages depended on IRAK1, with knockdown of IRAK4 or IRAK2 having less of an effect. Consistent with species-specific roles for these kinases, IRAK4 orthologs failed to rescue signaling in IRAK4-deficient macrophages from the other species, and only mouse macrophages required the kinase activity of IRAK4 to mediate TLR responses. The identification of a critical role for IRAK1 in TLR signaling in humans could potentially explain the association of IRAK1 with several autoimmune diseases. Furthermore, this study demonstrated how systematic screening can be used to identify important characteristics of innate immune responses across species, which could optimize therapeutic targeting to manipulate human TLR-dependent outputs. PMID:26732763

  7. 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. PMID:15869960

  8. 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. PMID:21712040

  9. 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. PMID:27174138

  10. Species-specific sequences of abalone lysin, the sperm protein that creates a hole in the egg envelope.

    PubMed Central

    Vacquier, V D; Carner, K R; Stout, C D

    1990-01-01

    Abalone eggs are contained within a rigid, elevated vitelline envelope through which the sperm must pass before reaching the egg cell membrane. Abalone spermatozoa possess an acrosomal protein called lysin that creates a hole in the egg vitelline envelope by a nonenzymatic mechanism. Lysins from two species of abalone, termed pink and red, which share the same habitat, exhibit species specificity in the dissolution of isolated egg envelopes. Cloning and sequencing the cDNAs for pink and red abalone lysins reveal transcript lengths of approximately 660 nucleotides. The open reading frames of 465 (pink) and 462 (red) nucleotides show a 13% difference. The 3' untranslated regions before the poly(A) tails are 170 (pink) and 165 (red) nucleotides long and differ from each other by about 7%. The protein sequences show nearly identical signal sequences of 18 amino acids for both lysins. The mature protein is 137 amino acids in the pink abalone and 136 in the red abalone; the two mature lysins differ in 29 of 137 amino acids (21%). The most variable region, which may account for lysin's species specificity, is at the NH2 terminus, where 11 of the 15 amino acids differ between the two species. Predictions of secondary structure indicate that both lysins contain four homologous amphiphilic alpha-helices. Images PMID:2377618