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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. X-ray induced photoconductivity in Vanadium Dioxide samples

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  6. High Resolution X-ray-Induced Acoustic Tomography

    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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  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. 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.

  17. 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.

  18. 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

  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. 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.

  1. 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).

  2. 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

  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. 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.

  2. 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.

  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. 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.

  5. 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).

  6. 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.

  7. 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.

  8. 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.

  9. 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

  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. 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

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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+.

  3. 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.}

  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-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

  15. 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

  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. 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

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

    PubMed

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

    2015-10-01

    Consumption of food products derived from porcine sources is strictly prohibited in Islam. Gelatin, mostly derived from bovine and porcine sources, has many applications in the food and pharmaceutical industries. To ensure that food products comply with halal regulations, development of valid and reliable analytical methods is very much required. In this study, a species-specific polymerase chain reaction (PCR) assay using conserved regions of mitochondrial DNA (cytochrome b gene) was performed to evaluate the halal authenticity of gelatin. After isolation of DNA from gelatin powders with known origin, conventional PCR using species-specific primers was carried out on the extracted DNA. The amplified expected PCR products of 212 and 271 bp were observed for porcine and bovine gelatin, respectively. The sensitivity of the method was tested on binary gelatin mixtures containing 0.1%, 1%, 10%, and 100% (w/w) of porcine gelatin within bovine gelatin and vice versa. Although most of the DNA is degraded due to the severe processing steps of gelatin production, the minimum level of 0.1% w/w of both porcine and bovine gelatin was detected. Moreover, eight food products labeled as containing bovine gelatin and eight capsule shells were subjected to PCR examination. The results showed that all samples contained bovine gelatin, and the absence of porcine gelatin was verified. This method of species authenticity is very useful to verify whether gelatin and gelatin-containing food products are derived from halal ingredients. PMID:25872445

  20. 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

  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. 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

  15. 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

  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. 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

  20. 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…

  1. 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.

  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. 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

  5. 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

  6. 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

  7. 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

  8. [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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  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. 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

  18. 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

  19. 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.

  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. 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

  3. 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

  4. 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

  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. 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

  8. 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

  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. 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

  13. 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

  14. 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

  15. 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

  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. 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

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

    PubMed Central

    Gallas, Genna; Waters, Elizabeth R.

    2015-01-01

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

  20. 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

    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

  2. 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

  3. 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

  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. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  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. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

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

    PubMed

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

    2016-05-01

    Absence of a municipal wastewater (WW) treatment plant results in the untreated WW discharge into the recipient. The present study investigated toxic effects and chemical composition of water extracts and fractions from untreated WW and recipient Danube River (DR). Samples were prepared by solid-phase extraction and silica gel fractionation and screened for EROD activity and cytotoxicity using aquatic models, comprising of fish liver cells (PLHC-1) and a model of the early development of zebrafish embryos, while rat (H4IIE) and human (HepG2) hepatoma cells served as mammalian models. Polar fraction caused cytotoxicity and increased the EROD activity in PLHC-1 cells, and increased mortality and developmental abnormalities in developing zebrafish embryos. In H4IIE, polar fraction induced inhibition of cell growth and increased EROD activity, whereas HepG2 exerted low or no response to the exposure. Non-polar and medium-polar fractions were ineffective. Tentative identification by GC/MS showed that WW is characterized by the hydrocarbons, alkylphenols, plasticizers, and a certain number of benzene derivatives and organic acids. In DR, smaller number of organic compounds was identified and toxicity was less pronounced than in WW treatments. The present study revealed the potent toxic effect of polar fraction of untreated WW, with biological responses varying in sensitivity across organisms. Obtained results confirmed that fraction- and species-specific toxicity should be considered when assessing health risk of environmental pollution. PMID:26829069

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  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. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  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 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  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. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Physical localisation of repetitive DNA sequences in Alstroemeria: karyotyping of two species with species-specific and ribosomal DNA.

    PubMed

    Kamstra, S A; Kuipers, A G; De Jeu, M J; Ramanna, M S; Jacobsen, E

    1997-10-01

    Fluorescence in situ hybridization (FISH) was used to localise two species-specific repetitive DNA sequences, A001-I and D32-13, and two highly conserved 25S and 5S rDNA sequences on the metaphase chromosomes of two species of Alstroemeria. The Chilean species, Alstroemeria aurea (2n = 16), has abundant constitutive heterochromatin, whereas the Brazilian species, Alstroemeria inodora, has hardly any heterochromatin. The A. aurea specific A001-I probe hybridized specifically to the C-band regions on all chromosomes. The FISH patterns on A. inodora chromosomes using species-specific probe D32-13 resembled the C-banding pattern and the A001-I pattern on A. aurea chromosomes. There were notable differences in number and distribution of rDNA sites between the two species. The 25S rDNA probe revealed 16 sites in A. aurea that closely colocalised with A001-I sites and 12 in A. inodora that were predominantly detected in the centromeric regions. FISH karyotypes of the two Alstroemeria species were constructed accordingly, enabling full identification of all individual chromosomes. These FISH karyotypes will be useful for monitoring the chromosomes of both Alstroemeria species in hybrids and backcross derivatives. PMID:9352644

  9. Species-specific patterns of diel migration into the Oxygen Minimum Zone by euphausiids in the Humboldt Current Ecosystem

    NASA Astrophysics Data System (ADS)

    Antezana, Tarsicio

    2009-12-01

    A series of stratified bongo net samples taken over a 2 day period at ca. 18°S, about 20 nm off the coast of Peru, South America, suggest species-specific patterns of diel vertical migration into the Oxygen Minimum Zone (OMZ) of the Humboldt Current Ecosystem (HCE). The OMZ was the most dramatic feature of the water column and seemed to determine the extent of migration: Stylocheiron affine migrated only to the shallow oxycline; whereas Euphausia mucronata, Euphausia eximia, Euphausia distinguenda and Euphausia tenera migrated to the core of the OMZ; and Nematoscelis gracilis to beneath the core of the OMZ. Some differences were also found in the timing and duration of the ascent and descent, and residence times in shallow and deep layers. E. mucronata, N. gracilis and E. distinguenda displayed a normal descent during sunrise, and ascent during sunset. E. eximia and E. tenera also descended during sunrise but seemed to begin their ascent earlier in the afternoon and consequently shortened their deep residence times. S. affine showed the most extended residence times at the shallow layer and the shortest vertical displacement. Day and night vertical stratification and differences in the timing of migration into and out of the OMZ of the HCE suggest a community structure based on habitat partitioning whereby species avoided co-occurrence in time and space. Species-specific patterns of vertical stratification and migratory chronology are examined with regard to body and gill sizes, feeding adaptations of euphausiids, and potential food resources at the OMZ.

  10. Selective MS screening reveals a sex pheromone in Caenorhabditis briggsae and species-specificity in indole ascaroside signalling.

    PubMed

    Dong, Chuanfu; Dolke, Franziska; von Reuss, Stephan H

    2016-08-14

    The indole ascarosides (icas) represent a highly potent class of nematode-derived modular signalling components that integrate structural inputs from amino acid, carbohydrate, and fatty acid metabolism. Comparative analysis of the crude exo-metabolome of hermaphroditic Caenorhabditis briggsae using a highly sensitive mass spectrometric screen reveals an indole ascaroside blend dominated by two new components. The structures of isolated icas#2 and icas#6.2 were determined by NMR spectroscopy and confirmed by total synthesis and chemical correlation. Low atto- to femtomolar amounts of icas#2 and icas#6.2 act in synergism to attract males indicating a function as sex pheromone. Comparative analysis of 14 Caenorhabditis species further demonstrates that species-specific indole ascaroside biosynthesis is highly conserved in the Elegans group. Functional characterization of the dominating indole ascarosides icas#2, icas#3, and icas#9 reveals a high degree of species-specificity and considerable variability with respect to gender-specificity, thus, confirming that indole ascarosides modulate different biological functions within the Elegans group. Although the nematode response was usually most pronounced towards conspecific signals, Caenorhabditis brenneri, the only species of the Elegans group that does not produce any indole ascarosides, exhibits a robust response to icas#2 suggesting the potential for interspecies interactions. PMID:27381649

  11. Identification of species in tribe Brassiceae by dot-blot hybridization using species-specific ITS1 probes.

    PubMed

    Tonosaki, K; Nishio, Takeshi

    2010-10-01

    Simple, reliable methods for identification of species are required for management of many species and lines in a plant gene bank. Species-specific probes were designed from published sequences of the ITS1 region in rDNA of 16 species in Brassica and its related genera, and used as probes for dot-blot hybridization with plant genomic DNA. All the probes detected species-specific signals at dot-blots of genomic DNAs of the 16 species in Brassica, Diplotaxis, Eruca, and Raphanus. Signals of the Brassica digenomic species in the U's triangle, i.e., B. napus, B. juncea, and B. carinata, were detected by the probes of their parental monogenomic species, i.e., B. rapa, B. nigra, and B. oleracea. The probe for B. oleracea showed signals of B. balearica, B. cretica, B. incana, B. insularis, and B. macrocarpa, which have the C genome as B. oleracea. Eruca vesicaria DNA was detected by the probe for E. sativa, which has been classified as a subspecies of E. vescaria. DNA of leaf tissue extracted by an alkaline solution and seed DNA prepared by the NaI method can be used directly for dot-blotting. Misidentification of species was revealed in 20 accessions in the Tohoku University Brassica Seed Bank. These results indicate dot-blot hybridization to be a simple and efficient technique for identification of plant species in a gene bank. PMID:20683723

  12. 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

  13. Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates.

    PubMed

    Dalmastri, Claudia; Pirone, Luisa; Tabacchioni, Silvia; Bevivino, Annamaria; Chiarini, Luigi

    2005-05-01

    In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species. PMID:15869960

  14. 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

  15. Coronavirus species specificity: murine coronavirus binds to a mouse-specific epitope on its carcinoembryonic antigen-related receptor glycoprotein.

    PubMed Central

    Compton, S R; Stephensen, C B; Snyder, S W; Weismiller, D G; Holmes, K V

    1992-01-01

    Like most coronaviruses, the coronavirus mouse hepatitis virus (MHV) exhibits strong species specificity, causing natural infection only in mice. MHV-A59 virions use as a receptor a 110- to 120-kDa glycoprotein (MHVR) in the carcinoembryonic antigen (CEA) family of glycoproteins (G. S. Dveksler, M. N. Pensiero, C. B. Cardellichio, R. K. Williams, G. S. Jiang, K. V. Holmes, and C. W. Dieffenbach, J. Virol. 65:6881-6891, 1991; and R. K. Williams, G. S. Jiang, and K. V. Holmes, Proc. Natl. Acad. Sci. USA 88:5533-5536, 1991). The role of virus-receptor interactions in determining the species specificity of MHV-A59 was examined by comparing the binding of virus and antireceptor antibodies to cell lines and intestinal brush border membranes (BBM) from many species. Polyclonal antireceptor antiserum (anti-MHVR) raised by immunization of SJL/J mice with BALB/c BBM recognized MHVR specifically in immunoblots of BALB/c BBM but not in BBM from adult SJL/J mice that are resistant to infection with MHV-A59, indicating a major difference in epitopes between MHVR and its SJL/J homolog which does not bind MHV (7). Anti-MHVR bound to plasma membranes of MHV-susceptible murine cell lines but not to membranes of human, cat, dog, monkey, or hamster cell lines. Cell lines from these species were resistant to MHV-A59 infection, and only the murine cell lines tested were susceptible. Pretreatment of murine fibroblasts with anti-MHVR prevented binding of radiolabeled virions to murine cells and prevented virus infection. Solid-phase virus-binding assays and virus overlay protein blot assays showed that MHV-A59 virions bound to MHVR on intestinal BBM from MHV-susceptible mouse strains but not to proteins on intestinal BBM from humans, cats, dogs, pigs, cows, rabbits, rats, cotton rats, or chickens. In immunoblots of BBM from these species, both polyclonal and monoclonal antireceptor antibodies that block MHV-A59 infection of murine cells recognized only the murine CEA-related glycoprotein

  16. In silico evidence for the species-specific conservation of mosquito retroposons: implications as a molecular biomarker

    PubMed Central

    Byarugaba, Wilson; Kajumbula, Henry; Wayengera, Misaki

    2009-01-01

    Background Mosquitoes are the transmissive vectors for several infectious pathogens that affect man. However, the control of mosquitoes through insecticide and pesticide spraying has proved difficult in the past. We hypothesized that, by virtue of their reported vertical inheritance among mosquitoes, group II introns – a class of small coding ribonucleic acids (scRNAs) – may form a potential species-specific biomarker. Structurally, introns are a six-moiety complex. Depending on the function of the protein encoded within the IV moiety, the highly mobile class of group II introns or retroposons is sub-divided into two: Restriction Endonuclease (REase)-like and Apurinic aPyramydinic Endonuclease (APE)-like. REase-like retroposons are thought to be the ancestors of APE retroposons. Our aim in this study was to find evidence for the highly species-specific conservation of the APE subclass of mosquito retroposons. Methods and Results In silico targeted sequence alignments were conducted across a 1,779-organism genome database (1,518 bacterial, 59 archeal, 201 eukaryotic, and the human), using three mosquito retroposon sequence tags (RST) as BLASTN queries [AJ970181 and AJ90201 of Culex pipien origin and AJ970301 of Anoplese sinensis origin]. At a calibration of E = 10, A & D = 100, default filtration and a homology cut-off of >95% identity, no hits were found on any of the 1,518 bacterial genomes. Eleven (100%) and 15 (100%) hits obtained on the 201-eukaryote genome database were homologs (>95% score) of C.pipien quinquefasciatus JHB retroposons, but none of An. sinensis. Twenty and 221 low score (30–43% identity) spurious hits were found at flanking ends of genes and contigs in the human genome with the C.pipien and An. sinensis RSTs respectively. Functional and positional inference revealed these to be possible relatives of human genomic spliceosomes. We advance two models for the application of mosquito RST: as precursors for developing molecular biomarkers for

  17. Development of species identification in ducklings: IV. Change in species-specific perception caused by auditory deprivation.

    PubMed

    Gottlieb, G

    1978-06-01

    The purpose of the present experiments was to identify the change in species-specific perception that underlies the aurally deprived ducklings' lack pf preference or discrimination in the mallard versus chicken call test. Among other acoustic differences, the mallard and chicken maternal calls differ in repetition rate (3.7 and 2.3 notes/sec, respectively). The present experiments showed the dimension of repetition rate to be uppermost in the perceptual hierarchy underlying the auditory aspect of species identification in Peking ducklings. The relatively narrow species-typical repetition-rate preferences of normal Peking ducklings (about 4--6 notes/sec) is lacking in the aurally deprived ducklings, and they respond to lower rates than usual (2.3 notes/sec). This broadening of the range of responsiveness on a perceptual dimension (repetition rate) that is basic to species identification accounts for the devocal ducklings' lack of discrimination in the mallard versus chicken call test. PMID:681560

  18. Detection of all Chlamydophila and Chlamydia spp. of veterinary interest using species-specific real-time PCR assays.

    PubMed

    Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad

    2010-12-01

    The aim of the present study was to analyse the occurrence of chlamydiae in several mammalian host species. Clinical samples that previously tested positive in a Chlamydiaceae-specific real-time PCR were retested using six species-specific real-time PCR assays to identify the chlamydial species involved. Chlamydophila (Cp.) abortus was the agent most frequently found in cattle, sheep, horses, goats, and pigs. Detection in cattle of Cp. psittaci (11% of samples) and Chlamydia (C.) suis (9%), as well as Cp. psittaci in a goat sample was somewhat unexpected. DNA of two different chlamydiae was identified in 56 (12.7%) of 440 samples tested. Cp. felis was the predominant species found in cats, while in guinea pigs and rabbits only Cp. caviae was detected. Interestingly, the latter two pathogens were also identified in samples from dogs. The data show that mixed chlamydial infections are not rare and suggest an extended host range of individual species. PMID:19733907

  19. New real-time PCR tests for species-specific detection of Chlamydophila psittaci and Chlamydophila abortus from tissue samples.

    PubMed

    Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad

    2009-08-01

    Chlamydophila psittaci and Chlamydophila abortus are the causative agents of avian chlamydiosis (psittacosis) and ovine enzootic abortion, respectively. Both pathogens are known to possess zoonotic potential. Due to their close genetic relatedness, direct and rapid species identification is difficult. In the present study, new real-time PCR assays are reported for both species. The tests are based on highly specific probes targeting the ompA gene region and were conducted as duplex PCRs including an internal amplification control. The Cp. psittaci assay successfully passed a proficiency test at national level. Examination of field samples revealed Cp. psittaci as the dominating species in birds, but also Cp. abortus in a few psittacines. Real-time PCR assays for species-specific detection of Cp. psittaci and Cp. abortus are suited for routine diagnosis, which renders them important tools for the recognition of outbreaks of psittacosis and ovine enzootic abortion. PMID:18413292

  20. Take time to smell the frogs: vocal sac glands of reed frogs (Anura: Hyperoliidae) contain species-specific chemical cocktails

    PubMed Central

    Starnberger, Iris; Poth, Dennis; Peram, Pardha Saradhi; Schulz, Stefan; Vences, Miguel; Knudsen, Jette; Barej, Michael F; Rödel, Mark-Oliver; Walzl, Manfred; Hödl, Walter

    2013-01-01

    Males of all reed frog species (Anura: Hyperoliidae) have a prominent, often colourful, gular patch on their vocal sac, which is particularly conspicuous once the vocal sac is inflated. Although the presence, shape, and form of the gular patch are well-known diagnostic characters for these frogs, its function remains unknown. By integrating biochemical and histological methods, we found strong evidence that the gular patch is a gland producing volatile compounds, which might be emitted while calling. Volatile compounds were confirmed by gas chromatography–mass spectrometry in the gular glands in 11 species of the hyperoliid genera Afrixalus, Heterixalus, Hyperolius, and Phlyctimantis. Comparing the gular gland contents of 17 specimens of four sympatric Hyperolius species yielded a large variety of 65 compounds in species-specific combinations. We suggest that reed frogs might use a complex combination of at least acoustic and chemical signals in species recognition and mate choice. PMID:24277973

  1. Species-specific leaf volatile compounds of obligate Macaranga myrmecophytes and host-specific aggressiveness of symbiotic Crematogaster ants.

    PubMed

    Inui, Yoko; Itioka, Takao

    2007-11-01

    Macaranga myrmecophytes harbor species-specific Crematogaster ants that defend host trees from herbivores. We examined ant aggressive behaviors when artificially damaged leaf pieces from another tree were offered to four sympatric species of obligate Macaranga myrmecophytes. The ants showed aggressive behavior in response to leaf pieces regardless of the leaf species; however, aggressiveness was higher when conspecific leaf pieces were offered than when nonhost species were offered. Thus, ants can recognize leaf damage and distinguish among damaged leaf species. Chemical analyses of volatile compounds emitted from damaged leaves that may induce ant defense showed that the composition of the minor compounds differed among the four Macaranga species, although there were many compounds in common. PMID:17929092

  2. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

    PubMed

    Ramond, Jean-Baptiste; Lako, Joseph D W; Stafford, William H L; Tuffin, Marla I; Cowan, Don A

    2015-08-01

    Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils. PMID:25721729

  3. Species-specific mutual regulation of p53 and miR-138 between human, rat and mouse

    PubMed Central

    Li, Jie; Xia, Wei; Su, Xueting; Qin, Xingliang; Chen, Ying; Li, Shaohua; Dong, Jie; Ding, Hongmei; Li, Hui; Huang, Aixue; Ge, Xingfeng; Hou, Lvbin; Wang, Chaonan; Sun, Leqiao; Bai, Chenjun; Shen, Xuelian; Fang, Tao; Liu, Yuanlin; Zhang, Yi; Zhang, Hongru; Zhang, Hongwen; Shao, Ningsheng

    2016-01-01

    In recent years, p53 was identified to regulate the expression of many miRNAs and was also regulated by miRNAs. In this paper, we found that miR-138 showed a pronounced increase after p53 activation in human non-small cell lung cancer (NSCLC) cells, which is mediated by p53 binding sites in the promoter region of its host gene, but this did not happen with rat and mouse cells. More interestingly, we found that p53 could be also regulated by miR-138 in mouse and rat cells, but not in the human NSCLC cells. Our results suggest the existence of species-specific differences of the regulations of miRNA against its targets and the regulations of miRNA itself by other proteins. PMID:27183959

  4. Detection and Identification of Gastrointestinal Lactobacillus Species by Using Denaturing Gradient Gel Electrophoresis and Species-Specific PCR Primers

    PubMed Central

    Walter, J.; Tannock, G. W.; Tilsala-Timisjarvi, A.; Rodtong, S.; Loach, D. M.; Munro, K.; Alatossava, T.

    2000-01-01

    Denaturing gradient gel electrophoresis (DGGE) of DNA fragments obtained by PCR amplification of the V2-V3 region of the 16S rRNA gene was used to detect the presence of Lactobacillus species in the stomach contents of mice. Lactobacillus isolates cultured from human and porcine gastrointestinal samples were identified to the species level by using a combination of DGGE and species-specific PCR primers that targeted 16S-23S rRNA intergenic spacer region or 16S rRNA gene sequences. The identifications obtained by this approach were confirmed by sequencing the V2-V3 region of the 16S rRNA gene and by a BLAST search of the GenBank database. PMID:10618239

  5. Species specificity of a monoclonal antibody produced to Naegleria fowleri and partial characterization of its antigenic determinant.

    PubMed

    Réveiller, F L; Marciano-Cabral, F; Pernin, P; Cabanes, P A; Legastelois, S

    2000-08-01

    Monoclonal antibody (Mab) 5D12 against Naegleria fowleri was analyzed for species specificity. Mab 5D12 reacted with a ubiquitous epitope present on the membrane of N. fowleri but not with soluble antigens. The Mab did not react with N. lovaniensis, N. gruberi, N. australiensis, or Acanthamoeba castellanii. The decreased reactivity of Mab 5D12 with N. fowleri observed after periodate oxidation, after digestion of carbohydrate moieties by three glycosidases, or after treatment of amebas with tunicamycin strongly suggests that the antigenic determinant has a polysaccharide component. Inhibition of the reactivity of Mab 5D12 by soluble saccharides supports the idea that N-acetyl or amino groups may play an important role in the recognition of the carbohydrate component of the epitope by the Mab. The specificity of Mab 5D12 makes this an ideal reagent for the identification of N. fowleri in environmental samples or in clinical specimens. PMID:10952262

  6. Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species.

    PubMed

    Ortea, Ignacio; Cañas, Benito; Gallardo, José M

    2009-11-01

    The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyses, is proposed for the identification of shrimp species with commercial interest. MALDI-TOF peptide mass fingerprint from arginine kinase tryptic digests were used for the identification of seven commercial, closely related species of Decapoda shrimps. Further identification and characterization of these peptides was performed by CID on an ESI-IT instrument, database search and de novo sequence interpretation, paying special attention to differential, species-specific peptides. Fisheries and manufacturers may take advantage of this methodology as a tool for a rapid and effective seafood product identification and authentication, providing and guaranteeing the quality and safety of the foodstuffs to consumers. PMID:19891510

  7. A novel 95-kilodalton antigen of Wuchereria bancrofti infective larvae identified by species-specific monoclonal antibodies.

    PubMed Central

    Burkot, T R; Kwan-Lim, G E; Maizels, R M

    1996-01-01

    CBA and BALB/c mice produced polyspecific and monospecific polyclonal antibody responses, respectively, following immunization with Wuchereria bancrofti stage-3 larvae. Two monoclonal antibodies (MAbs) were produced from the immunized BALB/c mouse. These MAbs (both isotype M) recognized a previously undescribed highly expressed W. bancrofti antigen present in stage-3 larvae. The epitopes bound by the MAbs appear to be species specific for W. bancrofti since the MAbs did not bind to antigens of either nine other nematode species or two vector species in Western blots (immunoblots). Phosphorylcholine epitopes, responsible for immunological cross-reactivity among nematodes, were identified only on a 200-kDa antigen and not on the 95-kDa molecule. The targets of these immunoglobulin M MAbs are not carbohydrate epitopes. PMID:8550196

  8. Molecular Determinants of Species Specificity in the Coronavirus Receptor Aminopeptidase N (CD13): Influence of N-Linked Glycosylation

    PubMed Central

    Wentworth, David E.; Holmes, Kathryn V.

    2001-01-01

    Aminopeptidase N (APN), a 150-kDa metalloprotease also called CD13, serves as a receptor for serologically related coronaviruses of humans (human coronavirus 229E [HCoV-229E]), pigs, and cats. These virus-receptor interactions can be highly species specific; for example, the human coronavirus can use human APN (hAPN) but not porcine APN (pAPN) as its cellular receptor, and porcine coronaviruses can use pAPN but not hAPN. Substitution of pAPN amino acids 283 to 290 into hAPN for the corresponding amino acids 288 to 295 introduced an N-glycosylation sequon at amino acids 291 to 293 that blocked HCoV-229E receptor activity of hAPN. Substitution of two amino acids that inserted an N-glycosylation site at amino acid 291 also resulted in a mutant hAPN that lacked receptor activity because it failed to bind HCoV-229E. Single amino acid revertants that removed this sequon at amino acids 291 to 293 but had one or five pAPN amino acid substitution(s) in this region all regained HCoV-229E binding and receptor activities. To determine if other N-linked glycosylation differences between hAPN, feline APN (fAPN), and pAPN account for receptor specificity of pig and cat coronaviruses, a mutant hAPN protein that, like fAPN and pAPN, lacked a glycosylation sequon at 818 to 820 was studied. This sequon is within the region that determines receptor activity for porcine and feline coronaviruses. Mutant hAPN lacking the sequon at amino acids 818 to 820 maintained HCoV-229E receptor activity but did not gain receptor activity for porcine or feline coronaviruses. Thus, certain differences in glycosylation between coronavirus receptors from different species are critical determinants in the species specificity of infection. PMID:11559807

  9. Hippo pathway genes developed varied exon numbers and coevolved functional domains in metazoans for species specific growth control

    PubMed Central

    2013-01-01

    Background The Hippo pathway controls growth by mediating cell proliferation and apoptosis. Dysregulation of Hippo signaling causes abnormal proliferation in both healthy and cancerous cells. The Hippo pathway receives inputs from multiple developmental pathways and interacts with many tissue-specific transcription factors, but how genes in the pathway have evolved remains inadequately revealed. Results To explore the origin and evolution of Hippo pathway, we have extensively examined 16 Hippo pathway genes, including upstream regulators and downstream targets, in 24 organisms covering major metazoan phyla. From simple to complex organisms, these genes are varied in the length and number of exons but encode conserved domains with similar higher-order organization. The core of the pathway is more conserved than its upstream regulators and downstream targets. Several components, despite existing in the most basal metazoan sponges, cannot be convincingly identified in other species. Potential recombination breakpoints were identified in some genes. Coevolutionary analysis reveals that most functional domains in Hippo genes have coevolved with interacting functional domains in other genes. Conclusions The two essential upstream regulators cadherins fat and dachsous may have originated in the unicellular organism Monosiga brevicollis and evolved more significantly than the core of the pathway. Genes having varied numbers of exons in different species, recombination events, and the gain and loss of some genes indicate alternative splicing and species-specific evolution. Coevolution signals explain some species-specific loss of functional domains. These results significantly unveil the structure and evolution of the Hippo pathway in distant phyla and provide valuable clues for further examination of Hippo signaling. PMID:23547742

  10. Species specific and environment induced variation of δ13C and δ15N in alpine plants

    PubMed Central

    Yang, Yang; Siegwolf, Rolf T. W.; Körner, Christian

    2015-01-01

    Stable carbon and nitrogen isotope signals in plant tissues integrate plant-environment interactions over long periods. In this study, we hypothesized that humid alpine life conditions are narrowing the scope for significant deviations from common carbon, water and nitrogen relations as captured by stable isotope signals. We explored the variation in δ13C and δ15N in 32 plant species from tissue type to ecosystem scale across a suite of locations at c. Two thousand five hundred meter elevation in the Swiss Alps. Foliar δ13C and δ15N varied among species by about 3–4‰ and 7–8‰ respectively. However, there was no overall difference in means of δ13C and δ15N for species sampled in different plant communities or when bulk plant dry matter harvests of different plant communities were compared. δ13C was found to be highly species specific, so that the ranking among species was mostly maintained across 11 habitats. However, δ15N varied significantly from place to place in all species (a range of 2.7‰) except in Fabaceae (Trifolium alpinum) and Juncaceae (Luzula lutea). There was also a substantial variation among individuals of the same species collected next to each other. No difference was found in foliar δ15N of non-legumes, which were either collected next to or away from the most common legume, T. alpinum. δ15N data place Cyperaceae and Juncaceae, just like Fabaceae, in a low discrimination category, well separated from other families. Soil δ15N was higher than in plants and increased with soil depth. The results indicate a high functional diversity in alpine plants that is similar to that reported for low elevation plants. We conclude that the surprisingly high variation in δ13C and δ15N signals in the studied high elevation plants is largely species specific (genetic) and insensitive to obvious environmental cues. PMID:26097487

  11. The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1β

    PubMed Central

    Rondeau, Jean-Michel; Ramage, Paul; Zurini, Mauro; Gram, Hermann

    2015-01-01

    Interleukin-1β (IL-1β) plays a key role in autoinflammatory diseases, such as systemic juvenile idiopathic arthritis (sJIA) or cryopyrin-associated periodic syndrome (CAPS). Canakinumab, a human monoclonal anti-IL-1β antibody, was recently approved for human use under the brand name Ilaris®. Canakinumab does not cross-react with IL-1β from mouse, rat, rabbit, or macaques. The crystal structure of the canakinumab Fab bound to human IL-1β was determined in an attempt to rationalize the species specificity. The X-ray analysis reveals a complex surface epitope with an intricate network of well-ordered water molecules at the antibody-antigen interface. The canakinumab paratope is largely pre-organized, as demonstrated by the structure determination of the free Fab. Glu 64 of human IL-1β is a pivotal epitope residue explaining the exquisite species specificity of canakinumab. We identified marmoset as the only non-human primate species that carries Glu 64 in its IL-1β and demonstrates full cross-reactivity of canakinumab, thereby enabling toxicological studies in this species. As demonstrated by the X-ray structure of the complex with IL-1β, canakinumab binds IL-1β on the opposite side with respect to the IL-1RAcP binding site, and in an approximately orthogonal orientation with respect to IL-1RI. However, the antibody and IL-1RI binding sites slightly overlap and the VH region of canakinumab would sterically interfere with the D1 domain of IL-1RI, as shown by a structural overlay with the IL-1β:IL-1RI complex. Therefore, direct competition with IL-1RI for IL-1β binding is the molecular mechanism of neutralization by canakinumab, which is also confirmed by competition assays with recombinant IL-1RI and IL-1RII. PMID:26284424

  12. Species-Specific Differential AhR Expression Protects Human Neural Progenitor Cells against Developmental Neurotoxicity of PAHs

    PubMed Central

    Gassmann, Kathrin; Abel, Josef; Bothe, Hanno; Haarmann-Stemmann, Thomas; Merk, Hans F.; Quasthoff, Kim N.; Rockel, Thomas Dino; Schreiber, Timm; Fritsche, Ellen

    2010-01-01

    Background Because of their lipophilicity, persistent organic pollutants (POPs) cross the human placenta, possibly affecting central nervous system development. Most POPs are known aryl hydrocarbon receptor (AhR) ligands and activators of AhR signaling. Therefore, AhR activation has been suggested to cause developmental neurotoxicity (DNT). Objective We studied the effects of AhR ligands on basic processes of brain development in two comparative in vitro systems to determine whether AhR-activation is the underlying mechanism for reported DNT of POPs in humans. Methods We employed neurosphere cultures based on human neural progenitor cells (hNPCs) and wild-type and AhR-deficient mouse NPCs (mNPCs) and studied the effects of different AhR agonists [3-methylcholanthrene (3-MC), benzo(a)pyrene [B(a)P], and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)] and an antagonist [3′-methoxy-4′-nitroflavone (MNF)] on neurosphere development. Moreover, we analyzed expression of AhR and genes involved in AhR signaling. Results In contrast to wild-type mNPCs, hNPCs and AhR-deficient mNPCs were insensitive to AhR agonism or antagonism. Although AhR modulation attenuated wild-type mNPC proliferation and migration, hNPCs and AhR-deficient mNPCs remained unaffected. Results also suggest that species-specific differences resulted from nonfunctional AhR signaling in hNPCs. Conclusion Our findings suggest that in contrast to wild-type mNPCs, hNPCs were protected against polycyclic aromatic hydrocarbon–induced DNT because of an absence of AhR. This difference may contribute to species-specific differences in sensitivity to POPs. PMID:20570779

  13. Bacterial Communities of Two Ubiquitous Great Barrier Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

    PubMed Central

    Kvennefors, E. Charlotte E.; Sampayo, Eugenia; Ridgway, Tyrone; Barnes, Andrew C.; Hoegh-Guldberg, Ove

    2010-01-01

    Background Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. Methodology/Principal Findings Denaturing Gradient Gel Electrophoresis (DGGE) of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by “White Syndrome” (WS) underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. Conclusions/Significance This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine invertebrate associates

  14. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms.

    PubMed

    Emmons-Bell, Maya; Durant, Fallon; Hammelman, Jennifer; Bessonov, Nicholas; Volpert, Vitaly; Morokuma, Junji; Pinet, Kaylinnette; Adams, Dany S; Pietak, Alexis; Lobo, Daniel; Levin, Michael

    2015-01-01

    The shape of an animal body plan is constructed from protein components encoded by the genome. However, bioelectric networks composed of many cell types have their own intrinsic dynamics, and can drive distinct morphological outcomes during embryogenesis and regeneration. Planarian flatworms are a popular system for exploring body plan patterning due to their regenerative capacity, but despite considerable molecular information regarding stem cell differentiation and basic axial patterning, very little is known about how distinct head shapes are produced. Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina). We use morphometric analysis to quantify the ability of physiological network perturbations to induce different species-specific head shapes from the same genome. Moreover, we present a computational agent-based model of cell and physical dynamics during regeneration that quantitatively reproduces the observed shape changes. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain, the characteristic distribution of adult stem cells (neoblasts), and the bioelectric gradients of resting potential within the anterior tissues. Interestingly, the shape change is not permanent; after regeneration is complete, intact animals remodel back to G. dorotocephala-appropriate head shape within several weeks in a secondary phase of remodeling following initial complete regeneration. We present a conceptual model to guide future work to delineate the molecular mechanisms by which bioelectric networks stochastically select among a small set of discrete head morphologies. Taken together

  15. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms

    PubMed Central

    Emmons-Bell, Maya; Durant, Fallon; Hammelman, Jennifer; Bessonov, Nicholas; Volpert, Vitaly; Morokuma, Junji; Pinet, Kaylinnette; Adams, Dany S.; Pietak, Alexis; Lobo, Daniel; Levin, Michael

    2015-01-01

    The shape of an animal body plan is constructed from protein components encoded by the genome. However, bioelectric networks composed of many cell types have their own intrinsic dynamics, and can drive distinct morphological outcomes during embryogenesis and regeneration. Planarian flatworms are a popular system for exploring body plan patterning due to their regenerative capacity, but despite considerable molecular information regarding stem cell differentiation and basic axial patterning, very little is known about how distinct head shapes are produced. Here, we show that after decapitation in G. dorotocephala, a transient perturbation of physiological connectivity among cells (using the gap junction blocker octanol) can result in regenerated heads with quite different shapes, stochastically matching other known species of planaria (S. mediterranea, D. japonica, and P. felina). We use morphometric analysis to quantify the ability of physiological network perturbations to induce different species-specific head shapes from the same genome. Moreover, we present a computational agent-based model of cell and physical dynamics during regeneration that quantitatively reproduces the observed shape changes. Morphological alterations induced in a genomically wild-type G. dorotocephala during regeneration include not only the shape of the head but also the morphology of the brain, the characteristic distribution of adult stem cells (neoblasts), and the bioelectric gradients of resting potential within the anterior tissues. Interestingly, the shape change is not permanent; after regeneration is complete, intact animals remodel back to G. dorotocephala-appropriate head shape within several weeks in a secondary phase of remodeling following initial complete regeneration. We present a conceptual model to guide future work to delineate the molecular mechanisms by which bioelectric networks stochastically select among a small set of discrete head morphologies. Taken together

  16. Isolation and characterization of a gene encoding a Chlamydia pneumoniae 76-kilodalton protein containing a species-specific epitope.

    PubMed Central

    Perez Melgosa, M; Kuo, C C; Campbell, L A

    1994-01-01

    Chlamydia pneumoniae is a human respiratory pathogen. Unlike the other two Chlamydia species, no species-specific antigen has been defined for C. pneumoniae. An immunoreactive clone containing a 0.8-kb fragment was isolated from a C. pneumoniae (AR-39) genomic library by using anti-C. pneumoniae rabbit immune serum. By Southern hybridization analysis of chromosomal digests of the different Chlamydia spp., the 0.8-kb fragment was shown to react specifically with C. pneumoniae. Subcloning of this fragment into the pGEX-1 lambda T expression vector resulted in the expression of a 62-kDa fusion protein. This fusion protein as well as the cleaved C. pneumoniae peptide were recognized by anti-C. pneumoniae rabbit immune serum, while the glutathione S-transferase moiety was not recognized. The fusion protein was used to produce monospecific rabbit antiserum. This antiserum was shown to react with a 76-kDa protein in all C. pneumoniae isolates tested, specifically recognize C. pneumoniae inclusions in tissue culture, and neutralize infectivity of C. pneumoniae in cell culture. No reactivity was observed with Chlamydia trachomatis or Chlamydia psittaci. To isolate the entire coding sequence of the 76-kDa protein, two partially overlapping fragments of C. pneumoniae DNA, a 3.2-kb HindIII fragment and a 1.2-kb PvuII fragment, were isolated, cloned, and sequenced. No significant sequence similarity was found with any previously reported nucleotide or amino acid sequence of the other Chlamydia species. This C. pneumoniae protein containing a species-specific epitope could play a role in pathogenesis and may be useful as a diagnostic tool. Images PMID:7509320

  17. New method for simultaneous species-specific identification of equine strongyles (nematoda, strongylida) by reverse line blot hybridization.

    PubMed

    Traversa, Donato; Iorio, Raffaella; Klei, Thomas R; Kharchenko, Vitaliy A; Gawor, Jakub; Otranto, Domenico; Sparagano, Olivier A E

    2007-09-01

    The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species. PMID:17626168

  18. New Method for Simultaneous Species-Specific Identification of Equine Strongyles (Nematoda, Strongylida) by Reverse Line Blot Hybridization▿

    PubMed Central

    Traversa, Donato; Iorio, Raffaella; Klei, Thomas R.; Kharchenko, Vitaliy A.; Gawor, Jakub; Otranto, Domenico; Sparagano, Olivier A. E.

    2007-01-01

    The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species. PMID:17626168

  19. Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Wang, Mingjun; Wang, Huilin; Tan, Hao; Zhang, Ziding; Webb, Geoffrey I.; Song, Jiangning

    2014-07-01

    Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation, and apoptosis. To fully understand acetylation mechanisms, identification of substrates and specific acetylation sites is crucial. Experimental identification is often time-consuming and expensive. Alternative bioinformatics methods are cost-effective and can be used in a high-throughput manner to generate relatively precise predictions. Here we develop a method termed as SSPKA for species-specific lysine acetylation prediction, using random forest classifiers that combine sequence-derived and functional features with two-step feature selection. Feature importance analysis indicates functional features, applied for lysine acetylation site prediction for the first time, significantly improve the predictive performance. We apply the SSPKA model to screen the entire human proteome and identify many high-confidence putative substrates that are not previously identified. The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.

  20. Electron microscopy and three-dimensional reconstruction of native thin filaments reveal species-specific differences in regulatory strand densities

    SciTech Connect

    Cammarato, Anthony; Craig, Roger; Lehman, William

    2010-01-01

    Throughout the animal kingdom striated muscle contraction is regulated by the thin filament troponin-tropomyosin complex. Homologous regulatory components are shared among vertebrate and arthropod muscles; however, unique protein extensions and/or components characterize the latter. The Troponin T (TnT) isoforms of Drosophila indirect flight and tarantula femur muscle for example contain distinct C-terminal extensions and are {approx}20% larger overall than their vertebrate counterpart. Using electron microscopy and three-dimensional helical reconstruction of native Drosophila, tarantula and frog muscle thin filaments we have identified species-specific differences in tropomyosin regulatory strand densities. The strands on the arthropod thin filaments were significantly larger in diameter than those from vertebrates, although not significantly different from each other. These findings reflect differences in the regulatory troponin-tropomyosin complex, which are likely due to the larger TnT molecules aligning and extending along much of the tropomyosin strands' length. Such an arrangement potentially alters the physical properties of the regulatory strands and may help establish contractile characteristics unique to certain arthropod muscles.

  1. Quantification of ferritin-bound iron in plant samples by isotope tagging and species-specific isotope dilution mass spectrometry.

    PubMed

    Hoppler, Matthias; Zeder, Christophe; Walczyk, Thomas

    2009-09-01

    Ferritin is nature's predominant iron storage protein. The molecule consists of a hollow protein shell composed of 24 subunits which is capable of storing up to 4500 iron atoms per molecule. Recently, this protein has been identified as a target molecule for increasing iron content in plant staple foods in order to combat dietary iron deficiency, a major public health problem in developing countries. Here, we present a novel technique for quantification of ferritin-bound iron in edible plant seeds using species-specific isotope dilution mass spectrometry (IDMS) by means of a biosynthetically produced (57)Fe-labeled ferritin spike and negative thermal ionization mass spectrometry (NTIMS). Native plant ferritin and added spike ferritin were extracted in 20 mM Tris buffer (pH 7.4) and separated by anion exchange chromatography (DEAE Sepharose), followed by isotopic analysis by thermal ionization mass spectrometry. The chosen IDMS approach was critically evaluated by assessing the (i) efficiency of analyte extraction, (ii) identical behavior of spike and analyte, and (iii) potential iron isotope exchange with natural iron. Repeatabilities that can be achieved are on the order of <5% RSD for quintuplicate analyses at an absolute detection limit of 60 ng of ferritin-bound iron for plant seeds. Studies in six different legumes revealed ferritin-iron contents ranging from 15% of total iron in red kidney beans up to 69% in lentils. PMID:19653660

  2. Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection

    PubMed Central

    Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Shah, Masaud; Choi, Sangdun

    2015-01-01

    TLR4 in complex with MD2 senses the presence of lipid A (LA) and initiates a signaling cascade that curb the infection. This complex is evolutionarily conserved and can initiate the immune system in response to a variety of LAs. In this study, molecular dynamics simulation (25 ns) was performed to elucidate the differential behavior of TLR4/MD2 complex in response to Rhodobacter sphaeroides lipid A (RsLA). Penta-acyl chain-containing RsLA is at the verge of agonist (6 acyl-chains) and antagonist (4 acyl-chains) structure, and activates the TLR4 pathway in horses and hamsters, while inhibiting in humans and murine. In the time-evolved coordinates, the promising factors that dictated the differential response included the local and global mobility pattern of complexes, solvent-accessible surface area of ligand, and surface charge distributions of TLR4 and MD2. We showed that the GlcN1-GlcN2 backbone acquires agonist (3FXI)-like configurations in horses and hamsters, while acquiring antagonist (2E59)-like configurations in humans and murine systems. Moreover, analysis of F126 behavior in the MD2 F126 loop (amino acids 123–129) and loop EF (81–89) suggested that certain sequence variations also contribute to species-specific response. This study underlines the TLR4 signaling mechanism and provides new therapeutic opportunities. PMID:25563849

  3. Species-specific oligonucleotides and multiplex PCR for forensic discrimination of two species of scallops, Placopecten magellanicus and Chlamys islandica.

    PubMed

    Marshall, H D; Johnstone, K A; Carr, S M

    2007-03-22

    Characterization of DNA that remains in seafood products after skin, scales, and shells are removed is widely used in forensic species identification, however, ordinary methods may be prohibitively expensive or time-consuming if large sample series need to be discriminated. Forensic discrimination of two species of bivalves commercially harvested from the North Atlantic, sea scallops (Placopecten magellanicus) and Icelandic scallops (Chlamys islandica), was made by means of species-specific oligonucleotides (SSOs) in a multiplex polymerase chain reaction (PCR). The test is a simultaneous in vitro amplification of a portion of the mitochondrial Cytochrome Oxidase I locus with a PCR anchor primer for a sequence identical in both species, and two alternative SSOs that selectively amplify either a 619-bp in Placopecten or a 459-bp DNA fragment in Chlamys. Fragment size and thus species identity are determined directly by gel electrophoresis. In the forensic application, analysis of more than 900 scallops from a series of samples seized from two fishing vessels showed significantly variable proportions of the species from the closed and open fisheries (Placopecten versus Chlamys, respectively). The multiplex SSO test provides a direct means of forensic identification of large population sample series, without the necessity of secondary DNA sequencing, RFLP mapping, or fingerprinting, and can be adapted to other loci and species. PMID:16822630

  4. Comparison of pollination and defensive buzzes in bumblebees indicates species-specific and context-dependent vibrations

    NASA Astrophysics Data System (ADS)

    De Luca, Paul A.; Cox, Darryl A.; Vallejo-Marín, Mario

    2014-04-01

    Bees produce vibrations in many contexts, including for defense and while foraging. Buzz pollination is a unique foraging behavior in which bees vibrate the anthers of flowers to eject pollen which is then collected and used as food. The relationships between buzzing properties and pollen release are well understood, but it is less clear to what extent buzzing vibrations vary among species, even though such information is crucial to understanding the functional relationships between bees and buzz-pollinated plants. Our goals in this study were (1) to examine whether pollination buzzes differ from those produced during defense, (2) to evaluate the similarity of buzzes between different species of bumblebees ( Bombus spp.), and (3) to determine if body size affects the expression of buzzing properties. We found that relative peak amplitude, peak frequency, and duration were significantly different between species, but only relative peak amplitude differed between pollination and defensive buzzes. There were significant interactions between species and buzz type for peak frequency and duration, revealing that species differed in their patterns of expression in these buzz properties depending on the context. The only parameter affected by body size was duration, with larger bees producing shorter buzzes. Our findings suggest that although pollination and defensive buzzes differ in some properties, variability in buzz structure also exhibits a marked species-specific component. Species differences in pollination buzzes may have important implications for foraging preferences in bumblebees, especially if bees select flowers best matched to release pollen for their specific buzzing characteristics.

  5. A global review of species-specific shark-fin-to-body-mass ratios and relevant legislation.

    PubMed

    Biery, L; Pauly, D

    2012-04-01

    In this review, shark-fin-to-body-mass ratios, which have been legislated by several countries as a means of regulating and monitoring shark fisheries, have been compiled and reviewed. Observed and legislated wet-fin-mass-to-round-mass (M(fw) :M(r) ) ratios have been collected for 50 species and eight countries. Wet to dry-fin mass conversion factors have also been reviewed. Existing shark fishery legislation was compiled by political entity and regional fishery management organizations (RFMO). The mean observed M(fw) :M(r) ratio for all species was 3·0%, but actual fin to body-mass ratios varied considerably by species and location. Species-specific mean ratios ranged from 1·1 to 10·9%, and estimated mean ratios ranged from 1·5 to 6·1% by country, depending on fin-cutting practices and the mix of exploited species. The mean conversion factor for wet to dry-fin mass was 0·43. Shark-related legislation was found to exist in 37 countries and the 22 maritime members of the European Union, and shark-related regulations have been designated by nine RFMOs. Results suggest that currently regulated ratios may not be appropriate for all species and fin-cutting practices, and regulations based on generalized ratios for all sharks may be inadequate. Alternative policies may be necessary for the effective management of global shark fisheries. PMID:22497402

  6. Understanding species-specific differences in substrate recognition by Escherichia coli and human prolyl-tRNA synthetases.

    PubMed

    Musier-Forsyth, K; Stehlin, C; Burke, B; Liu, H

    1997-01-01

    Class II human prolyl-tRNA synthetase (ProRS) aminoacylates in vitro transcribed human tRNA(Pro) with kinetic parameters that are similar to those previously determined for aminoacylation of Escherichia coli tRNA(Pro) by its cognate synthetase. As in the bacterial system, large decreases in aminoacylation by human ProRS occur upon mutating anticodon positions G35 and G36 of human tRNA(Pro). The N73 'discriminator' base and the first and third base pairs of the acceptor stem vary between the E.coli and human isoacceptor groups. In contrast to the E. coli synthetase, the human enzyme does not appear to recognize these elements, since mutations at these positions do not significantly affect cognate synthetase charging. E. coli ProRS does not cross-aminoacylate human tRNA(Pro), and the bacterial tRNA(Pro) is a poor substrate for the human enzyme. Mutations in both the tRNAs and the synthetases have been made in an effort to identify elements in each system responsible for blocking cross-species aminoacylation. Alignment of all known ProRS primary sequences from different species reveals particularly low overall sequence homology, as well as two distinct groups of enzymes. The sequence divergence between E. coli and human ProRSs helps to explain the species-specific differences in the RNA code for aminoacylation of tRNA(Pro). PMID:9478190

  7. Species-specific differences in adaptive phenotypic plasticity in an ecologically relevant trophic trait: hypertrophic lips in Midas cichlid fishes.

    PubMed

    Machado-Schiaffino, Gonzalo; Henning, Frederico; Meyer, Axel

    2014-07-01

    The spectacular species richness of cichlids and their diversity in morphology, coloration, and behavior have made them an ideal model for the study of speciation and adaptive evolution. Hypertrophic lips evolved repeatedly and independently in African and Neotropical cichlid radiations. Cichlids with hypertrophic lips forage predominantly in rocky crevices and it has been hypothesized that mechanical stress caused by friction could result in larger lips through phenotypic plasticity. To test the influence of the environment on the size and development of lips, we conducted a series of breeding and feeding experiments on Midas cichlids. Full-sibs of Amphilophus labiatus (thick-lipped) and Amphilophus citrinellus (thin-lipped) each were split into a control group which was fed food from the water column and a treatment group whose food was fixed to substrates. We found strong evidence for phenotypic plasticity on lip area in the thick-lipped species, but not in the thin-lipped species. Intermediate phenotypic values were observed in hybrids from thick- and thin-lipped species reared under "control" conditions. Thus, both a genetic, but also a phenotypic plastic component is involved in the development of hypertrophic lips in Neotropical cichlids. Moreover, species-specific adaptive phenotypic plasticity was found, suggesting that plasticity is selected for in recent thick-lipped species. PMID:24475874

  8. Mercury speciation analysis in human hair by species-specific isotope-dilution using GC-ICP-MS.

    PubMed

    Laffont, Laure; Maurice, Laurence; Amouroux, David; Navarro, Patricia; Monperrus, Mathilde; Sonke, Jeroen E; Behra, Philippe

    2013-03-01

    We optimized a mercury (Hg) speciation extraction method for human hair in combination with species-specific isotope-dilution analysis by gas chromatography-inductively coupled plasma-mass spectrometry (GC-ICP-MS). The method was validated on human hair reference material RM (IAEA-086), which is recommended for analysis of monomethylmercury (MMHg) and inorganic mercury (IHg). Three reagents, hydrochloric acid (HCl), nitric acid (HNO3), and tetramethylammonium hydroxide (TMAH), and three extraction procedures, at ambient temperature for 12 h, microwave-assisted at 75 °C for 6 min, and oven heated at 80 °C for 2 h were tested. Extraction efficiency, recovery, and potential species transformations were evaluated for each method. The most efficient procedures, with recovery of ~90 % for each species with limited demethylation (<5 %) and methylation (0 %), were HNO3 digestion, irrespective of temperature, and microwave-assisted TMAH extraction. Acidic extraction with HCl induces significant demethylation, with production of artifacts. To correct for potential demethylation artifacts we recommend spiking with isotopically enriched standards before the extraction step. PMID:22669307

  9. Method- and species-specific detection probabilities of fish occupancy in Arctic lakes: Implications for design and management

    USGS Publications Warehouse

    Haynes, Trevor B.; Rosenberger, Amanda E.; Lindberg, Mark S.; Whitman, Matthew; Schmutz, Joel A.

    2013-01-01

    Studies examining species occurrence often fail to account for false absences in field sampling. We investigate detection probabilities of five gear types for six fish species in a sample of lakes on the North Slope, Alaska. We used an occupancy modeling approach to provide estimates of detection probabilities for each method. Variation in gear- and species-specific detection probability was considerable. For example, detection probabilities for the fyke net ranged from 0.82 (SE = 0.05) for least cisco (Coregonus sardinella) to 0.04 (SE = 0.01) for slimy sculpin (Cottus cognatus). Detection probabilities were also affected by site-specific variables such as depth of the lake, year, day of sampling, and lake connection to a stream. With the exception of the dip net and shore minnow traps, each gear type provided the highest detection probability of at least one species. Results suggest that a multimethod approach may be most effective when attempting to sample the entire fish community of Arctic lakes. Detection probability estimates will be useful for designing optimal fish sampling and monitoring protocols in Arctic lakes.

  10. Species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of Porphyromonas gingivalis HmuY

    PubMed Central

    2010-01-01

    Background Porphyromonas gingivalis is a major etiological agent of chronic periodontitis. The aim of this study was to examine the species specificity, surface exposure, protein expression, immunogenicity, and participation in biofilm formation of the P. gingivalis heme-binding protein HmuY. Results HmuY is a unique protein of P. gingivalis since only low amino-acid sequence homology has been found to proteins encoded in other species. It is exposed on the cell surface and highly abundant in the outer membrane of the cell, in outer-membrane vesicles, and is released into culture medium in a soluble form. The protein is produced constitutively at low levels in bacteria grown under high-iron/heme conditions and at higher levels in bacteria growing under the low-iron/heme conditions typical of dental plaque. HmuY is immunogenic and elicits high IgG antibody titers in rabbits. It is also engaged in homotypic biofilm formation by P. gingivalis. Anti-HmuY antibodies exhibit inhibitory activity against P. gingivalis growth and biofilm formation. Conclusions Here it is demonstrated that HmuY may play a significant role not only in heme acquisition, but also in biofilm accumulation on abiotic surfaces. The data also suggest that HmuY, as a surface-exposed protein, would be available for recognition by the immune response during chronic periodontitis and the production of anti-HmuY antibodies may inhibit biofilm formation. PMID:20438645

  11. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.

    PubMed

    de Brevern, Alexandre G; Joseph, Agnel Praveen

    2011-05-01

    Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account. PMID:21333657

  12. Species-specific adaptations explain resilience of herbaceous understorey to increased precipitation variability in a Mediterranean oak woodland.

    PubMed

    Jongen, Marjan; Hellmann, Christine; Unger, Stephan

    2015-10-01

    To date, the implications of the predicted greater intra-annual variability and extremes in precipitation on ecosystem functioning have received little attention. This study presents results on leaf-level physiological responses of five species covering the functional groups grasses, forbs, and legumes in the understorey of a Mediterranean oak woodland, with increasing precipitation variability, without altering total annual precipitation inputs. Although extending the dry period between precipitation events from 3 to 6 weeks led to increased soil moisture deficit, overall treatment effects on photosynthetic performance were not observed in the studied species. This resilience to prolonged water stress was explained by different physiological and morphological strategies to withstand periods below the wilting point, that is, isohydric behavior in Agrostis, Rumex, and Tuberaria, leaf succulence in Rumex, and taproots in Tolpis. In addition, quick recovery upon irrigation events and species-specific adaptations of water-use efficiency with longer dry periods and larger precipitation events contributed to the observed resilience in productivity of the annual plant community. Although none of the species exhibited a change in cover with increasing precipitation variability, leaf physiology of the legume Ornithopus exhibited signs of sensitivity to moisture deficit, which may have implications for the agricultural practice of seeding legume-rich mixtures in Mediterranean grassland-type systems. This highlights the need for long-term precipitation manipulation experiments to capture possible directional changes in species composition and seed bank development, which can subsequently affect ecosystem state and functioning. PMID:26664676

  13. A multiplex set of species-specific primers for rapid identification of members of the genus Saccharomyces.

    PubMed

    Muir, Alastair; Harrison, Elizabeth; Wheals, Alan

    2011-11-01

    The Saccharomyces genus (previously Saccharomyces sensu stricto) formally comprises Saccharomyces arboricola, Saccharomyces bayanus, Saccharomyces cariocanus, Saccharomyces cerevisiae, Saccharomyces kudriavzevii, Saccharomyces mikatae, Saccharomyces paradoxus and Saccharomyces pastorianus. Species-specific primer pairs that produce a single band of known and different product size have been developed for each member of the clade with the exception of S. pastorianus, which is a polyphyletic allopolyploid hybrid only found in lager breweries, and for which signature sequences could not be reliably created. Saccharomyces cariocanus is now regarded as an American variant of S. paradoxus, and accordingly a single primer pair that recognizes both species was developed. A different orthologous and essential housekeeping gene was used to detect each species, potentially avoiding competition between PCR primers and overlap between amplicons. In multiplex format, two or more different species could be identified in a single reaction; double and triple hybrids could not always be correctly identified. Forty-two unidentified yeasts from sugar cane juice fermentations were correctly identified as S. cerevisiae. A colony PCR method was developed that is rapid, robust, inexpensive and capable of automation, requires no mycological expertise on the part of the user and is thus useful for large-scale preliminary screens. PMID:22093682

  14. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

    PubMed Central

    Islam, Md. Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

    2015-01-01

    MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. PMID:25861616

  15. Comparison of pollination and defensive buzzes in bumblebees indicates species-specific and context-dependent vibrations.

    PubMed

    De Luca, Paul A; Cox, Darryl A; Vallejo-Marín, Mario

    2014-04-01

    Bees produce vibrations in many contexts, including for defense and while foraging. Buzz pollination is a unique foraging behavior in which bees vibrate the anthers of flowers to eject pollen which is then collected and used as food. The relationships between buzzing properties and pollen release are well understood, but it is less clear to what extent buzzing vibrations vary among species, even though such information is crucial to understanding the functional relationships between bees and buzz-pollinated plants. Our goals in this study were (1) to examine whether pollination buzzes differ from those produced during defense, (2) to evaluate the similarity of buzzes between different species of bumblebees (Bombus spp.), and (3) to determine if body size affects the expression of buzzing properties. We found that relative peak amplitude, peak frequency, and duration were significantly different between species, but only relative peak amplitude differed between pollination and defensive buzzes. There were significant interactions between species and buzz type for peak frequency and duration, revealing that species differed in their patterns of expression in these buzz properties depending on the context. The only parameter affected by body size was duration, with larger bees producing shorter buzzes. Our findings suggest that although pollination and defensive buzzes differ in some properties, variability in buzz structure also exhibits a marked species-specific component. Species differences in pollination buzzes may have important implications for foraging preferences in bumblebees, especially if bees select flowers best matched to release pollen for their specific buzzing characteristics. PMID:24563100

  16. Toward an evolutionary perspective on conceptual representation: species-specific calls activate visual and affective processing systems in the macaque.

    PubMed

    Gil-da-Costa, Ricardo; Braun, Allen; Lopes, Marco; Hauser, Marc D; Carson, Richard E; Herscovitch, Peter; Martin, Alex

    2004-12-14

    Non-human primates produce a diverse repertoire of species-specific calls and have rich conceptual systems. Some of their calls are designed to convey information about concepts such as predators, food, and social relationships, as well as the affective state of the caller. Little is known about the neural architecture of these calls, and much of what we do know is based on single-cell physiology from anesthetized subjects. By using positron emission tomography in awake rhesus macaques, we found that conspecific vocalizations elicited activity in higher-order visual areas, including regions in the temporal lobe associated with the visual perception of object form (TE/TEO) and motion (superior temporal sulcus) and storing visual object information into long-term memory (TE), as well as in limbic (the amygdala and hippocampus) and paralimbic regions (ventromedial prefrontal cortex) associated with the interpretation and memory-encoding of highly salient and affective material. This neural circuitry strongly corresponds to the network shown to support representation of conspecifics and affective information in humans. These findings shed light on the evolutionary precursors of conceptual representation in humans, suggesting that monkeys and humans have a common neural substrate for representing object concepts. PMID:15583132

  17. Glucocorticoids Acutely Increase Brown Adipose Tissue Activity in Humans, Revealing Species-Specific Differences in UCP-1 Regulation.

    PubMed

    Ramage, Lynne E; Akyol, Murat; Fletcher, Alison M; Forsythe, John; Nixon, Mark; Carter, Roderick N; van Beek, Edwin J R; Morton, Nicholas M; Walker, Brian R; Stimson, Roland H

    2016-07-12

    The discovery of brown adipose tissue (BAT) in adult humans presents a new therapeutic target for metabolic disease; however, little is known about the regulation of human BAT. Chronic glucocorticoid excess causes obesity in humans, and glucocorticoids suppress BAT activation in rodents. We tested whether glucocorticoids regulate BAT activity in humans. In vivo, the glucocorticoid prednisolone acutely increased (18)fluorodeoxyglucose uptake by BAT (measured using PET/CT) in lean healthy men during mild cold exposure (16°C-17°C). In addition, prednisolone increased supraclavicular skin temperature (measured using infrared thermography) and energy expenditure during cold, but not warm, exposure in lean subjects. In vitro, glucocorticoids increased isoprenaline-stimulated respiration and UCP-1 in human primary brown adipocytes, but substantially decreased isoprenaline-stimulated respiration and UCP-1 in primary murine brown and beige adipocytes. The highly species-specific regulation of BAT function by glucocorticoids may have important implications for the translation of novel treatments to activate BAT to improve metabolic health. PMID:27411014

  18. Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection

    NASA Astrophysics Data System (ADS)

    Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Shah, Masaud; Choi, Sangdun

    2015-01-01

    TLR4 in complex with MD2 senses the presence of lipid A (LA) and initiates a signaling cascade that curb the infection. This complex is evolutionarily conserved and can initiate the immune system in response to a variety of LAs. In this study, molecular dynamics simulation (25 ns) was performed to elucidate the differential behavior of TLR4/MD2 complex in response to Rhodobacter sphaeroides lipid A (RsLA). Penta-acyl chain-containing RsLA is at the verge of agonist (6 acyl-chains) and antagonist (4 acyl-chains) structure, and activates the TLR4 pathway in horses and hamsters, while inhibiting in humans and murine. In the time-evolved coordinates, the promising factors that dictated the differential response included the local and global mobility pattern of complexes, solvent-accessible surface area of ligand, and surface charge distributions of TLR4 and MD2. We showed that the GlcN1-GlcN2 backbone acquires agonist (3FXI)-like configurations in horses and hamsters, while acquiring antagonist (2E59)-like configurations in humans and murine systems. Moreover, analysis of F126 behavior in the MD2 F126 loop (amino acids 123-129) and loop EF (81-89) suggested that certain sequence variations also contribute to species-specific response. This study underlines the TLR4 signaling mechanism and provides new therapeutic opportunities.

  19. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute.

    PubMed

    Islam, Md Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

    2015-01-01

    MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. PMID:25861616

  20. Development of species-specific PCR primers and polyphasic characterization of Lactobacillus sanfranciscensis isolated from Korean sourdough.

    PubMed

    Lee, Hyeongrho; Baek, Hyunwook; Lim, Sae Bom; Hur, Jin Soo; Shim, Sangmin; Shin, So-Yeon; Han, Nam Soo; Seo, Jin-Ho

    2015-05-01

    Lactobacillus sanfranciscensis is a bacterium used in sourdough that provides desirable properties such as better flavor and texture to the sourdough bread. Here, the intra-species diversity of L. sanfranciscensis strains isolated from Korean sourdough was studied using genotypic (multiplex-RAPD-PCR: multiplex-Randomly Amplified Polymorphic DNA-polymerase chain reaction) and phenotypic (VITEK2 Compact system) analyses. For this, a novel species-specific set of PCR primers was developed to identify L. sanfranciscensis using the recently published genome database. The primers were able to detect L. sanfranciscensis isolated from Korean sourdough with 100% accuracy. Genotyping and phenotyping analyses at the strain level demonstrated that Korean sourdough possesses various biotypes of L. sanfranciscensis strains. These strains were clustered into 5 subtypes (genotyping) or 7 subtypes (phenotyping). In summary, this strategy to construct novel primers reduced the chance of cross amplification and was able to identify the desired strain. The various strains isolated in this study can be used to develop a sourdough starter after the analysis of their fermentation characteristics. PMID:25702881

  1. Intramammary infection with coagulase-negative staphylococci at parturition: Species-specific prevalence, risk factors, and effect on udder health.

    PubMed

    De Visscher, A; Piepers, S; Haesebrouck, F; De Vliegher, S

    2016-08-01

    Coagulase-negative staphylococci (CNS) are the main cause of bovine intramammary infections (IMI) in many countries. Despite a high prevalence of CNS IMI at parturition, species-specific risk factor studies, relying on accurate identification methods, are lacking. Therefore, this observational study aimed at determining the prevalence and distribution of different CNS species causing IMI in fresh heifers and dairy cows in Flemish dairy herds and identifying associated species- and subgroup-specific risk factors at the herd, cow, and quarter level. The effect on udder health was investigated as well. Staphylococcus chromogenes, S. sciuri, and S. cohnii were the most frequently isolated species. The only CNS species causing IMI in fresh heifers and dairy cows in all herds was Staphylococcus chromogenes, whereas large between-herd differences in distribution were observed for the other species. Quarters from heifers and quarters with an inverted teat end had higher odds of being infected with S. chromogenes, S. simulans, or S. xylosus as well as with S. chromogenes solely. Prepartum teat apex colonization with S. chromogenes increased the likelihood of S. chromogenes IMI in the corresponding quarters at parturition. Quarters with dirty teat apices before calving were more likely to be infected with S. cohnii, S. equorum, S. saprophyticus, or S. sciuri, supporting the environmental nature of these CNS species. Three species (S. chromogenes, S. simulans, and S. xylosus) were associated with a higher quarter somatic cell count at parturition as compared with uninfected quarters. PMID:27236763

  2. Microbiome, Inflammation and Cancer

    PubMed Central

    Francescone, Ralph; Hou, Vivianty; Grivennikov, Sergei I.

    2014-01-01

    Inflammation has long been suspected to play a major role in the pathogenesis of cancer. Only recently however, have some mechanisms of its tumor promoting effects come to light. Microbes, both commensal and pathogenic, are critical regulators of the host immune system, and ultimately, of inflammation. Consequently, microbes have the potential power to influence tumor progression as well, through a wide variety of routes, including chronic activation of inflammation, alteration of tumor microenvironment, induction of genotoxic responses, and metabolism. In this review, we will provide a general overview of commensal microbiota, inflammation and cancer, and how microbes fit into this emerging field. PMID:24855005

  3. Omics of Brucella: Species-Specific sRNA-Mediated Gene Ontology Regulatory Networks Identified by Computational Biology.

    PubMed

    Vishnu, Udayakumar S; Sankarasubramanian, Jagadesan; Gunasekaran, Paramasamy; Sridhar, Jayavel; Rajendhran, Jeyaprakash

    2016-06-01

    Brucella is an intracellular bacterium that causes the zoonotic infectious disease, brucellosis. Brucella species are currently intensively studied with a view to developing novel global health diagnostics and therapeutics. In this context, small RNAs (sRNAs) are one of the emerging topical areas; they play significant roles in regulating gene expression and cellular processes in bacteria. In the present study, we forecast sRNAs in three Brucella species that infect humans, namely Brucella melitensis, Brucella abortus, and Brucella suis, using a computational biology analysis. We combined two bioinformatic algorithms, SIPHT and sRNAscanner. In B. melitensis 16M, 21 sRNA candidates were identified, of which 14 were novel. Similarly, 14 sRNAs were identified in B. abortus, of which four were novel. In B. suis, 16 sRNAs were identified, and five of them were novel. TargetRNA2 software predicted the putative target genes that could be regulated by the identified sRNAs. The identified mRNA targets are involved in carbohydrate, amino acid, lipid, nucleotide, and coenzyme metabolism and transport, energy production and conversion, replication, recombination, repair, and transcription. Additionally, the Gene Ontology (GO) network analysis revealed the species-specific, sRNA-based regulatory networks in B. melitensis, B. abortus, and B. suis. Taken together, although sRNAs are veritable modulators of gene expression in prokaryotes, there are few reports on the significance of sRNAs in Brucella. This report begins to address this literature gap by offering a series of initial observations based on computational biology to pave the way for future experimental analysis of sRNAs and their targets to explain the complex pathogenesis of Brucella. PMID:27223678

  4. Characterization of the Host Response to Pichinde Virus Infection in the Syrian Golden Hamster by Species-Specific Kinome Analysis*

    PubMed Central

    Falcinelli, Shane; Gowen, Brian B.; Trost, Brett; Napper, Scott; Kusalik, Anthony; Johnson, Reed F.; Safronetz, David; Prescott, Joseph; Wahl-Jensen, Victoria; Jahrling, Peter B.; Kindrachuk, Jason

    2015-01-01

    The Syrian golden hamster has been increasingly used to study viral hemorrhagic fever (VHF) pathogenesis and countermeasure efficacy. As VHFs are a global health concern, well-characterized animal models are essential for both the development of therapeutics and vaccines as well as for increasing our understanding of the molecular events that underlie viral pathogenesis. However, the paucity of reagents or platforms that are available for studying hamsters at a molecular level limits the ability to extract biological information from this important animal model. As such, there is a need to develop platforms/technologies for characterizing host responses of hamsters at a molecular level. To this end, we developed hamster-specific kinome peptide arrays to characterize the molecular host response of the Syrian golden hamster. After validating the functionality of the arrays using immune agonists of defined signaling mechanisms (lipopolysaccharide (LPS) and tumor necrosis factor (TNF)-α), we characterized the host response in a hamster model of VHF based on Pichinde virus (PICV1) infection by performing temporal kinome analysis of lung tissue. Our analysis revealed key roles for vascular endothelial growth factor (VEGF), interleukin (IL) responses, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, and Toll-like receptor (TLR) signaling in the response to PICV infection. These findings were validated through phosphorylation-specific Western blot analysis. Overall, we have demonstrated that hamster-specific kinome arrays are a robust tool for characterizing the species-specific molecular host response in a VHF model. Further, our results provide key insights into the hamster host response to PICV infection and will inform future studies with high-consequence VHF pathogens. PMID:25573744

  5. Characterization of the host response to pichinde virus infection in the Syrian golden hamster by species-specific kinome analysis.

    PubMed

    Falcinelli, Shane; Gowen, Brian B; Trost, Brett; Napper, Scott; Kusalik, Anthony; Johnson, Reed F; Safronetz, David; Prescott, Joseph; Wahl-Jensen, Victoria; Jahrling, Peter B; Kindrachuk, Jason

    2015-03-01

    The Syrian golden hamster has been increasingly used to study viral hemorrhagic fever (VHF) pathogenesis and countermeasure efficacy. As VHFs are a global health concern, well-characterized animal models are essential for both the development of therapeutics and vaccines as well as for increasing our understanding of the molecular events that underlie viral pathogenesis. However, the paucity of reagents or platforms that are available for studying hamsters at a molecular level limits the ability to extract biological information from this important animal model. As such, there is a need to develop platforms/technologies for characterizing host responses of hamsters at a molecular level. To this end, we developed hamster-specific kinome peptide arrays to characterize the molecular host response of the Syrian golden hamster. After validating the functionality of the arrays using immune agonists of defined signaling mechanisms (lipopolysaccharide (LPS) and tumor necrosis factor (TNF)-α), we characterized the host response in a hamster model of VHF based on Pichinde virus (PICV(1)) infection by performing temporal kinome analysis of lung tissue. Our analysis revealed key roles for vascular endothelial growth factor (VEGF), interleukin (IL) responses, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, and Toll-like receptor (TLR) signaling in the response to PICV infection. These findings were validated through phosphorylation-specific Western blot analysis. Overall, we have demonstrated that hamster-specific kinome arrays are a robust tool for characterizing the species-specific molecular host response in a VHF model. Further, our results provide key insights into the hamster host response to PICV infection and will inform future studies with high-consequence VHF pathogens. PMID:25573744

  6. Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets

    PubMed Central

    Marshall, Jeremy L.

    2016-01-01

    In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK) and apolipoprotein A-1 binding protein (APBP). These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of conspecific males to

  7. Fecal Microbiomes of Non-Human Primates in Western Uganda Reveal Species-Specific Communities Largely Resistant to Habitat Perturbation

    PubMed Central

    McCORD, ALEIA I.; CHAPMAN, COLIN A.; WENY, GEOFFREY; TUMUKUNDE, ALEX; HYEROBA, DAVID; KLOTZ, KELLY; KOBLINGS, AVERY S.; MBORA, DAVID N.M.; CREGGER, MELISSA; WHITE, BRYAN A.; LEIGH, STEVEN R.; GOLDBERG, TONY L.

    2014-01-01

    system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance. PMID:24285224

  8. Needles in the blue Sea: Sub-species specificity by targeted metaproteomics of the vast oceanic microbial metaproteome

    NASA Astrophysics Data System (ADS)

    Saito, M. A.; Dorsk, A.; Post, A.; McIlvin, M.; Moran, D. M.; Rappe, M. S.; DiTullio, G. R.

    2015-12-01

    Targeted metaproteomics is the application of mass spectrometry-based quantitative protein measurements to natural microbial populations. It has significant potential for providing novel biogeochemical insights, for example by measurement of specific biomarkers indicative of nutrient stress, as well as direct measurements of enzymes that can be used to provide estimates of potential reaction rates. High microbial diversity presents unique challenges to this method. We examined the feasibility of a targeted metaproteomics workflow in Pacific Ocean environments for two cyanobacterial nitrogen regulatory proteins, NtcA and P-II. Genomic analyses using new METATRYP software found the number of shared (redundant) tryptic peptides between different marine bacteria species to typically being 1% or less. Closely related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8+1.9% of their tryptic peptides, while shared intraspecies peptides were higher, with 13+15% shared peptides. Measurements of an NtcA peptide in the Pacific Ocean was found to target multiple cyanobacteria species, whereas a P-II peptide showed sub-species specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ~4e7, 1000-fold larger an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples. These oceanic quantitative protein distributions in the oceans demonstrate sub-species resolution is achievable combining in silico and empirical approaches.

  9. Community-Level and Species-Specific Associations between Phytoplankton and Particle-Associated Vibrio Species in Delaware's Inland Bays.

    PubMed

    Main, Christopher R; Salvitti, Lauren R; Whereat, Edward B; Coyne, Kathryn J

    2015-09-01

    Vibrio species are an abundant and diverse group of bacteria that form associations with phytoplankton. Correlations between Vibrio and phytoplankton abundance have been noted, suggesting that growth is enhanced during algal blooms or that association with phytoplankton provides a refuge from predation. Here, we investigated relationships between particle-associated Vibrio spp. and phytoplankton in Delaware's inland bays (DIB). The relative abundances of particle-associated Vibrio spp. and algal classes that form blooms in DIB (dinoflagellates, diatoms, and raphidophytes) were determined using quantitative PCR. The results demonstrated a significant correlation between particle-associated Vibrio abundance and phytoplankton, with higher correlations to diatoms and raphidophytes than to dinoflagellates. Species-specific associations were examined during a mixed bloom of Heterosigma akashiwo and Fibrocapsa japonica (Raphidophyceae) and indicated a significant positive correlation for particle-associated Vibrio abundance with H. akashiwo but a negative correlation with F. japonica. Changes in Vibrio assemblages during the bloom were evaluated using automated ribosomal intergenic spacer analysis (ARISA), which revealed significant differences between each size fraction but no significant change in Vibrio assemblages over the course of the bloom. Microzooplankton grazing experiments showed that losses of particle-associated Vibrio spp. may be offset by increased growth in the Vibrio population. Moreover, analysis of Vibrio assemblages by ARISA also indicated an increase in the relative abundance for specific members of the Vibrio community despite higher grazing pressure on the particle-associated population as a whole. The results of this investigation demonstrate links between phytoplankton and Vibrio that may lead to predictions of potential health risks and inform future management practices in this region. PMID:26070682

  10. Driving factors for the evolution of species-specific echolocation call design in new world free-tailed bats (molossidae).

    PubMed

    Jung, Kirsten; Molinari, Jesús; Kalko, Elisabeth K V

    2014-01-01

    Phylogeny, ecology, and sensorial constraints are thought to be the most important factors influencing echolocation call design in bats. The Molossidae is a diverse bat family with a majority of species restricted to tropical and subtropical regions. Most molossids are specialized to forage for insects in open space, and thus share similar navigational challenges. We use an unprecedented dataset on the echolocation calls of 8 genera and 18 species of New World molossids to explore how habitat, phylogenetic relatedness, body mass, and prey perception contribute to echolocation call design. Our results confirm that, with the exception of the genus Molossops, echolocation calls of these bats show a typical design for open space foraging. Two lines of evidence point to echolocation call structure of molossids reflecting phylogenetic relatedness. First, such structure is significantly more similar within than among genera. Second, except for allometric scaling, such structure is nearly the same in congeneric species. Despite contrasting body masses, 12 of 18 species call within a relatively narrow frequency range of 20 to 35 kHz, a finding that we explain by using a modeling approach whose results suggest this frequency range to be an adaptation optimizing prey perception in open space. To conclude, we argue that the high variability in echolocation call design of molossids is an advanced evolutionary trait allowing the flexible adjustment of echolocation systems to various sensorial challenges, while conserving sender identity for social communication. Unraveling evolutionary drivers for echolocation call design in bats has so far been hampered by the lack of adequate model organisms sharing a phylogenetic origin and facing similar sensorial challenges. We thus believe that knowledge of the echolocation call diversity of New World molossid bats may prove to be landmark to understand the evolution and functionality of species-specific signal design in bats. PMID

  11. Community-Level and Species-Specific Associations between Phytoplankton and Particle-Associated Vibrio Species in Delaware's Inland Bays

    PubMed Central

    Main, Christopher R.; Salvitti, Lauren R.; Whereat, Edward B.

    2015-01-01

    Vibrio species are an abundant and diverse group of bacteria that form associations with phytoplankton. Correlations between Vibrio and phytoplankton abundance have been noted, suggesting that growth is enhanced during algal blooms or that association with phytoplankton provides a refuge from predation. Here, we investigated relationships between particle-associated Vibrio spp. and phytoplankton in Delaware's inland bays (DIB). The relative abundances of particle-associated Vibrio spp. and algal classes that form blooms in DIB (dinoflagellates, diatoms, and raphidophytes) were determined using quantitative PCR. The results demonstrated a significant correlation between particle-associated Vibrio abundance and phytoplankton, with higher correlations to diatoms and raphidophytes than to dinoflagellates. Species-specific associations were examined during a mixed bloom of Heterosigma akashiwo and Fibrocapsa japonica (Raphidophyceae) and indicated a significant positive correlation for particle-associated Vibrio abundance with H. akashiwo but a negative correlation with F. japonica. Changes in Vibrio assemblages during the bloom were evaluated using automated ribosomal intergenic spacer analysis (ARISA), which revealed significant differences between each size fraction but no significant change in Vibrio assemblages over the course of the bloom. Microzooplankton grazing experiments showed that losses of particle-associated Vibrio spp. may be offset by increased growth in the Vibrio population. Moreover, analysis of Vibrio assemblages by ARISA also indicated an increase in the relative abundance for specific members of the Vibrio community despite higher grazing pressure on the particle-associated population as a whole. The results of this investigation demonstrate links between phytoplankton and Vibrio that may lead to predictions of potential health risks and inform future management practices in this region. PMID:26070682

  12. Driving Factors for the Evolution of Species-Specific Echolocation Call Design in New World Free-Tailed Bats (Molossidae)

    PubMed Central

    Jung, Kirsten; Molinari, Jesús

    2014-01-01

    Phylogeny, ecology, and sensorial constraints are thought to be the most important factors influencing echolocation call design in bats. The Molossidae is a diverse bat family with a majority of species restricted to tropical and subtropical regions. Most molossids are specialized to forage for insects in open space, and thus share similar navigational challenges. We use an unprecedented dataset on the echolocation calls of 8 genera and 18 species of New World molossids to explore how habitat, phylogenetic relatedness, body mass, and prey perception contribute to echolocation call design. Our results confirm that, with the exception of the genus Molossops, echolocation calls of these bats show a typical design for open space foraging. Two lines of evidence point to echolocation call structure of molossids reflecting phylogenetic relatedness. First, such structure is significantly more similar within than among genera. Second, except for allometric scaling, such structure is nearly the same in congeneric species. Despite contrasting body masses, 12 of 18 species call within a relatively narrow frequency range of 20 to 35 kHz, a finding that we explain by using a modeling approach whose results suggest this frequency range to be an adaptation optimizing prey perception in open space. To conclude, we argue that the high variability in echolocation call design of molossids is an advanced evolutionary trait allowing the flexible adjustment of echolocation systems to various sensorial challenges, while conserving sender identity for social communication. Unraveling evolutionary drivers for echolocation call design in bats has so far been hampered by the lack of adequate model organisms sharing a phylogenetic origin and facing similar sensorial challenges. We thus believe that knowledge of the echolocation call diversity of New World molossid bats may prove to be landmark to understand the evolution and functionality of species-specific signal design in bats. PMID

  13. Species-Specific Differences in the Expression and Regulation of α4β7 Integrin in Various Nonhuman Primates

    PubMed Central

    Byrareddy, Siddappa N.; Sidell, Neil; Arthos, James; Cicala, Claudia; Zhao, Chunxia; Little, Dawn M.; Dunbar, Paul; Yang, Gui X.; Pierzchalski, Keely; Kane, Maureen A.; Mayne, Ann E.; Song, Byeongwoon; Soares, Marcelo A.; Villinger, Francois; Fauci, Anthony S.; Ansari, Aftab A.

    2016-01-01

    Among nonhuman primates, SIV-infected Asian pigtailed macaques (PM) are relatively more susceptible to infection and disease progression than SIV-infected rhesus macaques (RM). In addition, SIV-infected African natural hosts such as the sooty mangabeys (SM) are resistant to disease. The mechanisms associated with such species-related variable clinical outcomes remain ill-defined but hold the potential to provide insights into the underlying mechanisms surrounding HIV pathogenesis. Recent findings indicate that the expression of the heterodimeric gut homing integrin α4β7 can influence both susceptibility and disease progression in RM. It was reasoned that differences in the frequencies/surface densities of α4β7-expressing lymphocytes might contribute to the differences in the clinical outcome of SIV infection among NHPs. In this article, we report that CD4+ T cells from PM constitutively express significantly higher levels of α4β7 than RM or SM. Retinoic acid, a key regulator of α4β7 expression, was paradoxically found at higher levels in the plasma of SM versus RM or PM. We also observed pairing of β7 with αE (αEβ7) on CD4+ T cells in the peripheral blood of SM, but not PM or RM. Finally, the differential mean density of expression of α4β7 in RM versus SM versus PM was predominantly dictated by species-specific sequence differences at the level of the β7 promoters, as determined by in vitro reporter/promoter construct transfection studies. We propose that differences in the regulation and expression of α4β7 may explain, in part, the differences in susceptibility and SIV disease progression in these NHP models. PMID:25948815

  14. Seedling transplants reveal species-specific responses of high-elevation tropical treeline trees to climate change.

    PubMed

    Rehm, Evan M; Feeley, Kenneth J

    2016-08-01

    The elevations at which tropical treelines occur are believed to represent the point where low mean temperatures limit the growth of upright woody trees. Consequently, tropical treelines are predicted to shift to higher elevations with global warming. However, treelines throughout the tropics have remained stationary despite increasing global mean temperatures. The goal of the study reported here was to build a more comprehensive understanding of the effects of mean temperature, low-temperature extremes, shading, and their interactions on seedling survival at tropical treelines. We conducted a seedling transplant study using three dominant canopy-forming treeline species in the southern tropical Andes. We found species-specific differences and contrasting responses in seedling survival to changes in mean temperature. The most abundant naturally occurring species at the seedling stage outside the treeline, Weinmannia fagaroides, showed a negative relationship between the survival of transplanted seedlings and mean temperature, the opposite of a priori expectations. Conversely, Clethra cuneata showed increased survival at higher mean temperatures, but survival also increased with higher absolute low temperatures and the presence of shade. Finally, the survival of Gynoxys nitida seedlings was insensitive to temperature but increased under shade. These findings show that multiple factors can determine the upper distributional limit of species forming the current tropical treeline. As such, predictions of future local and regional tropical treeline shifts may need to consider several factors beyond changes in mean temperature. If the treeline remains stationary and cloud forests are unable to expand into higher elevations, there may be severe species loss in this biodiversity hotspot. PMID:27071667

  15. Species-specific effects of polyploidisation and plant traits of Centaurea maculosa and Senecio inaequidens on rhizosphere microorganisms.

    PubMed

    Thébault, Aurélie; Frey, Beat; Mitchell, Edward A D; Buttler, Alexandre

    2010-08-01

    Invasive plant species represent a threat to terrestrial ecosystems, but their effects on the soil biota and the mechanisms involved are not yet well understood. Many invasive species have undergone polyploidisation, leading to the coexistence of various cytotypes in the native range, whereas, in most cases, only one cytotype is present in the introduced range. Since genetic variation within a species can modify soil rhizosphere communities, we studied the effects of different cytotypes and ranges (native diploid, native tetraploid and introduced tetraploid) of Centaurea maculosa and Senecio inaequidens on microbial biomass carbon, rhizosphere total DNA content and bacterial communities of a standard soil in relation to plant functional traits. There was no overall significant difference in microbial biomass between cytotypes. The variation of rhizosphere total DNA content and bacterial community structure according to cytotype was species specific. The rhizosphere DNA content of S. inaequidens decreased with polyploidisation in the native range but did not vary for C. maculosa. In contrast, the bacterial community structure of C. maculosa was affected by polyploidisation and its diversity increased, whereas there was no significant change for S. inaequidens. Traits of S. inaequidens were correlated to the rhizosphere biota. Bacterial diversity and total DNA content were positively correlated with resource allocation to belowground growth and late flowering, whereas microbial biomass carbon was negatively correlated to investment in reproduction. There were no correlations between traits of the cytotypes of C. maculosa and corresponding rhizosphere soil biota. This study shows that polyploidisation may affect rhizosphere bacterial community composition, but that effects vary among plant species. Such changes may contribute to the success of invasive polyploid genotypes in the introduced range. PMID:20229242

  16. Species-specific antibody responses to the recombinant 53-kilodalton excretory and secretory proteins in mice infected with Trichinella spp.

    PubMed

    Nagano, Isao; Wu, Zhiliang; Takahashi, Yuzo

    2008-03-01

    The 53-kDa proteins in larval excretory and secretory (E-S) products were expressed from five Trichinella species (T. spiralis, T. britovi, T. nativa, T. pseudospiralis, and T. papuae), using the Escherichia coli expression system, and the antibody responses to the 53-kDa recombinant proteins in mice infected with Trichinella spp. were analyzed by Western blotting. The 53-kDa protein is conserved among the five Trichinella species, with >60% similarity in amino acid sequences. The 53-kDa recombinant proteins of T. spiralis and T. pseudospiralis reacted to sera from mice infected with T. spiralis and T. pseudospiralis at 8 days postinfection (p.i.), respectively. An antibody against the 53-kDa recombinant protein of T. spiralis recognized the 53-kDa protein in the crude extracts from adult worms and 30-day p.i. muscle larvae and E-S products from muscle larvae of T. spiralis but did not recognize any proteins from T. pseudospiralis. The sera from the mice infected with T. spiralis strongly reacted with the 53-kDa recombinant protein of T. spiralis but did not react with the 53-kDa recombinant proteins of T. britovi, T. nativa, T. pseudospiralis, and T. papuae. Similarly, the sera from mice infected with T. britovi, T. nativa, T. pseudospiralis, or T. papuae strongly reacted with the 53-kDa recombinant proteins of T. britovi, T. nativa, T. pseudospiralis, or T. papuae, respectively. These results showed that the 53-kDa recombinant proteins provide early and species-specific antibody responses in mice infected with Trichinella spp. PMID:18184826

  17. Molecular and Ecological Evidence for Species Specificity and Coevolution in a Group of Marine Algal-Bacterial Symbioses

    PubMed Central

    Ashen, Jon B.; Goff, Lynda J.

    2000-01-01

    The phylogenetic relationships of bacterial symbionts from three gall-bearing species in the marine red algal genus Prionitis (Rhodophyta) were inferred from 16S rDNA sequence analysis and compared to host phylogeny also inferred from sequence comparisons (nuclear ribosomal internal-transcribed-spacer region). Gall formation has been described previously on two species of Prionitis, P. lanceolata (from central California) and P. decipiens (from Peru). This investigation reports gall formation on a third related host, Prionitis filiformis. Phylogenetic analyses based on sequence comparisons place the bacteria as a single lineage within the Roseobacter grouping of the α subclass of the division Proteobacteria (99.4 to 98.25% sequence identity among phylotypes). Comparison of symbiont and host molecular phylogenies confirms the presence of three gall-bearing algal lineages and is consistent with the hypothesis that these red seaweeds and their bacterial symbionts are coevolving. The species specificity of these associations was investigated in nature by whole-cell hybridization of gall bacteria and in the laboratory by using cross-inoculation trials. Whole-cell in situ hybridization confirmed that a single bacterial symbiont phylotype is present in galls on each host. In laboratory trials, bacterial symbionts were incapable of inducing galls on alternate hosts (including two non-gall-bearing species). Symbiont-host specificity in Prionitis gall formation indicates an effective ecological separation between these closely related symbiont phylotypes and provides an example of a biological context in which to consider the organismic significance of 16S rDNA sequence variation. PMID:10877801

  18. MIR retroposon exonization promotes evolutionary variability and generates species-specific expression of IGF-1 splice variants.

    PubMed

    Annibalini, Giosuè; Bielli, Pamela; De Santi, Mauro; Agostini, Deborah; Guescini, Michele; Sisti, Davide; Contarelli, Serena; Brandi, Giorgio; Villarini, Anna; Stocchi, Vilberto; Sette, Claudio; Barbieri, Elena

    2016-05-01

    Insulin-like growth factor (IGF) -1 is a pleiotropic hormone exerting mitogenic and anti-apoptotic effects. Inclusion or exclusion of exon 5 into the IGF-1 mRNA gives rise to three transcripts, IGF-1Ea, IGF-1Eb and IGF-1Ec, which yield three different C-terminal extensions called Ea, Eb and Ec peptides. The biological significance of the IGF-1 splice variants and how the E-peptides affect the actions of mature IGF-1 are largely unknown. In this study we investigated the origin and conservation of the IGF-1 E-peptides and we compared the pattern of expression of the IGF-1 isoforms in vivo, in nine mammalian species, and in vitro using human and mouse IGF-1 minigenes. Our analysis showed that only IGF-1Ea is conserved among all vertebrates, whereas IGF-1Eb and IGF-1Ec are an evolutionary novelty originated from the exonization of a mammalian interspersed repetitive-b (MIR-b) element. Both IGF-1Eb and IGF-1Ec mRNAs were constitutively expressed in all mammalian species analyzed but their expression ratio varies greatly among species. Using IGF-1 minigenes we demonstrated that divergence in cis-acting regulatory elements between human and mouse conferred species-specific features to the exon 5 region. Finally, the protein-coding sequences of exon 5 showed low rate of synonymous mutations and contain disorder-promoting amino acids, suggesting a regulatory role for these domains. In conclusion, exonization of a MIR-b element in the IGF-1 gene determined gain of exon 5 during mammalian evolution. Alternative splicing of this novel exon added new regulatory elements at the mRNA and protein level potentially able to regulate the mature IGF-1 across tissues and species. PMID:27048986

  19. Persistent organochlorines in 13 shark species from offshore and coastal waters of Korea: Species-specific accumulation and contributing factors.

    PubMed

    Lee, Hyun-Kyung; Jeong, Yunsun; Lee, Sunggyu; Jeong, Woochang; Choy, Eun-Jung; Kang, Chang-Keun; Lee, Won-Chan; Kim, Sang-Jo; Moon, Hyo-Bang

    2015-05-01

    Data on persistent organochlorines (OCs) in sharks are scarce. Concentrations of OCs such as polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were determined in the muscle tissue of 13 shark species (n=105) collected from offshore (Indian and Pacific Oceans) and coastal waters of Korea, to investigate species-specific accumulation of OCs and to assess the potential health risks associated with consumption of shark meat. Overall OC concentrations were highly variable not only among species but also within the same species of shark. The concentrations of PCBs, DDTs, chlordanes, hexachlorobenzene, and heptachlor in all shark species ranged from

  20. Characterization of Putative Iron Responsive Genes as Species-Specific Indicators of Iron Stress in Thalassiosiroid Diatoms

    PubMed Central

    Whitney, LeAnn P.; Lins, Jeremy J.; Hughes, Margaret P.; Wells, Mark L.; Chappell, P. Dreux; Jenkins, Bethany D.

    2011-01-01

    Iron (Fe) availability restricts diatom growth and primary production in large areas of the oceans. It is a challenge to assess the bulk Fe nutritional health of natural diatom populations, since species can differ in their physiological and molecular responses to Fe limitation. We assayed expression of selected genes in diatoms from the Thalassiosira genus to assess their potential utility as species-specific molecular markers to indicate Fe status in natural diatom assemblages. In this study, we compared the expression of the photosynthetic genes encoding ferredoxin (a Fe-requiring protein) and flavodoxin (a Fe-free protein) in culture experiments with Fe replete and Fe stressed Thalassiosira pseudonana (CCMP 1335) isolated from coastal waters and Thalassiosira weissflogii (CCMP 1010) isolated from the open ocean. In T. pseudonana, expression of flavodoxin and ferredoxin genes were not sensitive to Fe status but were found to display diel periodicities. In T. weissflogii, expression of flavodoxin was highly responsive to iron levels and was only detectable when cultures were Fe limited. Flavodoxin genes have been duplicated in most diatoms with available genome data and we show that T. pseudonana has lost its copy related to the Fe-responsive copy in T. weissflogii. We also examined the expression of genes for a putative high affinity, copper (Cu)-dependent Fe uptake system in T. pseudonana. Our results indicate that genes encoding putative Cu transporters, a multi-Cu oxidase, and a Fe reductase are not linked to Fe status. The expression of a second putative Fe reductase increased in Fe limited cultures, but this gene was also highly expressed in Fe replete cultures, indicating it may not be a useful marker in the field. Our findings highlight that Fe metabolism may differ among diatoms even within a genus and show a need to validate responses in different species as part of the development pipeline for genetic markers of Fe status in field populations. PMID

  1. Distribution and species-specific occurrence of cyathostomins (Nematoda, Strongylida) in naturally infected horses from Italy, United Kingdom and Germany.

    PubMed

    Traversa, Donato; Milillo, Piermarino; Barnes, Helen; von Samson-Himmelstjerna, Georg; Schurmann, Sandra; Demeler, Janina; Otranto, Domenico; Lia, Riccardo P; Perrucci, Stefania; Frangipane di Regalbono, Antonio; Beraldo, Paola; Amodie, Deborah; Rohn, Karl; Cobb, Rami; Boeckh, Albert

    2010-02-26

    A broad scale study was carried out in 2008 to evaluate the distribution and species-specific occurrence of cyathostomin populations in horse yards from Europe. In total 102 properties and 3123 horses were included in Italy (60 yards and 1646 animals), United Kingdom (22 yards and 737 animals) and Germany (20 yards and 740 animals). Individual faecal samples were examined with a McMaster technique while pooled samples were subjected to the microscopic examination of in vitro cultured larvae and to a Reverse Line Blot (RLB) assay able to molecularly identify the most diffused 13 species of cyathostomins. All yards were positive for the presence of cyathostomins both at the McMaster technique and at the microscopic examination of cultured larvae. One thousand and nine hundred thirty-one horses (61.8%) showed a positive faecal egg count, i.e. 1110 (67.4%), 463 (62.8%) and 358 (48.3%) from Italy, UK and Germany respectively. Out of the 1931 positive animals 1133 (36.3%) showed a faecal egg count per gram >150, specifically 694 (42.2%) from Italy, 237 (32.2%) from UK and 202 (27.3%) from Germany. The molecular results showed that all 13 species that can be detected by the RLB were found in each of the three countries, with a range of 3-13 species present in individual yards. The five most prevalent were Cylicocyclus nassatus, Cylicostephanus longibursatus, Cyathostomum catinatum, Cylicocyclus goldi and Cyathostomum pateratum. The relevance of these results and related biological and epidemiological features are discussed, together with their significance for both future studies of cyathostomins and further intervention programs aiming to control the spread of anthelmintic-resistant populations. PMID:19906489

  2. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    PubMed Central

    2011-01-01

    Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of

  3. Teat apex colonization with coagulase-negative Staphylococcus species before parturition: Distribution and species-specific risk factors.

    PubMed

    De Visscher, A; Piepers, S; Haesebrouck, F; De Vliegher, S

    2016-02-01

    Coagulase-negative staphylococci (CNS) are the main cause of bovine intramammary infections and are also abundantly present in extramammary habitats such as teat apices. Teat apex colonization (TAC) with CNS has already been explored in lactating dairy cows at the species level, whereas this is not true for dry cows and end-term heifers. Therefore, the aim of this observational study was to describe CNS TAC in nonlactating dairy cows and end-term heifers in Flemish dairy herds and to identify associated risk factors at the herd, cow, and quarter level. All CNS were molecularly identified to the species level using transfer RNA intergenic spacer PCR (tDNA-PCR) and sequencing of the 16S rRNA gene, allowing for species-specific statistical analyses using multivariable, multilevel logistic regression. Staphylococcus devriesei, Staphylococcus chromogenes, Staphylococcus haemolyticus, and Staphylococcus equorum were the most frequently isolated species. Staphylococcus chromogenes was the sole species colonizing teat apices of cows and heifers in all herds, whereas large between-herd differences were observed for the other species. Teat apices of red and white Holstein Friesians, of quarters dried off without an internal teat sealer, and swabbed in months with lower precipitation and higher ambient temperature were significantly more likely to be colonized by S. devriesei. Slightly dirty teat apices and teat apices swabbed in months with lower precipitation had higher odds of being colonized by S. chromogenes, whereas teat apices sampled in months with lower precipitation and higher ambient temperature were more likely to be colonized by S. haemolyticus. Dirty teat apices and teat apices swabbed in months with lower ambient temperature in combination with low precipitation had higher odds of being colonized by S. equorum. Diverse factors explaining CNS TAC, yet mostly related to humidity, ambient temperature, and hygiene, substantiate differences in epidemiological

  4. Utilization of elongation factor Tu gene (tuf) sequencing and species-specific PCR (SS-PCR) for the molecular identification of Acetobacter species complex.

    PubMed

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2014-02-01

    The aim of this study was to use tuf gene as a molecular target for species discrimination in the Acetobacter genus, as well as to develop species-specific PCR method for direct species identification of Acetobacter aceti. The results showed that most Acetobacter species could be clearly distinguished, and the average sequence similarity for the tuf gene (89.5%) among type strains was significantly lower than that of the 16S rRNA gene sequence (98.0%). A pair of species-specific primers were designed and used to specifically identify A. aceti, but none of the other Acetobacter strains. Our data indicate that the phylogenetic relationships of most strains in the Acetobacter genus can be resolved using tuf gene sequencing, and the novel species-specific primer pair could be used to rapidly and accurately identify the species of A. aceti by the PCR based assay. PMID:23969032

  5. Inflammation in Reproductive Disorders

    PubMed Central

    Weiss, Gerson; Goldsmith, Laura T.; Taylor, Robert N.; Bellet, Dominique; Taylor, Hugh S.

    2011-01-01

    Inflammatory disorders account for a significant percentage of gynecologic disease, particularly in reproductive age women. Inflammation is a basic method by which we respond to infection, irritation, or injury. Inflammation is now recognized as a type of nonspecific immune response, either acute or chronic. In gynecology, inflammation leads to anatomic disorders primarily as a result of infectious disease; however inflammation can affect ovulation and hormone production as well as be associated with endometriosis. Similarly, immune cell trafficking is an important component of cyclic endometrial development in each menstrual cycle. These immune cells are required for endometrial function, producing a vast array of inflammatory cytokines. Inflammation alters endometrial receptivity, however it may also play a role in tissue repair and remodeling. Finally, inflammation affects the trophoblast and trophoblast—endometrial interaction. Some components of the immune response are required for optimal fertility and normal tissue remodeling. A better understanding of the necessary role of inflammation in reproduction will allow more rational and targeted treatment of inflammatory disorders in reproductive medicine. PMID:19208790

  6. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR

    PubMed Central

    2011-01-01

    Background This study describes the use of malaria rapid diagnostic tests (RDTs) as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test) were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60), Plasmodium vivax (n = 10), Plasmodium ovale (n = 10) and Plasmodium malariae (n = 10). Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20) gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the best method of RDT

  7. An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians.

    PubMed

    Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2016-01-01

    Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events

  8. Aberration of mitosis by hexavalent chromium in some Fabaceae members is mediated by species-specific microtubule disruption.

    PubMed

    Eleftheriou, Eleftherios P; Michalopoulou, Vasiliki A; Adamakis, Ioannis-Dimosthenis S

    2015-05-01

    Because the detrimental effects of chromium (Cr) to higher plants have been poorly investigated, the present study was undertaken to verify the toxic attributes of hexavalent chromium [Cr(VI)] to plant mitotic microtubules (MTs), to determine any differential disruption of MTs during mitosis of taxonomically related species and to clarify the relationship between the visualized chromosomal aberrations and the Cr(VI)-induced MT disturbance. For this purpose, 5-day-old uniform seedlings of Vicia faba, Pisum sativum, Vigna sinensis and Vigna angularis, all belonging to the Fabaceae family, were exposed to 250 μM Cr(VI) supplied as potassium dichromate (K₂Cr₂O₇) for 24, 72 and 120 h and others in distilled water serving as controls. Root tip samples were processed for tubulin immunolabelling (for MT visualization) and DNA fluorescent staining (for chromosomal visualization). Microscopic preparations of cell squashes were then examined and photographed by confocal laser scanning microscopy (CLSM). Cr(VI) halted seedling growth turning roots brown and necrotic. Severe chromosomal abnormalities and differential disturbance of the corresponding MT arrays were found in all mitotic phases. In particular, in V. faba MTs were primarily depolymerized and replaced by atypical tubulin conformations, whereas in P. sativum, V. sinensis and V. angularis they became bundled in a time-dependent manner. In P. sativum, the effects were milder compared to those of the other species, but in all cases MT disturbance adversely affected the proper aggregation of chromosomes on the metaphase plate, their segregation at anaphase and organization of the new nuclei at telophase. Cr(VI) is very toxic to seedling growth. The particular effect depends on the exact stage the cell is found at the time of Cr(VI) entrance and is species-specific. Mitotic MT arrays are differentially deranged by Cr(VI) in the different species examined, even if they are taxonomically related, while their

  9. An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians

    PubMed Central

    Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2016-01-01

    Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events

  10. Pre-Clinical Assays Predict Pan-African Echis Viper Efficacy for a Species-Specific Antivenom

    PubMed Central

    Casewell, Nicholas R.; Cook, Darren A. N.; Wagstaff, Simon C.; Nasidi, Abdulsalami; Durfa, Nandul; Wüster, Wolfgang; Harrison, Robert A.

    2010-01-01

    Background Snakebite is a significant cause of death and disability in subsistent farming populations of sub-Saharan Africa. Antivenom is the most effective treatment of envenoming and is manufactured from IgG of venom-immunised horses/sheep but, because of complex fiscal reasons, there is a paucity of antivenom in sub-Saharan Africa. To address the plight of thousands of snakebite victims in savannah Nigeria, the EchiTAb Study Group organised the production, testing and delivery of antivenoms designed to treat envenoming by the most medically-important snakes in the region. The Echis saw-scaled vipers have a wide African distribution and medical importance. In an effort to maximise the clinical utility of scarce antivenom resources in Africa, we aimed to ascertain, at the pre-clinical level, to what extent the E. ocellatus-specific EchiTAbG antivenom, which was designed specifically for Nigeria, neutralised the lethal activity of venom from two other African species, E. pyramidum leakeyi and E. coloratus. Methodology/Principal Findings Despite apparently quite distinctive venom protein profiles, we observed extensive cross-species similarity in the immuno-reactivity profiles of Echis species-specific antisera. Using WHO standard pre-clinical in vivo tests, we determined that the monospecific EchiTAbG antivenom was as effective at neutralising the venom-induced lethal effects of E. pyramidum leakeyi and E. coloratus as it was against E. ocellatus venom. Under the restricted conditions of this assay, the antivenom was ineffective against the lethal effects of venom from the non-African Echis species, E. carinatus sochureki. Conclusions/Significance Using WHO-recommended pre-clinical tests we have demonstrated that the new anti-E. ocellatus monospecific antivenom EchiTAbG, developed in response to the considerable snakebite-induced mortality and morbidity in Nigeria, neutralised the lethal effects of venoms from Echis species representing each taxonomic group of this

  11. Vestibuloocular reflex of the adult flatfish. III. A species-specific reciprocal pattern of excitation and inhibition.

    PubMed

    Graf, W; Spencer, R; Baker, H; Baker, R

    2001-09-01

    In juvenile flatfish the vestibuloocular reflex (VOR) circuitry that underlies compensatory eye movements adapts to a 90 degrees relative displacement of vestibular and oculomotor reference frames during metamorphosis. VOR pathways are rearranged to allow horizontal canal-activated second-order vestibular neurons in adult flatfish to control extraocular motoneurons innervating vertical eye muscles. This study describes the anatomy and physiology of identified flatfish-specific excitatory and inhibitory vestibular pathways. In antidromically identified oculomotor and trochlear motoneurons, excitatory postsynaptic potentials (EPSPs) were elicited after electrical stimulation of the horizontal canal nerve expected to provide excitatory input. Electrotonic depolarizations (0.8-0.9 ms) preceded small amplitude (<0.5 mV) chemical EPSPs at 1.2-1.6 ms with much larger EPSPs (>1 mV) recorded around 2.5 ms. Stimulation of the opposite horizontal canal nerve produced inhibitory postsynaptic potentials (IPSPs) at a disynaptic latency of 1.6-1.8 ms that were depolarizing at membrane resting potentials around -60 mV. Injection of chloride ions increased IPSP amplitude, and current-clamp analysis showed the IPSP equilibrium potential to be near the membrane resting potential. Repeated electrical stimulation of either the excitatory or inhibitory horizontal canal vestibular nerve greatly increased the amplitude of the respective synaptic responses. These observations suggest that the large terminal arborizations of each VOR neuron imposes an electrotonic load requiring multiple action potentials to maximize synaptic efficacy. GABA antibodies labeled axons in the medial longitudinal fasciculus (MLF) some of which were hypothesized to originate from horizontal canal-activated inhibitory vestibular neurons. GABAergic terminal arborizations were distributed largely on the somata and proximal dendrites of oculomotor and trochlear motoneurons. These findings suggest that the species-specific

  12. A comparative analysis of transcriptomic, biochemical and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current concentrations of tropospheric ozone (O3) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific d...

  13. Species specific identification of spore-producing microbes using the gene sequence of small acid-soluble spore coat proteins for amplification based diagnostics

    DOEpatents

    McKinney, Nancy

    2002-01-01

    PCR (polymerase chain reaction) primers for the detection of certain Bacillus species, such as Bacillus anthracis. The primers specifically amplify only DNA found in the target species and can distinguish closely related species. Species-specific PCR primers for Bacillus anthracis, Bacillus globigii and Clostridium perfringens are disclosed. The primers are directed to unique sequences within sasp (small acid soluble protein) genes.

  14. Estrogens, inflammation and cognition.

    PubMed

    Au, April; Feher, Anita; McPhee, Lucy; Jessa, Ailya; Oh, Soojin; Einstein, Gillian

    2016-01-01

    The effects of estrogens are pleiotropic, affecting multiple bodily systems. Changes from the body's natural fluctuating levels of estrogens, through surgical removal of the ovaries, natural menopause, or the administration of exogenous estrogens to menopausal women have been independently linked to an altered immune profile, and changes to cognitive processes. Here, we propose that inflammation may mediate the relationship between low levels of estrogens and cognitive decline. In order to determine what is known about this connection, we review the literature on the cognitive effects of decreased estrogens due to oophorectomy or natural menopause, decreased estrogens' role on inflammation - both peripherally and in the brain - and the relationship between inflammation and cognition. While this review demonstrates that much is unknown about the intersection between estrogens, cognition, inflammation, we propose that there is an important interaction between these literatures. PMID:26774208

  15. Species-specific effects on throughfall kinetic energy below 12 subtropical tree species are related to leaf traits and tree architecture

    NASA Astrophysics Data System (ADS)

    Goebes, Philipp; Seitz, Steffen; Kühn, Peter; Kröber, Wenzel; Bruelheide, Helge; Li, Ying; von Oheimb, Goddert; Scholten, Thomas

    2015-04-01

    Soil erosion impacts environmental systems widely, especially in subtropical China where high erosion rates occur. The comprehension about the mechanisms that induce soil erosion on agricultural land is broad, but erosion processes below forests are only rarely understood. Especially throughfall kinetic energy (TKE) is influenced by forests and their structure as well as their succession in many ways. Today, many forests are monoculture tree stands due to economic reasons by providing timber, fuel and pulp wood. Therefore, this study investigates the role of different monoculture forest stands on TKE that were afforestated in 2008. The main questions are: Is TKE species-specific? What are characteristic leaf traits and tree architectural parameters that induce a species-specific effect on TKE and by what extend do they contribute to a mediation of species-specific effects on TKE? We measured TKE of 12 different species in subtropical China using sand-filled splash cups during five rainfall events in summer 2013. In addition, 14 leaf traits and tree architectural parameters were registered to link species-specific effects on TKE to vegetation parameters. Our results show that TKE is highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus mukorossi, while Schima superba showed lowest TKE. The latter species can be regarded as key species for reduced erosion occurrence. This species effect is mediated by leaf habit, leaf area, leaf pinnation, leaf margin, tree ground diameter, crown base height, tree height, number of branches and LAI as biotic factors and rainfall amount as abiotic factor. Moreover, leaf habit, tree height and LA show high effect sizes on TKE and can be considered as major drivers evoking TKE differences below vegetation.

  16. Vitamin D and inflammation

    PubMed Central

    Cannell, John J; Grant, William B; Holick, Michael F

    2014-01-01

    Several studies found an inverse relationship between 25-hydroxyvitamin D [25(OH)D] and markers of inflammation. A controversy exists as to whether vitamin D lowers inflammation or whether inflammation lowers 25(OH)D concentrations. Certainly 25(OH)D concentrations fall after major surgery. However, is this due to inflammation lowering 25(OH)D or is 25(OH)D being metabolically cleared by the body to quell inflammation. We searched the literature and found 39 randomized controlled trials (RCT) of vitamin D and markers of inflammation. Seventeen found significantly reduced inflammatory markers, 19 did not, one was mixed and one showed adverse results. With few exceptions, studies in normal subjects, obesity, type 2 diabetics, and stable cardiovascular disease did not find significant beneficial effects. However, we found that 6 out of 7 RCTS of vitamin D3 in highly inflammatory conditions (acute infantile congestive heart failure, multiple sclerosis, inflammatory bowel disease, cystic fibrosis, SLE, active TB and evolving myocardial infarction) found significant reductions. We found baseline and final 25(OH)D predicted RCTs with significant reduction in inflammatory markers. Vitamin D tends to modestly lower markers of inflammation in highly inflammatory conditions, when baseline 25(OH)D levels were low and when achieved 25(OH)D levels were higher. Future inquiries should: recruit subjects with low baseline 25(OH)D levels, subjects with elevated markers of inflammation, subjects with inflammatory conditions, achieve adequate final 25(OH)D levels, and use physiological doses of vitamin D. We attempted to identify all extant randomized controlled trials (RCTs) of vitamin D that used inflammatory markers as primary or secondary endpoints. PMID:26413186

  17. Atrial fibrillation and inflammation

    PubMed Central

    Ozaydin, Mehmet

    2010-01-01

    Atrial fibrillation (AF) is the most common clinical arrhythmia. Recent investigations have suggested that inflammation might have a role in the pathophysiology of AF. In this review, the association between inflammation and AF, and the effects of several agents that have anti-inflammatory actions, such as statins, polyunsaturated fatty acids, corticosteroids and angiotensin-converting enzyme inhibitors and angiotensin receptor blockers, have been investigated. PMID:21160591

  18. X-ray induced alterations in the differentiation and mineralization potential of murine preosteoblastic cells

    NASA Astrophysics Data System (ADS)

    Hu, Yueyuan; Lau, Patrick; Baumstark-Khan, Christa; Hellweg, Christine E.; Reitz, Günther

    2012-05-01

    To evaluate the effects of ionizing radiation (IR) on murine preosteoblastic cell differentiation, we directed OCT-1 cells to the osteoblastic lineage by treatment with a combination of β-glycerophosphate (β-GP), ascorbic acid (AA), and dexamethasone (Dex). In vitro mineralization was evaluated based on histochemical staining and quantification of the hydroxyapatite content of the extracellular bone matrix. Expression of mRNA encoding Runx2, transforming growth factor β1 (TGF-β1), osteocalcin (OCN), and p21CDKN1A was analyzed. Exposure to IR reduced the growth rate and diminished cell survival of OCT-1 cells under standard conditions. Notably, calcium content analysis revealed that deposition of mineralized matrix increased significantly under osteogenic conditions after X-ray exposure in a time-dependent manner. In this study, higher radiation doses exert significant overall effects on TGF-β1, OCN, and p21CDKN1A gene expression, suggesting that gene expression following X-ray treatment is affected in a dose-dependent manner. Additionally, we verified that Runx2 was suppressed within 24 h after irradiation at 2 and 4 Gy. Although further studies are required to verify the molecular mechanism, our observations strongly suggest that treatment with IR markedly alters the differentiation and mineralization process of preosteoblastic cells.

  19. Time-resolved x-ray imaging of x-ray induced dynamics in Xe clusters

    NASA Astrophysics Data System (ADS)

    Bucher, M.; Ferguson, K.; Gorkhover, T.; Carron, S.; Cryan, J.; Krzywinski, J.; Lutman, A.; Marinelli, A.; Bacellar, C.; Chatterley, A.; Ziemkiewicz, M.; Bernando, C.; Gomez, L.; Jones, C.; Kwok, J.; Tanyag, R. M. P.; Mueller, M.; Rupp, D.; Möller, T.; Gessner, O.; Vilesov, A.; Bostedt, C.

    2016-05-01

    Nanoparticles irradiated by intense x-ray pulses from the LCLS free-electron laser are immediately transformed into a highly excited nanoplasma. Within the first few femtoseconds of the x-ray pulse the particles are ionized and on longer time scales they disintegrate due to Coulomb forces. We performed an x-ray pump / x-ray probe experiment to investigate how the nanoplasma creation and disintegration changes the particle's diffraction response. As samples we used pristine Xe clusters as well as Xe clusters embedded in He droplets. The data show that for pristine clusters the higher diffraction orders diminish first and vanish completely as the nanoplasma expansion progresses. This effect is less prominent in the embedded clusters. We compare our results to previous studies on optically pumped clusters (T. Gorkhover et al., Nat. Photonics, 2016). This work is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under Contract No. DE-AC02-06CH11357.

  20. X-ray induced insulator-metal transitions in CMR manganites

    SciTech Connect

    Kiryukhin, V.; Casa, D.; Keimer, B.; Hill, J.P.; Vigliante, A.; Tomioka, Y.; Tokura, Y. |

    1997-12-01

    In this work the authors report a study of the photoinduced insulator-to-metal transition in manganese oxide perovskites of the formula Pr{sub 1{minus}x}Ca{sub x}MnO{sub 3}. The transition is closely related to the magnetic field induced insulator-to-metal transition (CMR effect) observed in these materials. It is accompanied by a dramatic change in the magnetic properties and lattice structure: the material changes from an insulating charge-ordered canted antiferromagnet to a ferromagnetic metal. The authors present an investigation of the transport and structural properties of these materials over the course of the transition (which usually takes about an hour to complete). The current-voltage characteristics exhibited by the material during the transition are highly nonlinear, indicating a large inhomogeneity of the transitional state. Possible practical applications of this novel type of transition are briefly discussed. They also report a high resolution X-ray diffraction study of the charge ordering in these materials. The temperature dependent charge ordering structure observed in these compounds is more complex than previously reported.

  1. Antioxidant protects blood-testis barrier against synchrotron radiation X-ray-induced disruption

    PubMed Central

    Zhang, Tingting; Liu, Tengyuan; Shao, Jiaxiang; Sheng, Caibin; Hong, Yunyi; Ying, Weihai; Xia, Weiliang

    2015-01-01

    Synchrotron radiation (SR) X-ray has wide biomedical applications including high resolution imaging and brain tumor therapy due to its special properties of high coherence, monochromaticity and high intensity. However, its interaction with biological tissues remains poorly understood. In this study, we used the rat testis as a model to investigate how SR X-ray would induce tissue responses, especially the blood-testis barrier (BTB) because BTB dynamics are critical for spermatogenesis. We irradiated the male gonad with increasing doses of SR X-ray and obtained the testicles 1, 10 and 20 d after the exposures. The testicle weight and seminiferous tubule diameter reduced in a dose- and time-dependent manner. Cryosections of testes were stained with tight junction (TJ) component proteins such as occludin, claudin-11, JAM-A and ZO-1. Morphologically, increasing doses of SR X-ray consistently induced developing germ cell sloughing from the seminiferous tubules, accompanied by shrinkage of the tubules. Interestingly, TJ constituent proteins appeared to be induced by the increasing doses of SR X-ray. Up to 20 d after SR X-ray irradiation, there also appeared to be time-dependent changes on the steady-state level of these protein exhibiting differential patterns at 20-day after exposure, with JAM-A/claudin-11 still being up-regulated whereas occludin/ZO-1 being down-regulated. More importantly, the BTB damage induced by 40 Gy of SR X-ray could be significantly attenuated by antioxidant N-Acetyl-L-Cysteine (NAC) at a dose of 125 mg/kg. Taken together, our studies characterized the changes of TJ component proteins after SR X-ray irradiation, illustrating the possible protective effects of antioxidant NAC to BTB integrity. PMID:26413412

  2. Imaging of voids in dielectric materials by x-ray induced partial discharge

    NASA Astrophysics Data System (ADS)

    Filho, V. Swinka; Robert, R.

    2002-03-01

    A nondestructive testing technique for imaging of voids and inclusions in dielectric materials for high-voltage application is described. Void partial discharge occurrence is induced by a narrow pulsed x-ray beam scanning the bulk of epoxy sample. Phase resolved partial discharge analysis is recorded as a function of the beam position. The data matrix is used to construct digital gray scale images, which gives information about location, dimensions, and partial discharge activity in each defect in dielectric materials. This nondestructive technique can be an important tool to evaluate the degradation state of the material.

  3. Low coercive field of polymer ferroelectric via x-ray induced phase transition

    SciTech Connect

    Lee, Hyeon Jun; Kim, Jihong; Lee, Hye Jeong; Kwak, Jeong Hun; Kim, Jae Myung; Lee, Sung Su; Kim, Dong-Yu; Jo, Ji Young; Kwon, Owoong; Kim, Yunseok

    2015-12-28

    We present an experimental strategy via X-ray irradiation combined with time-resolved X-ray diffraction to reduce a coercive field of ferroelectric thin films. We found in real-time that X-ray irradiation enables the irreversible phase transition from a polar to non-polar phase in ferroelectric poly(vinylidene fluoride-trifluoroethylene) thin films. The non-polar regions act as initial nucleation sites for opposite domains thus reducing the coercive field, directly related to the switching of domains, by 48%.

  4. Soft X-ray-induced decomposition of amino acids: An XPS, massspectrometry, and NEXAFS study

    SciTech Connect

    Zubavichus, Y.; Fuchs, O.; Weinhardt, L.; Heske, C.; Umbach, E.; Denlinger, J.D.; Grunze, M.

    2003-02-26

    Decomposition of five amino acids, viz. alanine, serine,cysteine, aspartic acid, and asparagine under soft X-ray irradiation (MgKα X-ray source) in ultra-high vacuum has been studied by meansof XPS and mass-spectrometry. A comparative analysis of changes in XPSline shapes, stoichiometry, and residual gas composition indicates thatthe molecules decompose via severalpathways. Dehydration,decarboxylation, decarbonylation, deamination, and desulfurization ofpristine molecules accompanied by desorption of H2, H2O, CO2, CO, NH3,H2S are observed with rates depending on the specific amino acid. NEXAFSspectra of cysteine at the C, O, N K- and S L2,3-edges complement the XPSand mass-spectrometry data and show that exposure of the sample to anintense soft X-ray synchrotron beam results in a formation of C-C and C-Ndouble and triple bonds. Qualitatively, the studied amino acids can bearranged in the following ascending order for radiation stability: serine

  5. Defects in sodalite-group minerals determined from X-ray-induced luminescence

    NASA Astrophysics Data System (ADS)

    Finch, Adrian A.; Friis, Henrik; Maghrabi, Mufeed

    2016-07-01

    The luminescence spectra of a suite of natural sodium framework silicates including four different sodalite variants and tugtupite have been collected during X-ray irradiation as a function of temperature between 20 and 673 K. The origin of the emission bands observed in these samples is attributed to F-centres (360 nm), paramagnetic oxygen defects (400 and 450 nm), S2 - ions (620 nm) and tetrahedral Fe3+ (730 nm). Luminescence in the yellow (550 nm) is tentatively attributed to Mn2+, and red luminescence in Cr-rich pink sodalite is possibly from Cr3+ activation. Sudden reduction in luminescence intensities of emission centres was observed for all minerals in the 60-120 K range. Since it is common to all the sodalite-group minerals, we infer it is a feature of the aluminosilicate framework. Sodalite luminescence has responses from substitutions on the framework (e.g. paramagnetic oxygen defects, Fe3+) which give sodalite properties akin to other framework silicates such as feldspar and quartz. However, the presence of the sodalite cage containing anions (such as F-centres, S2 - ions) imparts additional properties akin to alkali halides. The possibility of coupling between Fe3+ and S2 - is discussed. The overall luminescence behaviour of sodalite group can be understood in terms of competition between these centre types.

  6. /sup 20/neon ion- and x-ray-induced mammary carcinogenesis in female rats

    SciTech Connect

    Shellabarger, C.J.; Baum, J.W.; Holtzman, S.; Stone, J.P.

    1983-01-01

    One of the proposed uses of heavy ion irradiation is to image lesions of the human female breast. The rat model system was chosen to assess the carcinogenic potential of heavy ion irradiation in the belief that data obtained from rat studies would have a qualitatively predictive value for the human female. Accordingly, female rats were exposed to /sup 20/Ne ions at the BEVALAC and studied for the development of mammary neoplasia for 312 +- 2 days at Brookhaven along with rats exposed concurrently to x-irradiation or to no irradiation. As the dose of either type of radiation was increased the percent of rats with mammary adenocarcinomas, and the percent of rats with mammary fibroadenomas, tended to increase. At a prevalence of 20%, the RBE for /sup 20/Neon ions for mammary adenocarcinomas was estimated to be larger than 5 and for mammary fibroadenomas the RBE was estimated to be less than 2. No conclusion was reached concerning whether or not the RBE might vary with dose. We suggest that /sup 20/Ne ions do have a carcinogenic potential for rat mammary tissue and that this carcinogenic potential is likely to be greater than for x-irradiation. (DT)

  7. INVOLVEMENT OF P53 IN X-RAY INDUCED INTRACHROMOSOMAL RECOMBINATION IN MICE. (R825359)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  8. X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy

    SciTech Connect

    Ptasinska, Sylwia; Stypczynska, Agnieszka; Nixon, Tony; Mason, Nigel J.; Klyachko, Dimitri V.; Sanche, Leon

    2008-08-14

    In this work, the chemical changes in calf thymus DNA samples were analyzed by X-ray photoelectron spectroscopy (XPS). The DNA samples were irradiated for over 5 h and spectra were taken repeatedly every 30 min. In this approach the X-ray beam both damages and probes the samples. In most cases, XPS spectra have complex shapes due to contributions of C, N, and O atoms bonded at several different sites. We show that from a comparative analysis of the modification in XPS line shapes of the C 1s, O 1s, N 1s, and P 2p peaks, one can gain insight into a number of reaction pathways leading to radiation damage to DNA.

  9. Proton-induces and x-ray induced fluorescence analysis of scoliotic tissue

    SciTech Connect

    Panessa-Warren, B J; Kraner, H W; Jones, K W; Weiss, L S

    1980-02-01

    Adolescent idiopathic scoliosis is characterized by a curvature or assymetry of the spine which may become progressively more severe, with clinical symptoms appearing just prior to, or during, puberty. The incidence for scoliosis in the age group from 12 to 14 years of age has been reported as high as 8 to 10%, with more than 80% of the cases occurring in females. Although pathologic changes exist in muscles from both sides of the spinal curvature, and no statistically significant side differences have been reported, morphologic changes suggest that the concanve side is the most affected. This paper reports our preliminary data on the elemental composition of individual muscle fibers derived from convex, concave and gluteal scoliotic muscle, and erythrocytes from scoliotic and normal patients, analyzed by proton induced x-ray emission (PIXE) and x-ray fluorescence spectroscopy (XRF). A new type of specimen holder was designed for this study which offers low x-ray background, minimal absorption and maintenance of a moist environment around the specimen.

  10. Distribution of X-ray-induced chromosome breakpoints in Down syndrome lymphocytes

    SciTech Connect

    Shafik, H.M.; Au, W.W.; Whorton, E.B. Jr.; Legator, M.S. )

    1990-01-01

    Down syndrome (DS) individuals are known to be predisposed to develop leukemia and their lymphocytes are highly sensitive to the induction of chromosome aberrations by X-rays. A study was conducted to identify the chromosome breakpoints and to evaluate whether site specificity for chromosome breakage and rearrangement may exist which may explain the predisposition phenomenon. DS lymphocytes at the G1 phase of the cell cycle were irradiated with 300, 450, and 600 rad of X-rays. Cells were harvested after 3 days in culture and 193 G-banded karyotypes were analyzed to identify the induced chromosome abnormalities. Out of 273 breakpoints identified, 122 were involved in the formation of stable chromosome rearrangements and 151 in the formation of unstable abnormalities. The Poisson analysis of these breakpoints demonstrated that 16 chromosome bands located in chromosomes 1, 3, 7, 12, 17, 19 and X were preferentially involved in breakage and rearrangement (P less than 0.05). These 16 bands are also found to be locations of cancer breakpoints, oncogenes, or fragile sites. Many abnormal cells were observed to carry stable chromosome rearrangements only. Therefore, these cells are presumed to be compatible with survival and to be initiated in the transformation process. We propose that similar stable and site-specific chromosome rearrangements may exist in proliferating cells in DS individuals after exposure to clastogens and that this abnormality predisposes them to develop leukemia.

  11. Monochromatic X-Ray Induced Novel Synthesis of Plasmonic Nanostructure for Photovoltaic Application.

    PubMed

    Bharti, Amardeep; Bhardwaj, Richa; Agrawal, Ashish K; Goyal, Navdeep; Gautam, Sanjeev

    2016-01-01

    It has been universally delineated that the plasmonic metal nanoparticles can enhance the efficiency of photovoltaic cell by increasing the probability of energetic solar photons capturing phenomena using localized surface plasmonic resonance response. In this paper, we developed a novel in-situ simple approach to synthesize noble plasmonic silver nanoparticles (AgNP) from aqueous poly-vinyl-pyrrolidone solution of metal salt using radiolysis of water via synchrotron monochromatic X-ray irradiation without any chemical reducing agent. X-ray irradiation of water produces hydrated electrons (e(-)aq), superoxide (O(-)2) and atom radicals H*, which triggers the reaction and reduces metal salt. X-ray radiolysis based synthesis provides the control over the reaction and prevent the formation of secondary products as occurs in case of chemical reduction route. In the previous studies, synchrotron "white" X-rays had been examined for the synthesis of metal nanoparticles, but that technique limits only upto the material synthesis while in this work we explored the role of "monochromatic" X-rays for the production of bulk amount of nanoparticles which would also provide the feasibility of in-situ characterization. Transmission electron micrographs show that the synthesized AgNP appears spherical with diameter of 2-6 nm and is in agreement with the size estimation from uv-vis spectra by "Mie theory". PMID:27094793

  12. X-ray-induced sterility in Aedes albopictus (Diptera: Culicidae) and male longevity following irradiation.

    PubMed

    Yamada, H; Parker, A G; Oliva, C F; Balestrino, F; Gilles, J R L

    2014-07-01

    The mosquito Aedes albopictus (Skuse, 1895) is a potent vector of several arboviral diseases, most notably chikungunya and dengue fever. In the context of the sterile insect technique (SIT), the sterilization of the male mosquitoes before their release can be achieved by gamma-ray irradiation. As gamma-ray irradiators are becoming increasingly problematic to purchase and transport, the suitability of an X-ray irradiator as an alternative for the sterilization of Ae. albopictus males was studied. The sterilization of up to 200,000 pupae at one time can be achieved with relative ease, and the sterility results obtained were comparable with those achieved by gamma irradiation, where 99% sterility is induced with a dose of 40 Gy. A significant reduction of longevity was observed in the latter stages of the males' life after irradiation treatments, especially at doses > 40 Gy, which is consistent with the negative effects on longevity induced by similar radiation doses using gamma rays. Females irradiated at 40 Gy were not only 100% sterile, but also failed to oviposit entirely, i.e., all of the females laid 0 eggs. Overall, it was found that the X-ray irradiator is generally suitable for the sterilization process for sterile insect technique programs, as it showed a high processing capacity, practicality, high effectiveness, and reproducibility. PMID:25118413

  13. Monochromatic X-Ray Induced Novel Synthesis of Plasmonic Nanostructure for Photovoltaic Application

    PubMed Central

    Bharti, Amardeep; Bhardwaj, Richa; Agrawal, Ashish K.; Goyal, Navdeep; Gautam, Sanjeev

    2016-01-01

    It has been universally delineated that the plasmonic metal nanoparticles can enhance the efficiency of photovoltaic cell by increasing the probability of energetic solar photons capturing phenomena using localized surface plasmonic resonance response. In this paper, we developed a novel in-situ simple approach to synthesize noble plasmonic silver nanoparticles (AgNP) from aqueous poly-vinyl-pyrrolidone solution of metal salt using radiolysis of water via synchrotron monochromatic X-ray irradiation without any chemical reducing agent. X-ray irradiation of water produces hydrated electrons , superoxide and atom radicals , which triggers the reaction and reduces metal salt. X-ray radiolysis based synthesis provides the control over the reaction and prevent the formation of secondary products as occurs in case of chemical reduction route. In the previous studies, synchrotron “white” X-rays had been examined for the synthesis of metal nanoparticles, but that technique limits only upto the material synthesis while in this work we explored the role of “monochromatic” X-rays for the production of bulk amount of nanoparticles which would also provide the feasibility of in-situ characterization. Transmission electron micrographs show that the synthesized AgNP appears spherical with diameter of 2–6 nm and is in agreement with the size estimation from uv-vis spectra by “Mie theory”. PMID:27094793

  14. Three-dimensional model of x-ray induced microchannel plate output

    NASA Astrophysics Data System (ADS)

    Harding, E. C.; Drake, R. P.

    2006-10-01

    Microchannel plates are an important component in a type of imaging diagnostic known as an x-ray framing camera, used in x-ray radiography of high-energy-density physics experiments. A microchannel plate is responsible for detecting x rays and then converting them into amplified bursts of electrons, which are then imaged onto a phosphor-coated fiber optic screen. We present the preliminary development of a three-dimensional model of a single microchannel plate channel in attempt to simulate the pulse height distribution of the microchannel plate electron output. Using a novel technique, initial simulations are compared with experimental data from an ungated x-ray framing camera.

  15. Three-dimensional model of x-ray induced microchannel plate output

    SciTech Connect

    Harding, E. C.; Drake, R. P.

    2006-10-15

    Microchannel plates are an important component in a type of imaging diagnostic known as an x-ray framing camera, used in x-ray radiography of high-energy-density physics experiments. A microchannel plate is responsible for detecting x rays and then converting them into amplified bursts of electrons, which are then imaged onto a phosphor-coated fiber optic screen. We present the preliminary development of a three-dimensional model of a single microchannel plate channel in attempt to simulate the pulse height distribution of the microchannel plate electron output. Using a novel technique, initial simulations are compared with experimental data from an ungated x-ray framing camera.

  16. Monochromatic X-Ray Induced Novel Synthesis of Plasmonic Nanostructure for Photovoltaic Application

    NASA Astrophysics Data System (ADS)

    Bharti, Amardeep; Bhardwaj, Richa; Agrawal, Ashish K.; Goyal, Navdeep; Gautam, Sanjeev

    2016-04-01

    It has been universally delineated that the plasmonic metal nanoparticles can enhance the efficiency of photovoltaic cell by increasing the probability of energetic solar photons capturing phenomena using localized surface plasmonic resonance response. In this paper, we developed a novel in-situ simple approach to synthesize noble plasmonic silver nanoparticles (AgNP) from aqueous poly-vinyl-pyrrolidone solution of metal salt using radiolysis of water via synchrotron monochromatic X-ray irradiation without any chemical reducing agent. X-ray irradiation of water produces hydrated electrons , superoxide and atom radicals , which triggers the reaction and reduces metal salt. X-ray radiolysis based synthesis provides the control over the reaction and prevent the formation of secondary products as occurs in case of chemical reduction route. In the previous studies, synchrotron “white” X-rays had been examined for the synthesis of metal nanoparticles, but that technique limits only upto the material synthesis while in this work we explored the role of “monochromatic” X-rays for the production of bulk amount of nanoparticles which would also provide the feasibility of in-situ characterization. Transmission electron micrographs show that the synthesized AgNP appears spherical with diameter of 2–6 nm and is in agreement with the size estimation from uv-vis spectra by “Mie theory”.

  17. Prevailing Features of X-Ray-Induced Molecular Electron Spectra Revealed with Fullerenes

    NASA Astrophysics Data System (ADS)

    Camacho Garibay, Abraham; Saalmann, Ulf; Rost, Jan M.

    2014-08-01

    X-ray photoabsorption from intense short pulses by a molecule triggers complicated electron and subsequently ion dynamics, leading to photoelectron spectra, which are difficult to interpret. Illuminating fullerenes offers a way to separate out the electron dynamics since the cage structure confines spatially the origin of photo- and Auger electrons. Together with the sequential nature of the photoprocesses at intensities available at x-ray free-electron lasers, this allows for a remarkably detailed interpretation of the photoelectron spectra, as we will demonstrate. The general features derived can serve as a paradigm for less well-defined situations in other large molecules or clusters.

  18. Inflammation and keratoconus.

    PubMed

    McMonnies, Charles W

    2015-02-01

    Keratoconus (KC) has been traditionally classified as a noninflammatory disease. Barring loss of function, the other classic signs of inflammation (heat, redness, swelling, pain) are not usually obvious or even apparent in KC. This clinical perspective examines the evidence and implications of numerous inflammatory processes that have been recognized in the tears of KC patients as well as some inflammation relevant differences found in the KC cornea. The roles of inflammation in corneal trauma attributed to eye rubbing and/or contact lens wear are examined as is the significance of atopy, allergic disease, dry eye disease, degradative enzyme activity, wound healing, reduced anti-inflammatory capacity, and ultraviolet irradiation. It is possible that any comorbidity that is inflammatory in nature may add synergistically to other forms of KC-related inflammation and exacerbate its pathogenetic processes. For example, some features of inflammation in ocular rosacea and associated corneal thinning and distortion could have some possible relevance to KC. An analogy is drawn with osteoarthritis, which also involves significant inflammatory processes but, like KC, does not meet all the classic criteria for an inflammatory disease. Classifying KC as quasi-inflammatory (inflammatory-related) rather than a noninflammatory disease appears to be more appropriate and may help focus attention on the possibility of developing effective anti-inflammatory therapies for its management. PMID:25397925

  19. Inflammation and Insulin Resistance

    PubMed Central

    de Luca, Carl; Olefsky, Jerrold M.

    2008-01-01

    Obesity-induced chronic inflammation is a key component in the pathogenesis of insulin resistance and the Metabolic syndrome. In this review, we focus on the interconnection between obesity, inflammation and insulin resistance. Pro-inflammatory cytokines can cause insulin resistance in adipose tissue, skeletal muscle and liver by inhibiting insulin signal transduction. The sources of cytokines in insulin resistant states are the insulin target tissue themselves, primarily fat and liver, but to a larger extent the activated tissue resident macrophages. While the initiating factors of this inflammatory response remain to be fully determined, chronic inflammation in these tissues could cause localized insulin resistance via autocrine/paracrine cytokine signaling and systemic insulin resistance via endocrine cytokine signaling all of which contribute to the abnormal metabolic state. PMID:18053812

  20. Evolution of a developmental mechanism: species-specific regulation of the cell cycle and the timing of events during craniofacial osteogenesis

    PubMed Central

    Hall, Jane; Jheon, Andrew H.; Ealba, Erin L.; Eames, B. Frank; Butcher, Kristin D.; Mak, Siu-Shan; Ladher, Raj; Alliston, Tamara; Schneider, Richard A.

    2014-01-01

    Neural crest mesenchyme (NCM) controls species-specific pattern in the craniofacial skeleton but how this cell population accomplishes such a complex task remains unclear. To elucidate mechanisms through which NCM directs skeletal development and evolution, we made chimeras from quail and duck embryos, which differ markedly in their craniofacial morphology and maturation rates. We show that quail NCM, when transplanted into duck, maintains its faster timetable for development and autonomously executes molecular and cellular programs for the induction, differentiation, and mineralization of bone, including premature expression of osteogenic genes such as Runx2 and Col1a1. In contrast, the duck host systemic environment appears to be relatively permissive and supports osteogenesis independently by providing circulating minerals and a vascular network. Further experiments reveal that NCM establishes the timing of osteogenesis by regulating cell cycle progression in a stage- and species-specific manner. Altering the time-course of D-type cyclin expression mimics chimeras by accelerating expression of Runx2 and Col1a1. We also discover higher endogenous expression of Runx2 in quail coincident with their smaller craniofacial skeletons, and by prematurely over-expressing Runx2 in chick embryos we reduce the overall size of the craniofacial skeleton. Thus, our work suggests that NCM establishes species-specific size in the craniofacial skeleton by controlling cell cycle, Runx2 expression, and the timing of key events during osteogenesis. PMID:24262986

  1. The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA.

    PubMed

    Zhao, Zi-Hua; Cui, Bing-Yi; Li, Zhi-Hong; Jiang, Fan; Yang, Qian-Qian; Kučerová, Zuzana; Stejskal, Václav; Opit, George; Cao, Yang; Li, Fu-Jun

    2016-01-01

    Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-product Liposcelis spp. psocids (L. bostrychophila, L. entomophila, L. decolor, L. paeta, L. brunnea, L. corrodens, L. mendax, L. rufa, L. pearmani, and L. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA. PMID:26880378

  2. Species-specific expansion of C2H2 zinc-finger genes and their expression profiles in silkworm, Bombyx mori.

    PubMed

    Duan, Jun; Xia, Qingyou; Cheng, Daojun; Zha, Xingfu; Zhao, Ping; Xiang, Zhonghuai

    2008-12-01

    Most C2H2 zinc-finger proteins (ZFPs) function as sequence-specific DNA-binding transcription factors, and play important roles in a variety of biology processes, such as development, differentiation, and tumor suppression. By searching the silkworm genome with a HMM model of C2H2 zinc-fingers, we have identified a total of 338 C2H2 ZFPs. Most of the ZFP genes were clustered on chromosomes and showed uneven distribution in the genome. Over one third of genes were concentrated on chromosome 11, 15 and 24. Phylogenetic analysis classified all silkworm C2H2 ZFPs into 75 families; 63 of which belong to evolutionarily conserved families. In addition, 188 C2H2 ZFP genes (55.6%) are species-specific to the silkworm. A species-specific expansion of a family with 39 members in a tandem array on chromosome 24 may explain the higher number of species-specific ZFPs in silkworm compared to other organisms. The expression patterns of C2H2 ZFP genes were also examined by microarray analysis. Most of these genes were actively expressed among different tissues on day 3 of the fifth instar. The results provide insight into the biological functions of the silkworm C2H2 ZFP genes in metamorphism and development. PMID:18835444

  3. The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA

    PubMed Central

    Zhao, Zi-Hua; Cui, Bing-Yi; Li, Zhi-Hong; Jiang, Fan; Yang, Qian-Qian; Kučerová, Zuzana; Stejskal, Václav; Opit, George; Cao, Yang; Li, Fu-Jun

    2016-01-01

    Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-product Liposcelis spp. psocids (L. bostrychophila, L. entomophila, L. decolor, L. paeta, L. brunnea, L. corrodens, L. mendax, L. rufa, L. pearmani, and L. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA. PMID:26880378

  4. Genetic Analysis and Species Specific Amplification of the Artemisinin Resistance-Associated Kelch Propeller Domain in P. falciparum and P. vivax

    PubMed Central

    Talundzic, Eldin; Chenet, Stella M.; Goldman, Ira F.; Patel, Dhruviben S.; Nelson, Julia A.; Plucinski, Mateusz M.; Barnwell, John W.; Udhayakumar, Venkatachalam

    2015-01-01

    Plasmodium falciparum resistance to artemisinin has emerged in the Greater Mekong Subregion and now poses a threat to malaria control and prevention. Recent work has identified mutations in the kelch propeller domain of the P. falciparum K13 gene to be associated artemisinin resistance as defined by delayed parasite clearance and ex vivo ring stage survival assays. Species specific primers for the two most prevalent human malaria species, P. falciparum and P. vivax, were designed and tested on multiple parasite isolates including human, rodent, and non- humans primate Plasmodium species. The new protocol described here using the species specific primers only amplified their respective species, P. falciparum and P. vivax, and did not cross react with any of the other human malaria Plasmodium species. We provide an improved species specific PCR and sequencing protocol that could be effectively used in areas where both P. falciparum and P. vivax are circulating. To design this improved protocol, the kelch gene was analyzed and compared among different species of Plasmodium. The kelch propeller domain was found to be highly conserved across the mammalian Plasmodium species. PMID:26292024

  5. Genetic Analysis and Species Specific Amplification of the Artemisinin Resistance-Associated Kelch Propeller Domain in P. falciparum and P. vivax.

    PubMed

    Talundzic, Eldin; Chenet, Stella M; Goldman, Ira F; Patel, Dhruviben S; Nelson, Julia A; Plucinski, Mateusz M; Barnwell, John W; Udhayakumar, Venkatachalam

    2015-01-01

    Plasmodium falciparum resistance to artemisinin has emerged in the Greater Mekong Subregion and now poses a threat to malaria control and prevention. Recent work has identified mutations in the kelch propeller domain of the P. falciparum K13 gene to be associated artemisinin resistance as defined by delayed parasite clearance and ex vivo ring stage survival assays. Species specific primers for the two most prevalent human malaria species, P. falciparum and P. vivax, were designed and tested on multiple parasite isolates including human, rodent, and non- humans primate Plasmodium species. The new protocol described here using the species specific primers only amplified their respective species, P. falciparum and P. vivax, and did not cross react with any of the other human malaria Plasmodium species. We provide an improved species specific PCR and sequencing protocol that could be effectively used in areas where both P. falciparum and P. vivax are circulating. To design this improved protocol, the kelch gene was analyzed and compared among different species of Plasmodium. The kelch propeller domain was found to be highly conserved across the mammalian Plasmodium species. PMID:26292024

  6. Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

    PubMed Central

    Back, Chang-Gi; Lee, Seung-Yeol; Lee, Boo-Ja; Yea, Mi-Chi; Kim, Sang-Mok; Kang, In-Kyu; Cha, Jae-Soon; Jung, Hee-Young

    2015-01-01

    In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP), X. hyacinthi (XH) and X. campestris pv. zantedeschiae (XCZ), based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases. PMID:26361469

  7. Cryoglobulin-induced inflammation.

    PubMed

    Denko, C W

    1985-10-01

    Inflammation of the rat footpad followed injection of cryoglobulin in crystalline form (Type I) and injection of cryoglobulin in solution (Type II). Rats deficient in essential fatty acids responded with diminished swelling which corrected to normal levels by addition of prostaglandin E1 suggesting that this reaction is prostaglandin mediated. Addition of bradykinin produced no effect. Aggregated cryoglobulin proved more inflammogenic than non-aggregated cryoglobulin. Pre-treatment with choline salicylate and colchicine reduced swelling while pre-treatment with dipyridamole increased edema following cryoglobulin inoculation. Cryoglobulin is considered to be an acute phase reactant in inflammation. PMID:4083184

  8. Quercetin, Inflammation and Immunity

    PubMed Central

    Li, Yao; Yao, Jiaying; Han, Chunyan; Yang, Jiaxin; Chaudhry, Maria Tabassum; Wang, Shengnan; Liu, Hongnan; Yin, Yulong

    2016-01-01

    In vitro and some animal models have shown that quercetin, a polyphenol derived from plants, has a wide range of biological actions including anti-carcinogenic, anti-inflammatory and antiviral activities; as well as attenuating lipid peroxidation, platelet aggregation and capillary permeability. This review focuses on the physicochemical properties, dietary sources, absorption, bioavailability and metabolism of quercetin, especially main effects of quercetin on inflammation and immune function. According to the results obtained both in vitro and in vivo, good perspectives have been opened for quercetin. Nevertheless, further studies are needed to better characterize the mechanisms of action underlying the beneficial effects of quercetin on inflammation and immunity. PMID:26999194

  9. Crystal Formation in Inflammation.

    PubMed

    Franklin, Bernardo S; Mangan, Matthew S; Latz, Eicke

    2016-05-20

    The formation and accumulation of crystalline material in tissues is a hallmark of many metabolic and inflammatory conditions. The discovery that the phase transition of physiologically soluble substances to their crystalline forms can be detected by the immune system and activate innate immune pathways has revolutionized our understanding of how crystals cause inflammation. It is now appreciated that crystals are part of the pathogenesis of numerous diseases, including gout, silicosis, asbestosis, and atherosclerosis. In this review we discuss current knowledge of the complex mechanisms of crystal formation in diseased tissues and their interplay with the nutrients, metabolites, and immune cells that account for crystal-induced inflammation. PMID:26772211

  10. Natural resolution of inflammation.

    PubMed

    Freire, Marcelo O; Van Dyke, Thomas E

    2013-10-01

    Inflammation is a protective response essential for maintaining human health and for fighting disease. As an active innate immune reaction to challenge, inflammation gives rise to clinical cardinal signs: rubor, calor, dolor, tumor and functio laesa. Termination of acute inflammation was previously recognized as a passive process; a natural decay of pro-inflammatory signals. We now understand that the natural resolution of inflammation involves well-integrated, active, biochemical programs that return tissues to homeostasis. This review focuses on recent advances in the understanding of the role of endogenous lipid mediators that modulate cellular fate and inflammation. Biosynthesis of eicosanoids and other lipids in exudates coincides with changes in the types of inflammatory cells. Resolution of inflammation is initiated by an active class switch in lipid mediators, such as classic prostaglandins and leukotrienes, to the production of proresolution mediators. Endogenous pro-resolving lipid mediators, including arachidonic acid-derived lipoxins, aspirin-triggered lipoxins, ω3-eicosapentaenoic acid-derived resolvins of the E-series, docosahexaenoic acid-derived resolvins of the D-series, protectins and maresins, are biosynthesized during the resolution phase of acute inflammation. Depending on the type of injury and the type of tissue, the initial cells that respond are polymorphonuclear leukocytes, monocytes/macrophages, epithelial cells or endothelial cells. The selective interaction of specific lipid mediators with G protein-coupled receptors expressed on innate immune cells (e.g. G protein-coupled receptor 32, lipoxin A4 receptor/formyl peptide receptor2, chemokine-like receptor 1, leukotriene B4 receptor type 1 and cabannoid receptor 2) induces cessation of leukocyte infiltration; vascular permeability/edema returns to normal with polymorphonuclear neutrophil death (mostly via apoptosis), the nonphlogistic infiltration of monocyte/macrophages and the removal

  11. Quercetin, Inflammation and Immunity.

    PubMed

    Li, Yao; Yao, Jiaying; Han, Chunyan; Yang, Jiaxin; Chaudhry, Maria Tabassum; Wang, Shengnan; Liu, Hongnan; Yin, Yulong

    2016-03-01

    In vitro and some animal models have shown that quercetin, a polyphenol derived from plants, has a wide range of biological actions including anti-carcinogenic, anti-inflammatory and antiviral activities; as well as attenuating lipid peroxidation, platelet aggregation and capillary permeability. This review focuses on the physicochemical properties, dietary sources, absorption, bioavailability and metabolism of quercetin, especially main effects of quercetin on inflammation and immune function. According to the results obtained both in vitro and in vivo, good perspectives have been opened for quercetin. Nevertheless, further studies are needed to better characterize the mechanisms of action underlying the beneficial effects of quercetin on inflammation and immunity. PMID:26999194

  12. Basophils and allergic inflammation.

    PubMed

    Siracusa, Mark C; Kim, Brian S; Spergel, Jonathan M; Artis, David

    2013-10-01

    Basophils were discovered by Paul Ehrlich in 1879 and represent the least abundant granulocyte population in mammals. The relative rarity of basophils and their phenotypic similarities with mast cells resulted in this cell lineage being historically overlooked, both clinically and experimentally. However, recent studies in human subjects and murine systems have shown that basophils perform nonredundant effector functions and significantly contribute to the development and progression of TH2 cytokine-mediated inflammation. Although the potential functions of murine and human basophils have provoked some controversy, recent genetic approaches indicate that basophils can migrate into lymphoid tissues and, in some circumstances, cooperate with other immune cells to promote optimal TH2 cytokine responses in vivo. This article provides a brief historical perspective on basophil-related research and discusses recent studies that have identified previously unappreciated molecules and pathways that regulate basophil development, activation, and function in the context of allergic inflammation. Furthermore, we highlight the unique effector functions of basophils and discuss their contributions to the development and pathogenesis of allergic inflammation in human disease. Finally, we discuss the therapeutic potential of targeting basophils in preventing or alleviating the development and progression of allergic inflammation. PMID:24075190

  13. Dietary modulation of inflammation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inflammation is heightened innate immune response caused by infection or wound. It is a part of essential immune responses for host defense against invading pathogens and wound healing which are the key biological processes necessary for the survival of all multi-cellular organisms. In mammals, it i...

  14. Vasospasm in Cerebral Inflammation

    PubMed Central

    Eisenhut, Michael

    2014-01-01

    All forms of cerebral inflammation as found in bacterial meningitis, cerebral malaria, brain injury, and subarachnoid haemorrhage have been associated with vasospasm of cerebral arteries and arterioles. Vasospasm has been associated with permanent neurological deficits and death in subarachnoid haemorrhage and bacterial meningitis. Increased levels of interleukin-1 may be involved in vasospasm through calcium dependent and independent activation of the myosin light chain kinase and release of the vasoconstrictor endothelin-1. Another key factor in the pathogenesis of cerebral arterial vasospasm may be the reduced bioavailability of the vasodilator nitric oxide. Therapeutic trials in vasospasm related to inflammation in subarachnoid haemorrhage in humans showed a reduction of vasospasm through calcium antagonists, endothelin receptor antagonists, statins, and plasminogen activators. Combination of therapeutic modalities addressing calcium dependent and independent vasospasm, the underlying inflammation, and depletion of nitric oxide simultaneously merit further study in all conditions with cerebral inflammation in double blind randomised placebo controlled trials. Auxiliary treatment with these agents may be able to reduce ischemic brain injury associated with neurological deficits and increased mortality. PMID:25610703

  15. Obesity, Inflammation, and Cancer.

    PubMed

    Deng, Tuo; Lyon, Christopher J; Bergin, Stephen; Caligiuri, Michael A; Hsueh, Willa A

    2016-05-23

    Obesity, a worldwide epidemic, confers increased risk for multiple serious conditions, including cancer, and is increasingly recognized as a growing cause of preventable cancer risk. Chronic inflammation, a well-known mediator of cancer, is a central characteristic of obesity, leading to many of its complications, and obesity-induced inflammation confers additional cancer risk beyond obesity itself. Multiple mechanisms facilitate this strong association between cancer and obesity. Adipose tissue is an important endocrine organ, secreting several hormones, including leptin and adiponectin, and chemokines that can regulate tumor behavior, inflammation, and the tumor microenvironment. Excessive adipose expansion during obesity causes adipose dysfunction and inflammation to increase systemic levels of proinflammatory factors. Cells from adipose tissue, such as cancer-associated adipocytes and adipose-derived stem cells, enter the cancer microenvironment to enhance protumoral effects. Dysregulated metabolism that stems from obesity, including insulin resistance, hyperglycemia, and dyslipidemia, can further impact tumor growth and development. This review describes how adipose tissue becomes inflamed in obesity, summarizes ways these mechanisms impact cancer development, and discusses their role in four adipose-associated cancers that demonstrate elevated incidence or mortality in obesity. PMID:27193454

  16. Dietary Polyphenols, Inflammation and Cancer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A considerable amount of evidence indicates that tumorigenesis, the development and growth of tumors, is associated with inflammation. Nuclear factor-kappaB (NF-kappaB), a master regulator of infection and inflammation, has been identified as a key modulator in which inflammation could develop into ...

  17. Molecular identification of the economically important freshwater mussels (Mollusca-Bivalvia-Unionoida) of Thailand: developing species-specific markers from AFLPs.

    PubMed

    Vannarattanarat, S; Zieritz, A; Kanchanaketu, T; Kovitvadhi, U; Kovitvadhi, S; Hongtrakul, V

    2014-04-01

    Shells of certain freshwater mussel (Unionoida) species are highly demanded and serve as raw material for a range of decorative and pharmaceutical products. In Thailand, most animals for this purpose are currently harvested from wild populations, with unionoid culture still being in its infancy. Whilst reliable species identification is a prerequisite for developing a large-scale industry, identification by morphological means is hampered by extensive phenotypic plasticity and poor knowledge of species delimitations. To facilitate alternative molecular identification, we developed species-specific markers for the three Thai unionoids with considerable economic potential (CEP): that is, Chamberlainia hainesiana, Hyriopsis desowitzi and Hyriopsis myersiana. For this purpose, amplified fragment length polymorphism (AFLP) fingerprints using 24 specific primer pairs were generated for eight samples of each CEP species and four samples of the closely related, non-CEP species Contradens contradens. Cloning and sequencing of 13 CEP species-specific AFLP bands revealed fragment collision at three occasions. In total, 16 species-specific primer pairs were designed and tested on 92 Thai specimens spanning seven species and four genera. Thereby, specificity of (1) three primers to C. hainesiana, (2) one primer to H. desowitzi + Hyriopsis bialata, (3) one primer to H. myersiana + H. bialata and (4) four primers to all three Hyriopsis species tested was confirmed. Respective multiplex PCR protocols are provided. The developed primers enable cheap, quick and reliable identification of the Thai CEP species by one to three PCRs and offer a tool for a range of additional applications within mussel culture and ecological and evolutionary research on these important organisms. PMID:24313464

  18. COMPARISON OF A GENUS-SPECIFIC CONVENTIONAL PCR AND A SPECIES-SPECIFIC NESTED-PCR FOR MALARIA DIAGNOSIS USING FTA COLLECTED SAMPLES FROM KINGDOM OF SAUDI ARABIA.

    PubMed

    Al-Harthi, Saeed A

    2015-12-01

    Molecular tools are increasingly accepted as the most sensitive and reliable techniques for malaria diagnosis and epidemiological surveys. Also, collection of finger prick blood spots onto filter papers is the most simple and affordable method for samples preservation and posterior molecular analysis, especially in rural endemic regions where malaria remains a major health problem. Two malaria molecular diagnostic tests, a Plasmodium genus-specific conventional PCR and a Plasmodium species-specific Nested PCR, were evaluated using DNA templates prepared from Whatman-FTA cards' dry blood spots using both, Methanol-fixation/Heat-extraction and FTA commercial purification kit. A total of 121 blood samples were collected from six Saudi south-western endemic districts both, as thick and thin films for routine microscopic screening and onto FTA cards for molecular studies. Out of the 121 samples, 75 were P. falciparum positive by at least one technique. No other species of Plasmodium were detected. P. falciparum parasites were identified in 69/75 (92%) samples by microscopic screening in health care centers. P. genus-specific PCR was able to amplify P. falciparum DNA in 41/75 (55%) and 59/75 (79%) samples using Methanol-fixation/Heat-extraction and FTA purification kit, respectively. P. species-specific Nested PCR revealed 68/75 (91%) and 75/75 (100%) positive samples using DNA templates were isolated by Methanol-fixation/Heat- extraction and FTA purification methods, respectively. The species-specific Nested PCR applied to Whatman-FTA preserved and processed blood samples represents the best alternative to classical microscopy for malaria diagnosis, particularly in epidemiological screening. PMID:26939223

  19. Simultaneous sample preparation and species-specific isotope dilution mass spectrometry analysis of monomethylmercury and tributyltin in a certified oyster tissue.

    PubMed

    Monperrus, M; Rodriguez Martin-Doimeadios, R C; Scancar, J; Amouroux, D; Donard, O F X

    2003-08-15

    A rapid, accurate, sensitive, and simple method for simultaneous speciation analysis of mercury and tin in biological samples has been developed. Integrated simultaneous sample preparation for tin and mercury species includes open focused microwave extraction and derivatization via ethylation. Capillary gas chromatography-inductively plasma mass spectrometry (CGC-ICPMS) conditions and parameters affecting the analytical performance were carefully optimized both for species-specific isotope dilution analysis of MMHg and TBT and for conventional analysis of MBT and DBT201Hg-enriched monomethylmercury and 117Sn-enriched tributyltin were used for species-specific isotope dilution mass spectrometry (SIDMS) analysis. As important, accurate isotope dilution analysis requires equilibration between the spike and the analyte to achieve successful analytical procedures. Since the spike stabilization and solubilization are the most critical and time-consuming steps in isotope dilution analysis, different spiking procedures were tested. Simultaneous microwave-assisted spike stabilization and solubilization can be achieved within less than 5 min. This study originally introduces a method for the simultaneous speciation and isotope dilution of mercury and tin in biological tissues. The sample throughput of the procedure was drastically reduced by fastening sample preparation and GC separation steps. The accuracy of the method was tested by both external calibration analysis and species-specific isotope dilution analysis using the first biological reference material certified for multielemental speciation (oyster tissue, CRM 710, IRMM). The results obtained demonstrate that isotope dilution analysis is a powerful method allowing the simultaneous speciation of TBT and MMHg with high precision and excellent accuracy. Analytical problems related to low recovery during sample preparation are thus minimized by SIDMS. In addition, a rapid procedure allows us to establish a performant

  20. Mineralogical characterization of pristine, bio-eroded and fossil bivalve shell material for the evaluation of a species-specific alteration potential

    NASA Astrophysics Data System (ADS)

    Hippler, Dorothee; Goetschl, Katja Elisabeth; Gerstmann, Brigitte Simone; Rafael Garcia-March, Jose; Dietzel, Martin

    2015-04-01

    Biogenic carbonates of marine calcifiers can provide a wealth of information for the reconstruction of modern and palaeo-environments. However, their composite carbonate shells are often prone to different alteration processes that might occur during their lifetime, post-mortem or during early diagenesis. In order to use these calcifiers as palaeo-archives or proxy carriers, it is thus of crucial importance to assess their alteration potential. Here, we present the mineral phase composition of four different Mediterranean bivalve species (Spondylus, Lithophaga, Arca, Glycymeris) using spatially selected, powder XRD analysis, as well as in-situ high-resolution Raman spectroscopy. The sample set thereby comprises pristine-modern, bioeroded-modern, Holocene and Pleistocene specimens of the same bivalve species in order to characterize and evaluate the species-specific susceptibility to bioerosion and diagenetic alteration. We reveal species-specific shell compositions that are validated by both analytical methods. Differences in shell mineralogy occur between the outermost (periostracum), the outer (ostracum) and inner (hypostracum) layer, with the outer layer mainly composed of calcite and the inner layers of aragonite with variable portions of calcite. Considerable species-specific changes in mineralogy of the respective shell layers with increasing geological age are not found. Our results indicate that the original shell mineralogy (calcite, aragonite and carbonate fluorapatite) as well as the composition, structure and thickness of the respective shell layers are important factors favouring or preventing alteration to occur. Moreover, our findings highlight the effect of bioerosion during the alteration process. The analysis of distinct areas of the shells hinting at microbial activity reveals slight changes in shell mineralogy. We thus postulate that processes related to shell taphonomy are crucial for the shell's alteration/preservational potential and thus

  1. Distribution pattern of benthic invertebrates in Danish estuaries: The use of Taylor's power law as a species-specific indicator of dispersion and behavior

    NASA Astrophysics Data System (ADS)

    Kristensen, Erik; Delefosse, Matthieu; Quintana, Cintia O.; Banta, Gary T.; Petersen, Hans Christian; Jørgensen, Bent

    2013-03-01

    The lack of a common statistical approach describing the distribution and dispersion pattern of marine benthic animals has often hampered the comparability among studies. The purpose of this study is therefore to apply an alternative approach, Taylor's power law, to data on spatial and temporal distribution of 9 dominating benthic invertebrate species from two study areas, the estuaries Odense Fjord and Roskilde Fjord, Denmark. The slope (b) obtained from the power relationship of sample variance (s2) versus mean (μ) appears to be species-specific and independent of location and time. It ranges from a low of ~ 1 for large-bodied (> 1 mg AFDW) species (e.g. Marenzelleria viridis, Nereis diversicolor) to a high of 1.6-1.9 for small-bodied (< 1 mg AFDW) species (e.g. Pygospio elegans and Tubificoides benedii). Accordingly, b is apparently a valuable species-specific dispersion index based on biological factors such as behavior and intraspecific interactions. Thus, at the examined spatial scale, the more intense intraspecific interactions (e.g. territoriality) cause less aggregated distribution patterns among large- than small-bodied invertebrates. The species-specific interactions seem sufficiently strong to override environmental influences (e.g. water depth and sediment type). The strong linear relationship between the slope b and intercept log(a) from the power relationship is remarkably similar for all surveys providing a common slope of - 1.63 with the present sampling approach. We suggest that this relationship is an inherent characteristic of Taylor's power law, and that b as a dispersion index may be biased by e.g. sampling errors when this relationship is weak. The correlation strength between b and log(a) could therefore be envisioned as a data quality check.

  2. Gut Microbiota and Inflammation

    PubMed Central

    Hakansson, Asa; Molin, Goran

    2011-01-01

    Systemic and local inflammation in relation to the resident microbiota of the human gastro-intestinal (GI) tract and administration of probiotics are the main themes of the present review. The dominating taxa of the human GI tract and their potential for aggravating or suppressing inflammation are described. The review focuses on human trials with probiotics and does not include in vitro studies and animal experimental models. The applications of probiotics considered are systemic immune-modulation, the metabolic syndrome, liver injury, inflammatory bowel disease, colorectal cancer and radiation-induced enteritis. When the major genomic differences between different types of probiotics are taken into account, it is to be expected that the human body can respond differently to the different species and strains of probiotics. This fact is often neglected in discussions of the outcome of clinical trials with probiotics. PMID:22254115

  3. Nitric oxide and inflammation.

    PubMed

    Cirino, Giuseppe; Distrutti, Eleonora; Wallace, John L

    2006-04-01

    There are several pre-clinical studies on the involvement of NO in inflammation. From this large amount of information it is clear that virtually every cell and many immunological parameters are modulated by NO. Thus, the final outcome is that NO cannot be rigidly classified as an anti-inflammatory or pro-inflammatory molecule. This peculiar aspect of the pathophysiology of NO has hampered the development of new drugs based on the concepts developed. Recent therapeutic approach are targeted to increase endogenous NO by activating the gene and some promising early data are available. At the present stage one of the most promising approach in the inflammation field is represented by a new class of NO-releasing compounds namely NO-NSAIDs that have recently enrolled in phase 2 clinical studies. PMID:16613570

  4. Species-specific sensitivity to selenium-induced impairment of cortisol secretion in adrenocortical cells of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis)

    SciTech Connect

    Miller, L.L. Hontela, A.

    2011-06-01

    Species differences in physiological and biochemical attributes exist even among closely related species and may underlie species-specific sensitivity to toxicants. Rainbow trout (RT) are more sensitive than brook trout (BT) to the teratogenic effects of selenium (Se), but it is not known whether all tissues exhibit this pattern of vulnerability. In this study, primary cultures of RT and BT adrenocortical cells were exposed to selenite (Na{sub 2}SO{sub 3}) and selenomethionine (Se-Met) to compare cell viability and ACTH-stimulated cortisol secretion in the two fish species. Cortisol, the primary stress hormone in fish, facilitates maintenance of homeostasis when fish are exposed to stressors, including toxicants. Cell viability was not affected by Se, but selenite impaired cortisol secretion, while Se-Met did not (RT and BT EC{sub 50} > 2000 mg/L). RT cells were more sensitive (EC{sub 50} = 8.7 mg/L) to selenite than BT cells (EC{sub 50} = 90.4 mg/L). To identify the targets where Se disrupts cortisol synthesis, selenite-impaired RT and BT cells were stimulated with ACTH, dbcAMP, OH-cholesterol, and pregnenolone. Selenite acted at different steps in the cortisol biosynthesis pathway in RT and BT cells, confirming a species-specific toxicity mechanism. To test the hypothesis that oxidative stress mediates Se-induced toxicity, selenite-impaired RT cells were exposed to NAC, BSO and antioxidants (DETCA, ATA, Vit A, and Vit E). Inhibition of SOD by DETCA enhanced selenite-induced cortisol impairment, indicating that oxidative stress plays a role in Se toxicity; however, modifying GSH content of the cells did not have an effect. The results of this study, with two closely related salmonids, provided additional evidence for species-specific differences in sensitivity to Se which should be considered when setting thresholds and water quality guidelines. - Research Highlights: > We investigated species-specific sensitivity to Se in trout adrenocortical cells. > Selenite

  5. PET Imaging of Inflammation Biomarkers

    PubMed Central

    Wu, Chenxi; Li, Fang; Niu, Gang; Chen, Xiaoyuan

    2013-01-01

    Inflammation plays a significant role in many disease processes. Development in molecular imaging in recent years provides new insight into the diagnosis and treatment evaluation of various inflammatory diseases and diseases involving inflammatory process. Positron emission tomography using 18F-FDG has been successfully applied in clinical oncology and neurology and in the inflammation realm. In addition to glucose metabolism, a variety of targets for inflammation imaging are being discovered and utilized, some of which are considered superior to FDG for imaging inflammation. This review summarizes the potential inflammation imaging targets and corresponding PET tracers, and the applications of PET in major inflammatory diseases and tumor associated inflammation. Also, the current attempt in differentiating inflammation from tumor using PET is also discussed. PMID:23843893

  6. Phage display allows identification of zona pellucida-binding peptides with species-specific properties: novel approach for development of contraceptive vaccines for wildlife.

    PubMed

    Samoylova, Tatiana I; Cochran, Anna M; Samoylov, Alexandre M; Schemera, Bettina; Breiteneicher, Adam H; Ditchkoff, Stephen S; Petrenko, Valery A; Cox, Nancy R

    2012-12-31

    Multiple phage-peptide constructs, where the peptides mimic sperm epitopes that bind to zona pellucida (ZP) proteins, were generated via selection from a phage display library using a novel approach. Selections were designed to allow for identification of ZP-binding phage clones with potential species-specific properties, an important feature for wildlife oral vaccines as the goal is to control overpopulation of a target species while not affecting non-target species' reproduction. Six phage-peptide antigens were injected intramuscularly into pigs and corresponding immune responses evaluated. Administration of the antigens into pigs stimulated production of anti-peptide antibodies, which were shown to act as anti-sperm antibodies. Potentially, such anti-sperm antibodies could interfere with sperm delivery or function in the male or female genital tract, leading to contraceptive effects. Staining of semen samples collected from different mammalian species, including pig, cat, dog, bull, and mouse, with anti-sera from pigs immunized with ZP-binding phage allowed identification of phage-peptide constructs with different levels of species specificity. Based on the intensity of the immune responses and specificity of these responses in different species, two of the antigens with fusion peptide sequences GEGGYGSHD and GQQGLNGDS were recognized as the most promising candidates for development of contraceptive vaccines for wild pigs. PMID:23079080

  7. DNA barcoding, species-specific PCR and real-time PCR techniques for the identification of six Tribolium pests of stored products.

    PubMed

    Zhang, Tao; Wang, Yi-Jiao; Guo, Wei; Luo, Dan; Wu, Yi; Kučerová, Zuzana; Stejskal, Václav; Opit, George; Cao, Yang; Li, Fu-Jun; Li, Zhi-Hong

    2016-01-01

    Flour beetles of the genus Tribolium Macleay (Coleoptera: Tenebrionidae) are important stored product pests in China and worldwide. They are often found or are intercepted in grain depots, flour mills, and entry-exit ports, etc. Traditionally, Tribolium species are identified according to the morphological characteristics of the adult. However, it is almost impossible to rapidly identify adult fragments and non-adult stages based on external morphological characteristics. Molecular techniques for the rapid and accurate identification of Tribolium species are required, particularly for pest monitoring and the quarantine of stored products pests. Here, we establish DNA barcoding, species-specific PCR, and real-time PCR techniques for the identification of six stored-product pest Tribolium species including T. castaneum, T. confusum, T. destructor, T. madens, T. freemani and T. brevicornis. We detected the mitochondrial DNA cytochrome oxidase subunit I (COI) barcodes for Tribolium from 18 geographic populations and 101 individuals, built a Tribolium DNA barcode library, and designed species-specific primers and TaqMan probes for the above six Tribolium species. The three techniques were applied to identify Tribolium collected from stored samples and samples captured from quarantine ports. The results demonstrated that three techniques were all able to identify the six species of Tribolium both rapidly and accurately. PMID:27352804

  8. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    PubMed

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-01

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. PMID:27025952

  9. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications.

    PubMed

    Queirós, J; Godinho, R; Lopes, S; Gortazar, C; de la Fuente, J; Alves, P C

    2015-07-01

    Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations. PMID:25403329

  10. DNA barcoding, species-specific PCR and real-time PCR techniques for the identification of six Tribolium pests of stored products

    PubMed Central

    Zhang, Tao; Wang, Yi-Jiao; Guo, Wei; Luo, Dan; Wu, Yi; Kučerová, Zuzana; Stejskal, Václav; Opit, George; Cao, Yang; Li, Fu-Jun; Li, Zhi-Hong

    2016-01-01

    Flour beetles of the genus Tribolium Macleay (Coleoptera: Tenebrionidae) are important stored product pests in China and worldwide. They are often found or are intercepted in grain depots, flour mills, and entry-exit ports, etc. Traditionally, Tribolium species are identified according to the morphological characteristics of the adult. However, it is almost impossible to rapidly identify adult fragments and non-adult stages based on external morphological characteristics. Molecular techniques for the rapid and accurate identification of Tribolium species are required, particularly for pest monitoring and the quarantine of stored products pests. Here, we establish DNA barcoding, species-specific PCR, and real-time PCR techniques for the identification of six stored-product pest Tribolium species including T. castaneum, T. confusum, T. destructor, T. madens, T. freemani and T. brevicornis. We detected the mitochondrial DNA cytochrome oxidase subunit I (COI) barcodes for Tribolium from 18 geographic populations and 101 individuals, built a Tribolium DNA barcode library, and designed species-specific primers and TaqMan probes for the above six Tribolium species. The three techniques were applied to identify Tribolium collected from stored samples and samples captured from quarantine ports. The results demonstrated that three techniques were all able to identify the six species of Tribolium both rapidly and accurately. PMID:27352804

  11. Do Species-specific Hydraulic Traits Predict Ecosystem Response and Community Structure? Evidence From Co-occurring Bryophytes of a Sloping Wetland

    NASA Astrophysics Data System (ADS)

    Lintz, H. E.; Russell, M. C.; Hardman, A. C.

    2007-12-01

    Ecosystems comprise a complex assortment species, and each species has a unique set of physiological and anatomical characteristics or traits. Landscape-level forecasts of ecosystem response to climate change can benefit by accounting for species-specific traits. Here, we demonstrate how a hydraulic trait can be quantified and aggregrated to community and ecosystem levels using a model life form and system, bryophytes in a sloping wetland. Growth and reproduction of bryophytes depend on the quantity of external water held, which varies by species. Wetlands provide a soil substrate that supplies either an unlimited amount of water, or at minimum, a shallow water table for part of the year. We hypothesized and confirmed that external water holding capacity of bryophyte species (measured in the laboratory) corresponded to bryophyte community structure along a hydrology gradient in the wetland. In addition, we demonstrated that water holding capacity by species can be aggregated to the level of the wetland ecosystem to reveal an emergent community property, water holding capacity of the bryophyte mat. Our results support ecological theory presented by Paul Keddy (1999) that co-occurring organisms show similarity in resource acquisition along gradients of resource limitation. We promote a conceptual framework that incorporates species-specific traits as modeling currency that can bridge scales.

  12. Control of ocular inflammation.

    PubMed

    Wilkie, D A

    1990-05-01

    Although both topical and systemic anti-inflammatory agents have a place in veterinary ophthalmology, they play only a small role in overall patient management. They must be used appropriately to prevent ocular damage and loss of vision from inflammation and are not a replacement for a complete ophthalmic examination and specific treatment directed at the etiology of the problem. If used indiscriminately, they can result in local or systemic side effects or toxicities, many of which are worse than the initial problem for which they were selected. Just as topical corticosteroids are contraindicated with infectious keratitis, so are systemic corticosteroids contraindicated in patients with ocular inflammation resulting from a systemic infectious process. Anti-inflammatories must be used at the appropriate dosage and frequency. Use of corticosteroids that have low intraocular penetration for intraocular disease or corticosteroids with low potency is a waste of time and money. The most expensive medication is one that does not work. Avoid combination therapies when only a single medication is required. These do not save time or money and have the potential to result in the development of drug-related diseases. Diseases for which anti-inflammatory therapy has little or no indication include corneal scars, corneal edema, corneal pigmentation, corneal dystrophy, cataracts without inflammation, glaucoma, and retinal atrophy and degeneration. Last, remember that all commercially available ophthalmic medications are specifically formulated for use in the eye. Their pH, concentration, osmolality, and melting temperature all are designed to facilitate penetration. The use of dermal and otic preparations to treat ophthalmic problems is contraindicated. PMID:2194354

  13. Inflammation and Vascular Injury

    PubMed Central

    Simon, Daniel I.

    2014-01-01

    The invited special lecture at the 76th Annual Scientific Meeting of the Japanese Circulation Society focused on the central role of inflammation in vascular injury and repair. Early studies pioneered the concept that mechanical injury, such as balloon angioplasty and endovascular stent deployment, elicits an inflammatory response from the vessel wall. This hypothesis was developed and substantiated at a time when the prevailing dogma viewed restenosis following angioplasty as a primarily proliferative smooth muscle cell disease. Antibody targeting of Mac-1 reduced leukocyte accumulation and limited neointimal formation following balloon injury or stent implantation. Genetic absence of Mac-1 resulted in diminished leukocyte accumulation and neointimal thickening after carotid artery injury in mice. In the course of those studies, our laboratory made fundamental discoveries regarding the mechanism of leukocyte recruitment at sites of vascular injury and identified platelet glycoprotein (GP) Ibα, a component of the GPIb-IX-V complex, as the previously unknown platelet counter-receptor for Mac-1. Follow-on studies have focused extensively on the structure, function, and signaling of the leukocyte integrin Mac-1. The binding site for GPIbα in Mac-1 has been mapped and subsequently showed that leukocyte engagement of platelet GPIbα via Mac-1 is critical not only for the biological response to vascular injury, but also for thrombosis, vasculitis, glomerulonephritis, and multiple sclerosis, thereby advancing the hypothesis that virtually all inflammation is platelet-dependent. Furthermore, ligand engagement of Mac-1 initiates a novel gene program that promotes inflammation by activating NFκB and downregulating the expression of the forkhead transcription factor Foxp1 that controls monocyte differentiation. Small molecule inhibitors of Mac-1 function have been pursued, including targeting of Mac-1-GPIbα binding or the downstream tyrosine kinase spleen tyrosine kinase

  14. Polyglycolic acid induced inflammation

    PubMed Central

    Ceonzo, Kathleen; Gaynor, Anne; Shaffer, Lisa; Kojima, Koji; Vacanti, Charles A.; Stahl, Gregory L.

    2005-01-01

    Tissue and organ replacement have quickly outpaced available supply. Tissue bioengineering holds the promise for additional tissue availability. Various scaffolds are currently used, whereas polyglycolic acid (PGA), which is currently used in absorbable sutures and orthopedic pins, provides an excellent support for tissue development. Unfortunately, PGA can induce a local inflammatory response following implantation, so we investigated the molecular mechanism of inflammation in vitro and in vivo. Degraded PGA induced an acute peritonitis, characterized by neutrophil (PMN) infiltration following intraperitoneal injection in mice. Similar observations were observed using the metabolite of PGA, glycolide. Dissolved PGA or glycolide, but not native PGA, activated the classical complement pathway in human sera, as determined by classical complement pathway hemolytic assays, C3a and C5a production, C3 and immunoglobulin deposition. To investigate whether these in vitro observations translated to in vivo findings, we used genetically engineered mice. Intraperitoneal administration of glycolide or dissolved PGA in mice deficient in C1q, factor D, C1q and factor D or C2 and factor B demonstrated significantly reduced PMN infiltration compared to congenic controls (WT). Mice deficient in C6 also demonstrated acute peritonitis. However, treatment of WT or C6 deficient mice with a monoclonal antibody against C5 prevented the inflammatory response. These data suggest that the hydrolysis of PGA to glycolide activates the classical complement pathway. Further, complement is amplified via the alternative pathway and inflammation is induced by C5a generation. Inhibition of C5a may provide a potential therapeutic approach to limit the inflammation associated with PGA derived materials following implantation. PMID:16548688

  15. Basophils in inflammation.

    PubMed

    Schwartz, Christian; Eberle, Joerg U; Voehringer, David

    2016-05-01

    Basophils are functionally closely related to mast cells. Both cell types express the high-affinity IgE receptor (FcεRI) and rapidly release preformed mediator from intracellular stores upon IgE-mediated activation. However, in contrast to mast cells basophils finish their maturation in the bone marrow and have a lifespan of only 2-3 days. Basophil numbers increase in response to IL-3 or TSLP and migrate into tissues to promote type 2 immune responses. Here we review recent advances regarding the pro- and anti-inflammatory functions of basophils in murine models and human allergic inflammation of the skin, lung and intestine. PMID:25959388

  16. [Inflammation and obesity (lipoinflammation)].

    PubMed

    Izaola, Olatz; de Luis, Daniel; Sajoux, Ignacio; Domingo, Joan Carles; Vidal, Montse

    2015-01-01

    Obesity is a chronic disease with multiple origins. It is a widespread global phenomenon carrying potentially serious complications which requires a multidisciplinary approach due to the significant clinical repercussions and elevated health costs associated with the disease. The most recent evidence indicates that it shares a common characteristic with other prevalent, difficult-to-treat pathologies: chronic, low-grade inflammation which perpetuates the disease and is associated with multiple complications. The current interest in lipoinflammation or chronic inflammation associated with obesity derives from an understanding of the alterations and remodelling that occurs in the adipose tissue, with the participation of multiple factors and elements throughout the process. Recent research highlights the importance of some of these molecules, called pro-resolving mediators, as possible therapeutic targets in the treatment of obesity. This article reviews the evidence published on the mechanisms that regulate the adipose tissue remodelling process and lipoinflammation both in obesity and in the mediators that are directly involved in the appearance and resolution of the inflammatory process. PMID:26040339

  17. Myopia and Inflammation

    PubMed Central

    Herbort, Carl P.; Papadia, Marina; Neri, Piergiorgio

    2011-01-01

    The correlation between myopia and intraocular inflammation has rarely been explored. The aim of this article is to review myopic changes induced by inflammatory diseases and inflammatory diseases related to myopia, followed by a discussion on inflammatory choroidal neovascularization. Clinical cases are used to illustrate these conditions. The review does not include inflammatory conditions caused by surgical interventions employed for treatment of myopia. Uveitic conditions that can induce a myopic shift include sclero-choroidal inflammation, lens induced myopia due to steroid cataracts, juvenile idiopathic arthritis (JIA) induced myopia, and transient drug induced myopia due to sulfonamides and acetazolamide used for treatment of ocular toxoplasmosis and inflammatory cystoid macular edema, respectively. Most inflammatory conditions related to myopia are conditions involving the choriocapillaris. These include multifocal choroiditis and/or punctate inner choroiditis, multiple evanescent white dot syndrome and acute idiopathic blind spot enlargement. It can be hypothesized that fragility of the choriocapillaris due to particular anatomic changes due to myopia, together with unknown immunogenetic factors predispose myopic eyes to primary inflammatory choriocapillaropathies. PMID:22454750

  18. Myopia and inflammation.

    PubMed

    Herbort, Carl P; Papadia, Marina; Neri, Piergiorgio

    2011-10-01

    The correlation between myopia and intraocular inflammation has rarely been explored. The aim of this article is to review myopic changes induced by inflammatory diseases and inflammatory diseases related to myopia, followed by a discussion on inflammatory choroidal neovascularization. Clinical cases are used to illustrate these conditions. The review does not include inflammatory conditions caused by surgical interventions employed for treatment of myopia. Uveitic conditions that can induce a myopic shift include sclero-choroidal inflammation, lens induced myopia due to steroid cataracts, juvenile idiopathic arthritis (JIA) induced myopia, and transient drug induced myopia due to sulfonamides and acetazolamide used for treatment of ocular toxoplasmosis and inflammatory cystoid macular edema, respectively. Most inflammatory conditions related to myopia are conditions involving the choriocapillaris. These include multifocal choroiditis and/or punctate inner choroiditis, multiple evanescent white dot syndrome and acute idiopathic blind spot enlargement. It can be hypothesized that fragility of the choriocapillaris due to particular anatomic changes due to myopia, together with unknown immunogenetic factors predispose myopic eyes to primary inflammatory choriocapillaropathies. PMID:22454750

  19. Strategies for managing periodontal inflammation.

    PubMed

    Schonfeld, Steven E

    2010-04-01

    Most of the tissue destruction in periodontal disease is caused by the patient's inflammatory response. Classical approaches to controlling inflammation rely on attempts to eliminate pathogenic bacteria that incite the inflammatory response through mechanical or chemical means. This approach still has a place in treating periodontal inflammation today. Emerging and future approaches will rely more on modifying the inflammatory response itself, by limiting the activity of proinflammatory pathways and by amplifying pathways that resolve inflammation. PMID:20509367

  20. [Concentration of species alien (bovine) IgG in the blood serum of foals after the intake of non-species specific colostrum preparation].

    PubMed

    Warko, G; Becht, H; Bostedt, H

    1993-12-01

    Sixteen vital foals with free access to maternal colostrum received a additional non-species-specific commercial colostrum additive within the first 18 hours of their life. The additive had been prepared from bovine colostrum. At birth no bovine IgG was detectable. The concentration of bovine IgG reached its maximum 18 hours post natum with XG = 74.6 mg/dl. 96 hours after birth IgG levels had dropped to XG = 20.9 mg/dl. The correlation of bovine IgG with GGT-activity was highly significant. Formation of antibodies against bovine IgG could not be demonstrated. It is not possible to increase igG in the circulation of newborn foals to satisfactory levels with IgG of bovine origin in the used commercial colostrum additive. PMID:8129698

  1. U2504 Determines the Species Specificity of the A-site Cleft Antibiotics: The sStructures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

    SciTech Connect

    Gurel, G.; Blaha, G; Moore, P; Steitz,

    2009-01-01

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  2. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome

    SciTech Connect

    Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.; Yale

    2009-06-30

    Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the Asite cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

  3. Assessing the potential impact of water-based drill cuttings on deep-water calcareous red algae using species specific impact categories and measured oceanographic and discharge data.

    PubMed

    Nilssen, Ingunn; dos Santos, Francisco; Coutinho, Ricardo; Gomes, Natalia; Cabral, Marcelo Montenegro; Eide, Ingvar; Figueiredo, Marcia A O; Johnsen, Geir; Johnsen, Ståle

    2015-12-01

    The potential impact of drill cuttings on the two deep water calcareous red algae Mesophyllum engelhartii and Lithothamnion sp. from the Peregrino oil field was assessed. Dispersion modelling of drill cuttings was performed for a two year period using measured oceanographic and discharge data with 24 h resolution. The model was also used to assess the impact on the two algae species using four species specific impact categories: No, minor, medium and severe impact. The corresponding intervals for photosynthetic efficiency (ΦPSIImax) and sediment coverage were obtained from exposure-response relationship for photosynthetic efficiency as function of sediment coverage for the two algae species. The temporal resolution enabled more accurate model predictions as short-term changes in discharges and environmental conditions could be detected. The assessment shows that there is a patchy risk for severe impact on the calcareous algae stretching across the transitional zone and into the calcareous algae bed at Peregrino. PMID:26412110

  4. Predicting Incursion of Plant Invaders into Kruger National Park, South Africa: The Interplay of General Drivers and Species-Specific Factors

    PubMed Central

    Jarošík, Vojtěch; Pyšek, Petr; Foxcroft, Llewellyn C.; Richardson, David M.; Rouget, Mathieu; MacFadyen, Sandra

    2011-01-01

    Background Overcoming boundaries is crucial for incursion of alien plant species and their successful naturalization and invasion within protected areas. Previous work showed that in Kruger National Park, South Africa, this process can be quantified and that factors determining the incursion of invasive species can be identified and predicted confidently. Here we explore the similarity between determinants of incursions identified by the general model based on a multispecies assemblage, and those identified by species-specific models. We analyzed the presence and absence of six invasive plant species in 1.0×1.5 km segments along the border of the park as a function of environmental characteristics from outside and inside the KNP boundary, using two data-mining techniques: classification trees and random forests. Principal Findings The occurrence of Ageratum houstonianum, Chromolaena odorata, Xanthium strumarium, Argemone ochroleuca, Opuntia stricta and Lantana camara can be reliably predicted based on landscape characteristics identified by the general multispecies model, namely water runoff from surrounding watersheds and road density in a 10 km radius. The presence of main rivers and species-specific combinations of vegetation types are reliable predictors from inside the park. Conclusions The predictors from the outside and inside of the park are complementary, and are approximately equally reliable for explaining the presence/absence of current invaders; those from the inside are, however, more reliable for predicting future invasions. Landscape characteristics determined as crucial predictors from outside the KNP serve as guidelines for management to enact proactive interventions to manipulate landscape features near the KNP to prevent further incursions. Predictors from the inside the KNP can be used reliably to identify high-risk areas to improve the cost-effectiveness of management, to locate invasive plants and target them for eradication. PMID:22194893

  5. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor.

    PubMed

    Esfandiari, Leyla; Wang, Siqing; Wang, Siqi; Banda, Anisha; Lorenzini, Michael; Kocharyan, Gayane; Monbouquette, Harold G; Schmidt, Jacob J

    2016-01-01

    A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids. PMID:27455337

  6. Sleep Loss and Inflammation

    PubMed Central

    Simpson, Norah S.; Meier-Ewert, Hans K.; Haack, Monika

    2012-01-01

    Controlled, experimental studies on the effects of acute sleep loss in humans have shown that mediators of inflammation are altered by sleep loss. Elevations in these mediators have been found to occur in healthy, rigorously screened individuals undergoing experimental vigils of more than 24 hours, and have also been seen in response to various durations of sleep restricted to between 25 and 50% of a normal 8 hour sleep amount. While these altered profiles represent small changes, such sub-clinical shifts in basal inflammatory cytokines are known to be associated with the future development of metabolic syndrome disease in healthy, asymptomatic individuals. Although the mechanism of this altered inflammatory status in humans undergoing experimental sleep loss is unknown, it is likely that autonomic activation and metabolic changes play key roles. PMID:21112025

  7. Frailty, Inflammation and Immunosenescence.

    PubMed

    Fulop, Tamas; McElhaney, Janet; Pawelec, Graham; Cohen, Alan A; Morais, José A; Dupuis, Gilles; Baehl, Sarra; Camous, Xavier; Witkowski, Jacek M; Larbi, Anis

    2015-01-01

    Frailty is a still-evolving concept of a complex phenomenon. There are several algorithms and strategies for assessing frailty syndrome, but currently, no universally accepted definition or measurement protocol has been determined. Consequently, the biological cause(s) of frailty are also poorly defined. Much circumstantial experimental data point to the dysregulation of several key physiological systems, including the neuroendocrine, musculoskeletal, metabolic and immune/inflammatory systems, resulting from alterations in functional reserves. Immune dysregulation and inflammation as causes of frailty have gained some support from the results of longitudinal studies, but a true causal relationship has not been established. This chapter will describe the immune/inflammatory alterations found in frailty and their putative causal relationships with this state. PMID:26301977

  8. Inflammation and Epilepsy

    PubMed Central

    Vezzani, Annamaria

    2005-01-01

    In recent years, increasing evidence has indicated that immune and inflammatory reactions occur in brain in various central nervous system (CNS) diseases. Furthermore, inflammatory processes, such as the production of proinflammatory cytokines and related molecules, have been described in brain after seizures induced in experimental models and in clinical cases of epilepsy. Although little is known about the role of inflammation in epilepsy, it has been hypothesized that activation of the innate immune system and associated inflammatory reactions in brain may mediate some of the molecular and structural changes occurring during and after seizure activity. Whether the innate immune response that takes place in epileptic tissue is beneficial or noxious to the CNS is still an open and intriguing question that should be addressed by further investigations. PMID:16059445

  9. Infections, inflammation and epilepsy.

    PubMed

    Vezzani, Annamaria; Fujinami, Robert S; White, H Steve; Preux, Pierre-Marie; Blümcke, Ingmar; Sander, Josemir W; Löscher, Wolfgang

    2016-02-01

    Epilepsy is the tendency to have unprovoked epileptic seizures. Anything causing structural or functional derangement of brain physiology may lead to seizures, and different conditions may express themselves solely by recurrent seizures and thus be labelled "epilepsy." Worldwide, epilepsy is the most common serious neurological condition. The range of risk factors for the development of epilepsy varies with age and geographic location. Congenital, developmental and genetic conditions are mostly associated with the development of epilepsy in childhood, adolescence and early adulthood. Head trauma, infections of the central nervous system (CNS) and tumours may occur at any age and may lead to the development of epilepsy. Infections of the CNS are a major risk factor for epilepsy. The reported risk of unprovoked seizures in population-based cohorts of survivors of CNS infections from developed countries is between 6.8 and 8.3 %, and is much higher in resource-poor countries. In this review, the various viral, bacterial, fungal and parasitic infectious diseases of the CNS which result in seizures and epilepsy are discussed. The pathogenesis of epilepsy due to brain infections, as well as the role of experimental models to study mechanisms of epileptogenesis induced by infectious agents, is reviewed. The sterile (non-infectious) inflammatory response that occurs following brain insults is also discussed, as well as its overlap with inflammation due to infections, and the potential role in epileptogenesis. Furthermore, autoimmune encephalitis as a cause of seizures is reviewed. Potential strategies to prevent epilepsy resulting from brain infections and non-infectious inflammation are also considered. PMID:26423537

  10. Identification of beta-subunit of bacterial RNA-polymerase--a non-species-specific bacterial protein--as target of antibodies in primary biliary cirrhosis.

    PubMed

    Roesler, Kai-Wolfgang; Schmider, Wolfgang; Kist, Manfred; Batsford, Stephen; Schiltz, Emile; Oelke, Mathias; Tuczek, Anja; Dettenborn, Therese; Behringer, Dirk; Kreisel, Wolfgang

    2003-03-01

    Several observations suggest that bacteria induce autoimmunity in primary biliary cirrhosis (PBC). Since no PBC-specific bacterial species could be identified, it can be speculated that the triggers are non-species-specific bacterial proteins. This hypothesis would imply that several or even all bacterial species can trigger PBC. Therefore, we investigated whether PBC exhibits immune reactions to non-species-specific bacterial antigens. Yersinia enterocolitica O3 was screened for the presence of proteins that were labeled by immunoblotting using PBC sera. We focused our investigations on a 160-kDa protein, which was further enriched and characterized by partial N-terminal amino acid sequencing. The prevalence of antibodies to this protein was determined by immunoblotting in a variety of diseases. The 160-kDa protein was identified as the beta-subunit of bacterial RNA-polymerase, a highly conserved bacterial protein with a very high degree of sequence identity among all bacterial species. Antibodies to the beta-subunit of bacterial RNA polymerase were specific for this protein. Until now no mammalian protein could be found that cross-reacts with these antibodies. The prevalence of antibodies to the beta-subunit of bacterial RNA polymerase (ARPA) using the protein from Yersinia enterocolitica O3 (serum dilution 1:1000) was: healthy controls (HC, N = 101) 7.9%, primary biliary cirrhosis (PBC, N = 61) 32.8%, autoimmune hepatitis type 1 (AIH, N = 46) 26.1%, alcoholic liver cirrhosis (ALC, N = 44) 9.1%, Crohn's disease (CD, N = 38) 7.9%, ulcerative colitis (UC, N = 24) 8.3%, primary sclerosing cholangitis + UC (PSC/UC, N = 11) 0%, acute yersiniosis (Yers, N = 36) 19.4%, acute infection with Campylobacter jejuni (Camp, N = 10) 0%, acute Q-fever (QF, N = 16) 6.25%, chronic hepatitis C (HCV, N = 39) 7.7%, c-ANCA-positive vasculitis (Vasc, N = 40) 15%, systemic lupus erythematosus (SLE, N = 28) 10.7%, and malaria tropica (MT, N = 24) 16.7%. There was no significant

  11. Inference about species richness and community structure using species-specific occupancy models in the National Swiss Breeding Bird Survey MUB

    USGS Publications Warehouse

    Kery, M.; Royle, J. Andrew

    2009-01-01

    Species richness is the most widely used biodiversity measure. Virtually always, it cannot be observed but needs to be estimated because some species may be present but remain undetected. This fact is commonly ignored in ecology and management, although it will bias estimates of species richness and related parameters such as occupancy, turnover or extinction rates. We describe a species community modeling strategy based on species-specific models of occurrence, from which estimates of important summaries of community structure, e.g., species richness, occupancy, or measures of similarity among species or sites, are derived by aggregating indicators of occurrence for all species observed in the sample, and for the estimated complement of unobserved species. We use data augmentation for an efficient Bayesian approach to estimation and prediction under this model based on MCMC in WinBUGS. For illustration, we use the Swiss breeding bird survey (MHB) that conducts 2?3 territory-mapping surveys in a systematic sample of 267 1 km2 units on quadrat-specific routes averaging 5.1 km to obtain species-specific estimates of occupancy, and estimates of species richness of all diurnal species free of distorting effects of imperfect detectability. We introduce into our model species-specific covariates relevant to occupancy (elevation, forest cover, route length) and sampling (season, effort). From 1995 to 2004, 185 diurnal breeding bird species were known in Switzerland, and an additional 13 bred 1?3 times since 1900. 134 species were observed during MHB surveys in 254 quadrats surveyed in 2001, and our estimate of 169.9 (95% CI 151?195) therefore appeared sensible. The observed number of species ranged from 4 to 58 (mean 32.8), but with an estimated 0.7?11.2 (mean 2.6) further, unobserved species, the estimated proportion of detected species was 0.48?0.98 (mean 0.91). As is well known, species richness declined at higher elevation and fell above the timberline, and most

  12. Species-specific and seasonal differences in chlorophyll fluorescence and photosynthetic light response among three evergreen species in a Madrean sky island mixed conifer forest

    NASA Astrophysics Data System (ADS)

    Potts, D. L.; Minor, R. L.; Braun, Z.; Barron-Gafford, G. A.

    2012-12-01

    Unlike the snowmelt-dominated hydroclimate of more northern mountainous regions, the hydroclimate of the Madrean sky islands is characterized by snowmelt and convective storms associated with the North American Monsoon. These mid-summer storms trigger biological activity and are important drivers of primary productivity. For example, at the highest elevations where mixed conifer forests occur, ecosystem carbon balance is influenced by monsoon rains. Whereas these storms' significance is increasingly recognized at the ecosystem scale, species-specific physiological responses to the monsoon are poorly known. Prior to and following monsoon onset, we measured pre-dawn and light-adapted chlorophyll fluorescence as well as photosynthetic light response in southwestern white pine (Pinus strobiformis), ponderosa pine (Pinus ponderosa), and Douglas fir (Pseudotsuga menziesii) in a Madrean sky island mixed conifer forest near Tucson, Arizona. Photochemical quenching (qp), an indicator of the proportion of open PSII reaction centers, was greatest in P. strobiformis and least in P. menziesii and increased in response to monsoon rains (repeated-measures ANOVA; species, F2,14 = 6.17, P = 0.012; time, F2,14= 8.17, P = 0.013). In contrast, non-photochemical quenching (qN), an indicator of heat dissipation ability, was greatest in P. ponderosa and least in P. menziesii, but was not influenced by monsoon onset (repeated-measures ANOVA; species, F2,12 = 4.18, P = 0.042). Estimated from leaf area-adjusted photosynthetic light response curves, maximum photosynthetic rate (Amax) was greatest in P. ponderosa and least in P. menziesii (repeated-measures ANOVA; species, F2,8= 40.8, P = 0.001). Surprisingly, while the monsoon positively influenced Amax among P. ponderosa and P. strobiformis, Amax of P. menziesii declined with monsoon onset (repeated-measures ANOVA; species x time, F2,8 = 13.8, P = 0.002). Calculated as the initial slope of the photosynthetic light response curve, light

  13. Epilepsy and brain inflammation.

    PubMed

    Vezzani, Annamaria; Aronica, Eleonora; Mazarati, Andrey; Pittman, Quentin J

    2013-06-01

    During the last decade, experimental research has demonstrated a prominent role of glial cells, activated in brain by various injuries, in the mechanisms of seizure precipitation and recurrence. In particular, alterations in the phenotype and function of activated astrocytes and microglial cells have been described in experimental and human epileptic tissue, including modifications in potassium and water channels, alterations of glutamine/glutamate cycle, changes in glutamate receptor expression and transporters, release of neuromodulatory molecules (e.g. gliotransmitters, neurotrophic factors), and induction of molecules involved in inflammatory processes (e.g. cytokines, chemokines, prostaglandins, complement factors, cell adhesion molecules) (Seifert et al., 2006; Vezzani et al., 2011; Wetherington et al., 2008). In particular, brain injury or proconvulsant events can activate microglia and astrocytes to release a number of proinflammatory mediators, thus initiating a cascade of inflammatory processes in brain tissue. Proinflammatory molecules can alter neuronal excitability and affect the physiological functions of glia by paracrine or autocrine actions, thus perturbing the glioneuronal communications. In experimental models, these changes contribute to decreasing the threshold to seizures and may compromise neuronal survival (Riazi et al., 2010; Vezzani et al., 2008). In this context, understanding which are the soluble mediators and the molecular mechanisms crucially involved in glio-neuronal interactions is instrumental to shed light on how brain inflammation may contribute to neuronal hyperexcitability in epilepsy. This review will report the clinical observations in drug-resistant human epilepsies and the experimental findings in adult and immature rodents linking brain inflammation to the epileptic process in a causal and reciprocal manner. By confronting the clinical evidence with the experimental findings, we will discuss the role of specific soluble

  14. Inflammation and endometrial bleeding.

    PubMed

    Berbic, M; Ng, C H M; Fraser, I S

    2014-12-01

    Most of the key physiological processes in the human reproductive tract involve a significant inflammatory component. These processes include follicle development, ovulation, implantation, pregnancy, labor, postpartum, remodeling and menstruation. In this context, the term 'inflammation' usually means an influx of leukocytes ('immune cells'), often of different types, into a reproductive tract tissue. These examples of inflammation are not overtly associated with any infective process. There may also be evidence that these invading leukocytes have altered their functions to take on specific and relevant local regulatory roles. Specific sequential changes in different leukocytes can be demonstrated within human endometrium during the different phases of the normal menstrual cycle. Leukocytes are fairly sparse in numbers through the proliferative phase, but increase substantially into and through the secretory phase, so much so that around 40% of all stromal cells in the premenstrual phase are leukocytes, mainly uterine natural killer cells, a large granulated lymphocyte. Other leukocytes which play key roles in menstruation appear to be macrophages, mast cells, dendritic cells, neutrophils, eosinophils and regulatory T cells. Premenstrual withdrawal of progesterone increases the endometrial expression of inflammatory mediators, including IL-8 and MCP-1, which are believed to drive endometrial leukocyte recruitment at this time. Macrophages and neutrophils are rich sources of defensins and whey acid protein motif proteins, which play important roles in ensuring microbial protection while the epithelial barrier is disrupted. Mast cells are increasingly activated as the menstrual phase approaches, and leukocyte proteases trigger a cascade of matrix metalloproteinases and degradation of extracellular matrix. Dendritic cells and other antigen-presenting cells (e.g. macrophages) almost certainly facilitate clearance of cellular debris from the uterine cavity, and reduce

  15. Species-specific bioaccumulation of halogenated organic pollutants and their metabolites in fish serum from an e-waste site, South China.

    PubMed

    Zeng, Yan-Hong; Luo, Xiao-Jun; Zheng, Xiao-Bo; Tang, Bin; Wu, Jiang-Ping; Mai, Bi-Xian

    2014-10-01

    Halogenated organic pollutants (HOPs)-including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenylethers (PBDEs), polybromobiphenyls (PBBs), dechlorane plus (DP), tetrabromobisphenol A (TBBPA), and hexabromocyclododecanes (HBCDs) as well as PCB metabolites (methylsulfone [MeSO2-]) and hydroxylated (OH-) PCBs and OH-PBDEs-were determined in the serum of mud carp and northern snakehead from an electronic-waste (e-waste) site in South China. The average concentrations (mean ± SD) of ΣPCBs, ΣPBDEs, ΣOCPs, ΣPBBs, ΣTBBPA, ΣHBCDs, and ΣDP were 1410 ± 324, 70 ± 20, 3.0 ± 0.4, 2.8 ± 0.8, 1.6 ± 0.4, 1.0 ± 0.2, and 0.3 ± 0.03 ng/g wet weight (ww) in mud carp and 6430 ± 781, 468 ± 49, 22.4 ± 1.1, 7.0 ± 0.6, 2.9 ± 2.3, 5.5 ± 1.1, and 4.6 ± 0.6 ng/g ww in northern snakehead, respectively. MeSO2-PCBs, OH-PCBs, and OH-PBDEs were detected at a total concentration of 0.44 ± 0.03 and 9.7 ± 0.3 ng/g ww in mud carp and northern snakehead, respectively. The congener profiles of PCBs, PBDEs, OH/MeSO2-PCBs, and OH-PBDEs were found to be significantly different between the two fish species, possibly as a result of species-specific bioaccumulation and/or metabolism of the HOPs. Chirality of ten PCB congeners and α-HBCD, as well as the f anti values of DP in the serum samples, supported the species-specific biotransformation of HOPs. Furthermore, the presence of covaried and counter-varied enantiomeric fractions of PCBs between the two fish species indicated species- and congener-specific enantiomer enrichment of PCBs. PMID:24859045

  16. Species-specific physiological response by the cold-water corals Lophelia pertusa and Madrepora oculata to variations within their natural temperature range

    NASA Astrophysics Data System (ADS)

    Naumann, Malik S.; Orejas, Covadonga; Ferrier-Pagès, Christine

    2014-01-01

    The scleractinian cold-water corals (CWC) Lophelia pertusa and Madrepora oculata represent two major deep-sea reef-forming species that act as key ecosystem engineers over a wide temperature range, extending from the northern Atlantic (ca. 5-9 °C) to the Mediterranean Sea (ca. 11-13 °C). Recent research suggests that environmental parameters, such as food supply, settling substrate availability or aragonite saturation state may represent important precursors controlling habitat suitability for CWC. However, the effect of one principal environmental factor, temperature, on CWC key physiological processes is still unknown. In order to evaluate this effect on calcification, respiration, and dissolved organic carbon (DOC) net flux, colonies of Mediterranean L. pertusa and M. oculata were acclimated in aquaria to three temperatures (12, 9 and 6 °C), by consecutive decrements of 1 month duration. L. pertusa and M. oculata maintained at Mediterranean control conditions (i.e. 12 °C) displayed constant rates, on average respiring 4.8 and 4.0 μmol O2 cm-2 coral surface area d-1, calcifying 22.3 and 12.3 μmol CaCO3 g-1 skeletal dry weight d-1 and net releasing 2.6 and 3.1 μmol DOC cm-2 coral surface area d-1, respectively. Respiration of L. pertusa was not affected by lowered temperatures, while M. oculata respiration declined significantly (by 48%) when temperature decreased to 9 °C and 6 °C relative to controls. L. pertusa calcification at 9 °C was similar to controls, but decreased significantly (by 58%) at 6 °C. For M. oculata, calcification declined by 41% at 9 °C and by 69% at 6 °C. DOC net flux was similar throughout the experiment for both CWC. These findings reveal species-specific physiological responses by CWC within their natural temperature range. L. pertusa shows thermal acclimation in respiration and calcification, while these mechanisms appear largely absent in M. oculata. Conclusively, species-specific thermal acclimation may significantly affect

  17. The central leucine-rich repeat region of chicken TLR16 dictates unique ligand specificity and species-specific interaction with TLR2.

    PubMed

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

    2007-06-01

    The ligand specificity of human TLR (hTLR) 2 is determined through the formation of functional heterodimers with either hTLR1 or hTLR6. The chicken carries two TLR (chTLR) 2 isoforms, type 1 and type 2 (chTLR2t1 and chTLR2t2), and one putative TLR1/6/10 homologue (chTLR16) of unknown function. In this study, we report that transfection of HeLa cells with the various chicken receptors yields potent NF-kappaB activation for the receptor combination of chTLR2t2 and chTLR16 only. The sensitivity of this complex was strongly enhanced by human CD14. The functional chTLR16/chTLR2t2 complex responded toward both the hTLR2/6-specific diacylated peptide S-(2,3-bispalmitoyloxypropyl)-Cys-Gly-Asp-Pro-Lys-His-Pro-Lys-Ser-Phe (FSL-1) and the hTLR2/1 specific triacylated peptide tripalmitoyl-S-(bis(palmitoyloxy)propyl)-Cys-Ser-(Lys)(3)-Lys (Pam(3)CSK(4)), indicating that chTLR16 covers the functions of both mammalian TLR1 and TLR6. Dissection of the species specificity of TLR2 and its coreceptors showed functional chTLR16 complex formation with chTLR2t2 but not hTLR2. Conversely, chTLR2t2 did not function in combination with hTLR1 or hTLR6. The use of constructed chimeric receptors in which the defined domains of chTLR16 and hTLR1 or hTLR6 had been exchanged revealed that the transfer of leucine-rich repeats (LRR) 6-16 of chTLR16 into hTLR6 was sufficient to confer dual ligand specificity to the human receptor and to establish species-specific interaction with chTLR2t2. Collectively, our data indicate that diversification of the central LRR region of the TLR2 coreceptors during evolution has put constraints on both their ligand specificity and their ability to form functional complexes with TLR2. PMID:17513760

  18. Development of stably transfected human and rat hepatoma cell lines for the species-specific assessment of xenobiotic response enhancer module (XREM)-dependent induction of drug metabolism.

    PubMed

    Fery, Yvonne; Mueller, Stefan O; Schrenk, Dieter

    2010-11-01

    Based on our current knowledge, PXR holds a key position in the induction of a selective battery of enzymes and transporters of drug metabolism. In order to prevent serious adverse drug effects or unpredicted drug-drug interactions (DDI), it is compulsory to investigate the possible inducing potency of drugs under development. Furthermore, analysis of the inducing potency of environmental pollutants and new or manufactured chemicals is part of toxicological risk assessment. In non-transfected human HepG2 and rat H4IIE hepatoma cells, we examined the characteristics of expression of 45 genes involved in drug metabolism. A few gene products such as CYP2B6 or CYP3A4 mRNA were prominent in HepG2 cells while their major rat counterparts were, e.g., CYP2B3 or CYP3A1/3A3. Furthermore, a number of xenobiotic receptors including PXR were expressed in both cell lines. A number of genes were regulated in a cell type and species-specific manner after incubation with the prototypical PXR agonists rifampicin or dexamethasone, respectively. Then, we established cell-based reporter gene assays for screening for PXR-dependent induction of drug metabolism. HepG2 and H4IIE cells were stably transfected with a reporter gene containing PXR responsive elements (XREMs) which mediate the induction of PXR target genes such as CYP3A enzymes. With both stable cell lines the CYP inducers clotrimazole, dexamethasone, omeprazole, phenobarbital, rifampicin, as well as the drug candidate EMD 392949 and the brominated flame retardants hexabromocylododecane (HBCD) and a pentabromodiphenyl ether (pentaBDE) mixture were screened. In the human HepG2-XREM3 and rat H4IIE-XREM3 cells, clotrimazole and HBCD were found as common activators of the human and rat PXR whereas pentaBDE was more effective with the human cell system. Omeprazole and phenobarbital did not induce the rat PXR-dependent reporter gene expression in H4IIE-XREM3 cells, while a moderate increase was found in HepG2-XREM3 cells. EMD 392949

  19. A species-specific activation of Toll-like receptor signaling in bovine and sheep bronchial epithelial cells triggered by Mycobacterial infections.

    PubMed

    Ma, Yan; Han, Fei; Liang, Jinping; Yang, Jiali; Shi, Juan; Xue, Jing; Yang, Li; Li, Yong; Luo, Meihui; Wang, Yujiong; Wei, Jun; Liu, Xiaoming

    2016-03-01

    Pulmonary tuberculosis caused by a Mycobacterium infection remains a major public health problem in most part of the world, in part owing to the transmission of its pathogens between hosts including human, domestic and wild animals. To date, molecular mechanisms of the pathogenesis of TB are still incompletely understood. In addition to alveolar macrophages, airway epithelial cells have also been recently recognized as main targets for Mycobacteria infections. In an effort to understand the pathogen-host interaction between Mycobacteria and airway epithelial cells in domestic animals, in present study, we investigated the Toll-like receptor (TLR) signaling in bovine and sheep airway epithelial cells in response to an infection of Mycobacterium tuberculosis avirulent H37Ra stain or Mycobacterium bovis BCG vaccine strain, using primary air-liquid interface (ALI) bronchial epithelial culture models. Our results revealed a host and pathogen species-specific TLR-mediated recognition of pathogen-associated molecular patterns (PAMPs), induction and activation of TLR signaling pathways, and substantial induction of inflammatory response in bronchial epithelial cells in response to Mycobacteria infections between these two species. Interestingly, the activation TLR signaling in bovine bronchial epithelial cells induced by Mycobacteria infection was mainly through a myeloid differentiation factor 88 (MyD88)-independent TLR signaling pathway, while both MyD88-dependent and independent TLR signaling cascades could be induced in sheep epithelial cells. Equally noteworthy, a BCG infection was able to induce both MyD88-dependent and independent signaling in sheep and bovine airway epithelial cells, but more robust inflammatory responses were induced in sheep epithelial cells relative to the bovines; whereas an H37Ra infection displayed an ability to mainly trigger a MyD88-independent TLR signaling cascade in these two host species, and induce a more extent expression of

  20. [Non-species-specific effects of unacylated homoserine lactone and hexylresorcinol, low molecular weight autoregulators, on the growth and development of bacteria].

    PubMed

    Muliukin, A L; Filippova, S N; Kozlova, A N; Surgucheva, N A; Bogdanova, T I; Tsaplina, I A; El'-Registan, G I

    2006-01-01

    We conducted a comparative study of the effects of alpha-amino-gamma-butyrolactone, the common structural element of extracellular microbial regulators of the homoserine lactone (HSL) group, and of 4-n-hexylresorcinol, an autoregulator of the alkylhydroxybenzene (AHB) group, on the growth and development of gram-positive and gram-negative bacteria. We revealed non-species-specific effects of HSL and AHB and characterized their concentration dependencies. The addition of 10(-5)-10(-3) M HSL or 10(-5)-10(-4) M AHB during the exponential growth phase of the cultures grown on balanced media resulted in cell division arrest and accelerated the transition to the stationary phase that culminated in endospore formation in Bacillus cereus, Alicyclobacillus tolerans, and Sulfobacillus thermosulfidooxidans. When bacilli grew under the cultivation conditions that resulted in a low-zero spore percentage, 10(-4)-10(-3) M HSL cancelled the inhibition of spore formation. In the gram-negative bacteria Pseudomonas aurantiaca and Azotobacter vinelandii, AHB at concentrations of 10(-4) to (1.5-2.5) 10(-4) M induced the formation of dormant cells. Studies with the actinobacterium Streptomyces avermitilis revealed that the HSL effect varied depending on the age of the test cultures. The addition of 10(-4) M HSL during the lag phase of a submerged streptomycete culture accelerated its transition to the stationary phase and induced the formation of endospores, the dormant cells that are regarded as alternatives to exospores (conidia). If HSL (3.64 and 4.55 mg per 1cm2 disc) was locally added to a surface S. avermitilis culture, the growing mycelium formed rings that differed in their density, in the extent of the development of aerial mycelium, and in the presence/absence of exospores. Ring-shaped growth of streptomycete mycelia was also induced by 0.075-0.75 mg of AHB; however, unlike HSL, AHB repressed exospore formation. The data on non-species-specific effects of HSL and AHB suggest

  1. [Pathophysiology of inflammation].

    PubMed

    Sahlmann, C-O; Ströbel, P

    2016-02-15

    Inflammation results from activation of the immune system in response to a broad range of different stimuli. The immune system is a highly complex and evolutionary optimized defense system with cellular and humoral components. The course of an inflammatory response is influenced by the immune condition of the host, the virulence e. g. of an infectious agent, and the fine tuning of the local tissue reaction, which may be influenced by individual genetic factors. Immunity is a compromise between insufficient (immunodeficiency) or exaggerated (autoimmunity) immune reactions. The dynamic balance between these two extremes is achieved through stringent T- and B-cell selection in the bone marrow and thymus on the one hand and through "checkpoint control" in peripheral lymphatic tissues. Many tumors have ways to suppress local immune responses and to escape destruction through the immune system (one of the so-called "hallmarks of cancer"). In recent years, different approaches have successfully been able to reverse this local immunosuppression. First clinical trials using these strategies have shown highly promising results indicating that the therapeutic use of the immune system will be a very effective instrument in the arsenal of cancer treatment agents. PMID:26875429

  2. Thermography in ocular inflammation

    PubMed Central

    Kawali, Ankush A

    2013-01-01

    Background and Objectives: The purpose of this study was to evaluate ocular inflammatory and non-inflammatory conditions using commercially available thermal camera. Materials and Methods: A non-contact thermographic camera (FLIR P 620) was used to take thermal pictures of seven cases of ocular inflammation, two cases of non-inflammatory ocular pathology, and one healthy subject with mild refractive error only. Ocular inflammatory cases included five cases of scleritis, one case of postoperative anterior uveitis, and a case of meibomian gland dysfunction with keratitis (MGD-keratitis). Non-inflammatory conditions included a case of conjunctival benign reactive lymphoid hyperplasia (BRLH) and a case of central serous chorio-retinopathy. Thermal and non-thermal photographs were taken, and using analyzing software, the ocular surface temperature was calculated. Results: Patient with fresh episode of scleritis revealed high temperature. Eyes with MGD-keratitis depicted lower temperature in clinically more affected eye. Conjunctival BRLH showed a cold lesion on thermography at the site of involvement, in contrast to cases of scleritis with similar clinical presentation. Conclusion: Ocular thermal imaging is an underutilized diagnostic tool which can be used to distinguish inflammatory ocular conditions from non-inflammatory conditions. It can also be utilized in the evaluation of tear film in dry eye syndrome. Its applications should be further explored in uveitis and other ocular disorders. Dedicated “ocular thermographic” camera is today's need of the hour. PMID:24347863

  3. Mast cells and inflammation.

    PubMed

    Theoharides, Theoharis C; Alysandratos, Konstantinos-Dionysios; Angelidou, Asimenia; Delivanis, Danae-Anastasia; Sismanopoulos, Nikolaos; Zhang, Bodi; Asadi, Shahrzad; Vasiadi, Magdalini; Weng, Zuyi; Miniati, Alexandra; Kalogeromitros, Dimitrios

    2012-01-01

    Mast cells are well known for their role in allergic and anaphylactic reactions, as well as their involvement in acquired and innate immunity. Increasing evidence now implicates mast cells in inflammatory diseases where they are activated by non-allergic triggers, such as neuropeptides and cytokines, often exerting synergistic effects as in the case of IL-33 and neurotensin. Mast cells can also release pro-inflammatory mediators selectively without degranulation. In particular, IL-1 induces selective release of IL-6, while corticotropin-releasing hormone secreted under stress induces the release of vascular endothelial growth factor. Many inflammatory diseases involve mast cells in cross-talk with T cells, such as atopic dermatitis, psoriasis and multiple sclerosis, which all worsen by stress. How mast cell differential responses are regulated is still unresolved. Preliminary evidence suggests that mitochondrial function and dynamics control mast cell degranulation, but not selective release. Recent findings also indicate that mast cells have immunomodulatory properties. Understanding selective release of mediators could explain how mast cells participate in numerous diverse biologic processes, and how they exert both immunostimulatory and immunosuppressive actions. Unraveling selective mast cell secretion could also help develop unique mast cell inhibitors with novel therapeutic applications. This article is part of a Special Issue entitled: Mast cells in inflammation. PMID:21185371

  4. Mechanisms Underlying Inflammation in Neurodegeneration

    PubMed Central

    Glass, Christopher K.; Saijo, Kaoru; Winner, Beate; Marchetto, Maria Carolina; Gage, Fred H.

    2010-01-01

    Inflammation is associated with many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. In this Review, we discuss inducers, sensors, transducers, and effectors of neuroinflammation that contribute to neuronal dysfunction and death. Although inducers of inflammation may be generated in a disease-specific manner, there is evidence for a remarkable convergence in the mechanisms responsible for the sensing, transduction, and amplification of inflammatory processes that result in the production of neurotoxic mediators. A major unanswered question is whether pharmacological inhibition of inflammation pathways will be able to safely reverse or slow the course of disease. PMID:20303880

  5. Phytoplankton IF-FISH: Species-specific labeling of cellular proteins by immunofluorescence (IF) with simultaneous species identification by fluorescence immunohybridization (FISH).

    PubMed

    Meek, Megan E; Van Dolah, Frances M

    2016-05-01

    Phytoplankton rarely occur as unialgal populations. Therefore, to study species-specific protein expression, indicative of physiological status in natural populations, methods are needed that will both assay for a protein of interest and identify the species expressing it. Here we describe a protocol for IF-FISH, a dual labeling procedure using immunofluorescence (IF) labeling of a protein of interest followed by fluorescence in situ hybridization (FISH) to identify the species expressing that protein. The protocol was developed to monitor expression of the cell cycle marker proliferating cell nuclear antigen (PCNA) in the red tide dinoflagellate, Karenia brevis, using a large subunit (LSU) rRNA probe to identify K. brevis in a mixed population of morphologically similar Karenia species. We present this protocol as proof of concept that IF-FISH can be successfully applied to phytoplankton cells. This method is widely applicable for the analysis of single-cell protein expression of any protein of interest within phytoplankton communities. PMID:26948044

  6. Rapid Genus- and Species-Specific Identification of Cronobacter spp. by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

    PubMed Central

    Stephan, Roger; Ziegler, Dominik; Pflüger, Valentin; Vogel, Guido; Lehner, Angelika

    2010-01-01

    Cronobacter spp. are Gram-negative opportunistic food-borne pathogens and are known as rare but important causes of life-threatening neonatal infections. Rapid and reliable identification of Cronobacter species and their differentiation from phenotypically similar, nonpathogenic Enterobacter turicensis, Enterobacter helveticus, and Enterobacter pulveris have become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid genus and species identification of the six Cronobacter species recognized so far. To this end, we developed a reference MS database library that includes 54 Cronobacter target strains as well as 17 nontarget strains. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2,000 to 30,000 Da). Genus- and species-specific biomarker protein mass patterns were determined. The defined biomarker mass patterns (Spectral Archive and Microbial Identification System [SARAMIS] SuperSpectrum) were validated using 36 strains from various Cronobacter species as well as eight nontarget strains. For all strains the mass spectrometry-based identification scheme yielded identical results as with a PCR-based identification system. All strains were correctly identified, and no nontarget strain was misidentified as Cronobacter. Our study demonstrates that MALDI-TOF MS is a reliable and powerful tool for the rapid identification of Cronobacter strains to the genus and species level. PMID:20554814

  7. A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops

    PubMed Central

    Yendrek, Craig R.; Koester, Robert P.

    2015-01-01

    Current concentrations of tropospheric ozone ([O3]) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific differences are largely unknown. Here, a physiological screen has been performed on multiple varieties of legume species. Three varieties of garden pea (Pisum sativum L.) were resilient to elevated [O3]. Garden pea showed no change in photosynthetic capacity or leaf longevity when exposed to elevated [O3], in contrast to varieties of soybean (Glycine max (L.) Merr.) and common bean (Phaseolus vulgaris L.). Global transcriptomic and targeted biochemical analyses were then done to examine the mechanistic differences in legume responses to elevated [O3]. In all three species, there was an O3-mediated reduction in specific leaf weight and total non-structural carbohydrate content, as well as increased abundance of respiration-related transcripts. Differences specific to garden pea included a pronounced increase in the abundance of GLUTATHIONE REDUCTASE transcript, as well as greater contents of foliar glutathione, apoplastic ascorbate, and sucrose in elevated [O3]. These results suggest that garden pea may have had greater capacity for detoxification, which prevented net losses in CO2 fixation in an elevated [O3] environment. PMID:26324463

  8. Differentiation of Meat Samples from Domestic Horses (Equus caballus) and Asiatic Wild Asses (Equus hemionus) Using a Species-Specific Restriction Site in the Mitochondrial Cytochrome b Region

    PubMed Central

    Kuehn, Ralph; Kaczensky, Petra; Lkhagvasuren, Davaa; Pietsch, Stephanie; Walzer, Chris

    2011-01-01

    Recent studies suggest that Asiatic wild asses (Equus hemionus) are being increasingly poached in a commercial fashion. Part of the meat is believed to reach the meat markets in the capital Ulaanbaatar. To test this hypothesis, we collected 500 meat samples between February and May 2006. To differentiate between domestic horse (Equus caballus) and wild ass meat, we developed a restriction fragment length polymorphism (RFLP) assay based on the polymerase chain reaction (PCR). We amplified and sequenced a cytochrome b fragment (335 bp) and carried out a multialignment of the generated sequences for the domestic horse, the Asiatic wild ass, the domestic donkey (Equus asinus) and the Przewalski’s horse (Equus ferus przewalskii). We detected a species-specific restriction site (AatII) for the Asiatic wild ass, resulting in a specific restriction fragment length polymorphism (RFLP) band pattern. This RFLP assay represents a rapid and cost-effective method to detect wild ass meat. All of the 500 meat samples we collected and analysed within this pilot project proved to be domestic horsemeat as declared by the sales people. Thus, either the assumption that wild ass meat is sold as “cheap horse meat” is wrong, or we picked the wrong markets, products or season. PMID:22059088

  9. Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein.

    PubMed Central

    Emili, A; Greenblatt, J; Ingles, C J

    1994-01-01

    We have used protein-blotting and protein affinity chromatography to demonstrate that each of the two glutamine-rich activation domains of the human transcription factor Sp1 can bind specifically and directly to the C-terminal evolutionarily conserved domain of the human TATA box-binding protein (TBP). These activation domains of Sp1 also bind directly to Drosophila TBP but bind much less strongly to TBP from the yeast Saccharomyces cerevisiae. The abilities of the Sp1 activation domains to interact directly with the TBPs of various species correlate well with their abilities to activate transcription in extracts derived from the same species. We also show that a glutamine-rich transcriptional activating region of the Drosophila protein Antennapedia binds directly to TBP in a species-specific manner that reflects its ability to activate transcription in vivo. These results support the notion that TBP is a direct and important target of glutamine-rich transcriptional activators. Images PMID:8114696

  10. A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops.

    PubMed

    Yendrek, Craig R; Koester, Robert P; Ainsworth, Elizabeth A

    2015-12-01

    Current concentrations of tropospheric ozone ([O3]) pollution negatively impact plant metabolism, which can result in decreased crop yields. Interspecific variation in the physiological response of plants to elevated [O3] exists; however, the underlying cellular responses explaining species-specific differences are largely unknown. Here, a physiological screen has been performed on multiple varieties of legume species. Three varieties of garden pea (Pisum sativum L.) were resilient to elevated [O3]. Garden pea showed no change in photosynthetic capacity or leaf longevity when exposed to elevated [O3], in contrast to varieties of soybean (Glycine max (L.) Merr.) and common bean (Phaseolus vulgaris L.). Global transcriptomic and targeted biochemical analyses were then done to examine the mechanistic differences in legume responses to elevated [O3]. In all three species, there was an O3-mediated reduction in specific leaf weight and total non-structural carbohydrate content, as well as increased abundance of respiration-related transcripts. Differences specific to garden pea included a pronounced increase in the abundance of GLUTATHIONE REDUCTASE transcript, as well as greater contents of foliar glutathione, apoplastic ascorbate, and sucrose in elevated [O3]. These results suggest that garden pea may have had greater capacity for detoxification, which prevented net losses in CO2 fixation in an elevated [O3] environment. PMID:26324463

  11. Evolution of a Species-Specific Determinant within Human CRM1 that Regulates the Post-transcriptional Phases of HIV-1 Replication

    PubMed Central

    Hué, Stéphane; Roberts, Roland G.; Bergeron, Julien R. C.; Malim, Michael H.

    2011-01-01

    The human immunodeficiency virus type-1 (HIV-1) Rev protein regulates the nuclear export of intron-containing viral RNAs by recruiting the CRM1 nuclear export receptor. Here, we employed a combination of functional and phylogenetic analyses to identify and characterize a species-specific determinant within human CRM1 (hCRM1) that largely overcomes established defects in murine cells to the post-transcriptional stages of the HIV-1 life cycle. hCRM1 expression in murine cells promotes the cytoplasmic accumulation of intron-containing viral RNAs, resulting in a substantial stimulation of the net production of infectious HIV-1 particles. These stimulatory effects require a novel surface-exposed element within HEAT repeats 9A and 10A, discrete from the binding cleft previously shown to engage Rev's leucine-rich nuclear export signal. Moreover, we show that this element is a unique feature of higher primate CRM1 proteins, and discuss how this sequence has evolved from a non-functional, ancestral sequence. PMID:22114565

  12. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies

    PubMed Central

    Lhermie, Guillaume; El Garch, Farid; Toutain, Pierre-Louis; Ferran, Aude A.; Bousquet-Mélou, Alain

    2015-01-01

    We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting. PMID:26506096

  13. Bacterial Species-Specific Activity of a Fluoroquinolone against Two Closely Related Pasteurellaceae with Similar MICs: Differential In Vitro Inoculum Effects and In Vivo Efficacies.

    PubMed

    Lhermie, Guillaume; El Garch, Farid; Toutain, Pierre-Louis; Ferran, Aude A; Bousquet-Mélou, Alain

    2015-01-01

    We investigated the antimicrobial activity of a fluoroquinolone against two genetically close bacterial species belonging to the Pasteurellaceae family. Time-kill experiments were used to measure the in vitro activity of marbofloxacin against two strains of Mannheimia haemolytica and Pasteurella multocida with similar MICs. We observed that marbofloxacin was equally potent against 105 CFU/mL inocula M. haemolytica and P. multocida. However, an inoculum effect was observed with P. multocida, meaning that marbofloxacin activity was decreased against a 108 CFU/mL inoculum, whereas no inoculum effect was observed with M. haemolytica. Marbofloxacin activity was also tested in a lung infection model with immunocompromised mice intratracheally infected with 109 CFU of each bacteria. At the same dose, the clinical and bacteriological outcomes were much better for mice infected with M. haemolytica than for those infected with P. multocida. Moreover, bacteriological eradication was obtained with a lower marbofloxacin dose for mice infected with M. haemolytica. Our results suggest that the differential in vivo marbofloxacin efficacy observed with the two bacterial species of similar MIC could be explained by a differential inoculum effect. Consequently, MICs determined on 105 CFU inocula were not predictive of the differences in antibiotic efficacies against high bacterial inocula of closely related bacterial strains. These results could stimulate further investigations on bacterial species-specific antibiotic doses in a clinical setting. PMID:26506096

  14. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    PubMed

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-01-01

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species. PMID:26662418

  15. Species-specific responses of late Miocene Discoaster spp. to enhanced biosilica productivity conditions in the equatorial Pacific and the Mediterranean

    NASA Astrophysics Data System (ADS)

    Backman, Jan; Raffi, Isabella; Ciummelli, Marina; Baldauf, Jack

    2013-08-01

    Census data of a major Cenozoic calcareous nannofossil genus ( Discoaster) have been acquired from Site U1338, located near the Equator in the eastern Pacific Ocean and drilled in 2009 during Integrated Ocean Drilling Program (IODP) Expedition 321. The investigated 147.53 m thick upper Miocene sediment sequence is primarily composed of biogenic carbonate and biogenic silica. Diatom biostratigraphic data were used to develop a revised biomagnetostratigraphic age model, resulting in more variable late Miocene sedimentation rates. Carbonate content variations mainly reflect dilution by biogenic silica production, although intense carbonate dissolution affects a few shorter intervals. Abundance variations of discoasters show no distinct correlation with either carbonate or biosilica contents. The two dominant Discoaster taxa are D. brouweri and D. variabilis, except for a 12 m thick interval where D. bellus outnumbers the sum of all other discoasters by a factor of 4.6. Data presented indicate that first D. hamatus and then D. berggrenii both evolved from D. bellus. Three unusual morphotypes, here referred to as Discoaster A, B and C, increase in relative abundance during episodes of enhanced biosilica production in the upper half of the investigated sequence (Messinian). Strikingly similar morphotypes have been observed previously in Messinian age sediments from the Mediterranean, characterized by alternating deposition of biogenic carbonate and biosilica. This suggests a species-specific response among some of the late Miocene discoasters to broader oceanographic and climatic forcing that promoted episodes of enhanced deposition of biogenic silica.

  16. An Intrinsically Disordered Region of the DNA Repair Protein Nbs1 Is a Species-Specific Barrier to Herpes Simplex Virus 1 in Primates.

    PubMed

    Lou, Dianne I; Kim, Eui Tae; Meyerson, Nicholas R; Pancholi, Neha J; Mohni, Kareem N; Enard, David; Petrov, Dmitri A; Weller, Sandra K; Weitzman, Matthew D; Sawyer, Sara L

    2016-08-10

    Humans occasionally transmit herpes simplex virus 1 (HSV-1) to captive primates, who reciprocally harbor alphaherpesviruses poised for zoonotic transmission to humans. To understand the basis for the species-specific restriction of HSV-1 in primates, we simulated what might happen during the cross-species transmission of HSV-1 and found that the DNA repair protein Nbs1 from only some primate species is able to promote HSV-1 infection. The Nbs1 homologs that promote HSV-1 infection also interact with the HSV-1 ICP0 protein. ICP0 interaction mapped to a region of structural disorder in the Nbs1 protein. Chimeras reversing patterns of disorder in Nbs1 reversed titers of HSV-1 produced in the cell. By extending this analysis to 1,237 virus-interacting mammalian proteins, we show that proteins that interact with viruses are highly enriched in disorder, suggesting that viruses commonly interact with host proteins through intrinsically disordered domains. PMID:27512903

  17. Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges.

    PubMed

    Massatti, Rob; Knowles, L Lacey

    2016-08-01

    Deterministic processes may uniquely affect codistributed species' phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet-adapted species. However, in the dry-adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species-specific responses to climate change. PMID:27317885

  18. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.

    PubMed

    Bolaños, Luis M; Rosenblueth, Mónica; Castillo-Ramírez, Santiago; Figuier-Huttin, Gilles; Martínez-Romero, Esperanza

    2016-05-01

    Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species. PMID:26058415

  19. Molecular barcoding of venomous snakes and species-specific multiplex PCR assay to identify snake groups for which antivenom is available in Thailand.

    PubMed

    Supikamolseni, A; Ngaoburanawit, N; Sumontha, M; Chanhome, L; Suntrarachun, S; Peyachoknagul, S; Srikulnath, K

    2015-01-01

    DNA barcodes of mitochondrial COI and Cytb genes were constructed from 54 specimens of 16 species for species identification. Intra- and interspecific sequence divergence of the COI gene (10 times) was greater than that of the Cytb gene (4 times), which suggests that the former gene may be a better marker than the latter for species delimitation in snakes. The COI barcode cut-off scores differed by more than 3% between most species, and the minimum interspecific divergence was greater than the maximum intraspecific divergence. Clustering analysis indicated that most species fell into monophyletic clades. These results suggest that these species could be reliably differentiated using COI DNA barcodes. Moreover, a novel species-specific multiplex PCR assay was developed to distinguish between Naja spp, Ophiophagus hannah, Trimeresurus spp, Hydrophiinae, Daboia siamensis, Bungarus fasciatus, and Calloselasma rhodostoma. Antivenom for these species is produced and kept by the Thai Red Cross for clinical use. Our novel PCR assay could easily be applied to venom and saliva samples and could be used effectively for the rapid and accurate identification of species during forensic work, conservation study, and medical research. PMID:26535713

  20. Molecular analysis of biofilms on the surface of neonatal endotracheal tubes based on 16S rRNA PCR-DGGE and species-specific PCR.

    PubMed

    Li, Hongdong; Song, Chao; Liu, Dong; Ai, Qing; Yu, Jialin

    2015-01-01

    Ventilator-associated pneumonia (VAP) results in considerable morbidity and mortality in neonatal intensive care units. VAP is associated with polymicrobial biofilms that form on endotracheal tubes (ETTs). We aimed to evaluate the diversity and the bacterial community in biofilms on ETTs extubated from mechanically ventilated newborns. ETTs (N = 29) and aerobic sputum cultures were obtained from 20 mechanically ventilated newborns. Denaturing gradient gel electrophoresis (DGGE) was used to characterize the bacterial species in the biofilms on the ETTs. Species-specific PCR was used to detect common oropharyngeal Streptococcus species and known ETT-associated pathogens. DGGE profiling of ETT biofilms showed multiple banding patterns indicating a diverse bacterial community. The dominant bacterial species were Klebsiella spp. (29/29), Streptococcus spp. (27/29), and Pseudomonas spp. (24/29). The most frequently occurring Streptococcus species was Streptococcus mitis (N = 18). Oropharyngeal bacteria were present in 25 of 29 ETT specimens. Streptococcus spp. often co-existed with K. pneumoniae and/or P. aeruginosa. In contrast, only one bacterial species was isolated from each sputum culture, K. pneumoniae or Acinetobacter baumannii. Our results demonstrated that Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the most frequent microbes on the surface of neonatal ETTs. The co-existence of oral commensals and pathogenic bacteria on the same tubes may play a crucial role for biofilm formation. PMID:26379907

  1. COI barcode based species-specific primers for identification of five species of stored-product pests from genus Cryptolestes (Coleoptera: Laemophloeidae).

    PubMed

    Varadínová, Z; Wang, Y J; Kučerová, Z; Stejskal, V; Opit, G; Cao, Y; Li, F J; Li, Z H

    2015-04-01

    Flat grain beetles of the genus Cryptolestes (Coleoptera: Laemophloeidae) are one of the economically most important stored-product pests which feed on many kinds of agricultural products, especially grains. Nine of more than 40 described Cryptolestes species are recognized as stored-product pests and two of the pest species have a cosmopolitan distribution. Given the rapid growth in global trade of food products, ecological barriers to the spread of pests are easily overcome. Therefore, development of reliable systems for routine quarantine inspection and early infestation detection is vital. In the present study, we established a new rapid and accurate cytochrome c oxidase subunit I-based system for molecular identification of five common stored-product Cryptolestes species, namely, Cryptolestes capensis, Cryptolestes ferrugineus, Cryptolestes pusilloides, Cryptolestes pusillus and Cryptolestes turcicus. Five species-specific primer pairs for traditional uniplex polymerase chain reaction assay are described and their specificity and sensitivity for the identification process is evaluated using larval samples of 12 different populations from three continents (Asia, Europe and North America). PMID:25609404

  2. Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet.

    PubMed

    Gao, D; Schmidt, T; Jung, C

    2000-12-01

    Repetitive DNA sequences have been isolated from a Sau3AI plasmid library of tetraploid Beta corolliflora (2n = 4x = 36), a wild relative of sugar beet (B. vulgaris). The library was screened by differential hybridization with genomic DNA of B. corolliflora and B. vulgaris. When used as probes for Southern hybridization of genomic DNA, six clones were determined to represent highly repetitive DNA families present only in the B. corolliflora genome. Five other sequences were highly repetitive in B. corolliflora and low or single copy in B. vulgaris. The insert size varied between 43 bp and 448 bp. Two sequences pBC1279 and pBC1944 displayed strong homology to a previously cloned satellite DNA from B. nana. With one exception, sequences are tandemly arranged as revealed by a typical ladder pattern after genomic Southern hybridization. The chromosomal distribution of five probes was determined by fluorescence in situ hybridization (FISH) of mitotic metaphases from B. corolliflora and a triploid hybrid between B. vulgaris and B. corolliflora. Three sequences were spread along all chromosome arms of B. corolliflora while one sequence was present on only six chromosomes. The chromosome-specific sequence pBC216 was found in close vicinity to the 5S rDNA located on B. corolliflora chromosome IV. This set of species-specific sequences has the potential to be used as probes for the identification of monosomic alien addition lines and for marker-assisted gene transfer from wild beet to cultivated beet. PMID:11195340

  3. Species-specific relative AHR1 binding affinities of 2,3,4,7,8-pentachlorodibenzofuran explain avian species differences in its relative potency.

    PubMed

    Farmahin, Reza; Jones, Stephanie P; Crump, Doug; Hahn, Mark E; Giesy, John P; Zwiernik, Matthew J; Bursian, Steven J; Kennedy, Sean W

    2014-04-01

    Results of recent studies showed that 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are equipotent in domestic chicken (Gallus gallus domesticus) while PeCDF is more potent than TCDD in ring-necked pheasant (Phasianus colchicus) and Japanese quail (Coturnix japonica). To elucidate the mechanism(s) underlying these differences in relative potency of PeCDF among avian species, we tested the hypothesis that this is due to species-specific differential binding affinity of PeCDF to the aryl hydrocarbon receptor 1 (AHR1). Here, we modified a cell-based binding assay that allowed us to measure the binding affinity of dioxin-like compounds (DLCs) to avian AHR1 expressed in COS-7 (fibroblast-like cells). The results of the binding assay show that PeCDF and TCDD bind with equal affinity to chicken AHR1, but PeCDF binds with greater affinity than TCDD to pheasant (3-fold) and Japanese quail (5-fold) AHR1. The current report introduces a COS-7 whole-cell binding assay and provides a mechanistic explanation for differential relative potencies of PeCDF among species of birds. PMID:24434118

  4. The vectorial competence of Phlebotomus sergenti is specific for Leishmania tropica and is controlled by species-specific, lipophosphoglycan-mediated midgut attachment.

    PubMed

    Kamhawi, S; Modi, G B; Pimenta, P F; Rowton, E; Sacks, D L

    2000-07-01

    The vectorial competence of Phlebotomus sergenti for 3 Old World species of Leishmania, L. tropica, L. major and L. donovani, was investigated in vivo and by in vitro midgut binding assays using living promastigotes and purified lipophosphoglycan (LPG). P. sergenti consistently showed a high specificity for L. tropica strains, which were able to develop mature, potentially transmissible infections. The loss of infection with L. major and L. donovani correlated with the excretion of the digested bloodmeal. These strains were able to produce sustained infections in the midguts of their appropriate vectors, P. papatasi and P. argentipes, respectively. In in vitro binding assays, a significantly higher number of L. tropica procyclic promastigotes attached to the midgut lining of P. sergenti, compared to those of L. major and L. donovani (P < 0.05). The prediction that the species specificity of midgut attachment is controlled by polymorphic structures on the parasite LPG was supported by the finding that P. sergenti midguts were intensely stained following incubation with purified phosphoglycan (PG) from L. tropica compared with PGs from L. major or L. donovani. The results provide further evidence that LPG structural polymorphisms are driven by the species diversity of molecules present on the sandfly midgut that function as parasite attachment sites. PMID:11085222

  5. Species-specific expansion and molecular evolution of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene family in plants.

    PubMed

    Li, Wei; Liu, Wei; Wei, Hengling; He, Qiuling; Chen, Jinhong; Zhang, Baohong; Zhu, Shuijin

    2014-01-01

    The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in Zea mays, Gossypium raimondii, Populus trichocarpa and Glycine max after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom. PMID:24722776

  6. Lamin in inflammation and aging.

    PubMed

    Tran, Joseph R; Chen, Haiyang; Zheng, Xiaobin; Zheng, Yixian

    2016-06-01

    Aging is characterized by a progressive loss of tissue function and an increased susceptibility to injury and disease. Many age-associated pathologies manifest an inflammatory component, and this has led to the speculation that aging is at least in part caused by some form of inflammation. However, whether or not inflammation is truly a cause of aging, or is a consequence of the aging process is unknown. Recent work using Drosophila has uncovered a mechanism where the progressive loss of lamin-B in the fat body upon aging triggers systemic inflammation. This inflammatory response perturbs the local immune response of the neighboring gut tissue and leads to hyperplasia. Here, we will discuss the literature connecting lamins to aging and inflammation. PMID:27023494

  7. Inflammation in diabetic kidney disease

    PubMed Central

    García-García, Patricia M; Getino-Melián, María A; Domínguez-Pimentel, Virginia; Navarro-González, Juan F

    2014-01-01

    Diabetes mellitus entails significant health problems worldwide. The pathogenesis of diabetes is multifactorial, resulting from interactions of both genetic and environmental factors that trigger a complex network of pathophysiological events, with metabolic and hemodynamic alterations. In this context, inflammation has emerged as a key pathophysiology mechanism. New pathogenic pathways will provide targets for prevention or future treatments. This review will focus on the implications of inflammation in diabetes mellitus, with special attention to inflammatory cytokines. PMID:25126391

  8. [Antifungal susceptibility profiles of Candida species to triazole: application of new CLSI species-specific clinical breakpoints and epidemiological cutoff values for characterization of antifungal resistance].

    PubMed

    Karabıçak, Nilgün; Alem, Nihal

    2016-01-01

    The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antifungal Susceptibility Testing has newly introduced species-specific clinical breakpoints (CBPs) for fluconazole and voriconazole. When CBPs can not be determined, wild-type minimal inhibitory concentration (MIC) distributions are detected and epidemiological cutoff values (ECVs) provide valuable means for the detection of emerging resistance. The aim of this study is to determine triazole resistance patterns in Candida species by the recently revised CLSI CBPs. A total of 140 Candida strains isolated from blood cultures of patients with invasive candidiasis hospitalized in various intensive care units in Turkey and sent to our reference laboratory between 2011-2012, were included in the study. The isolates were identified by conventional methods, and susceptibility testing was performed against fluconazole, itraconazole and voriconazole, by the 24-h CLSI broth microdilution (BMD) method. Azole resistance rates for all Candida species were determined using the new species-specific CLSI CBPs and ECVs criteria, when appropriate. The species distribution of the isolates were as follows; C.parapsilosis (n= 31 ), C.tropicalis (n= 26 ), C.glabrata (n= 21), C.albicans (n= 18), C.lusitaniae (n= 16), C.krusei (n= 16), C.kefyr (n= 9), C.guilliermondii (n= 2), and C.dubliniensis (n= 1). According to the newly determined CLSI CBPs for fluconazole and C.albicans, C.parapsilosis, C.tropicalis [susceptible (S), ≤ 2 µg/ml; dose-dependent susceptible (SDD), 4 µg/ml; resistant (R), ≥ 8 µg/ml], and C.glabrata (SDD, ≤ 32 µg/ml; R≥ 64 µg/ml) and for voriconazole and C.albicans, C.parapsilosis, C.tropicalis (S, ≤ 0.12 µg/ml; SDD, 0.25-0.5 µg/ml; R, ≥ 1 µg/ml), and C.krusei (S, ≤ 0.5 µg/ml; SDD, 1 µg/ml; R, ≥ 2 µg/ml), it was found that three of C.albicans, one of C.parapsilosis and one of C.glabrata isolates were resistant to fluconazole, while two of C.albicans and two of C

  9. Is splash erosion potential species specific? Measuring of splash erosion potential under forest in different succession stages along a biodiversity gradient in the humid subtropics

    NASA Astrophysics Data System (ADS)

    Geißler, C.; Kühn, P.; Scholten, T.

    2009-04-01

    It is widely accepted that (forest) vegetation is a key control for the type and intensity of soil erosion. The current paradigm is that natural or quasi-natural vegetation protects the soil from erosion and that agricultural vegetation or land use generally enhances erosion. The latter was in focus of most research during the last decades and less interest was paid on natural systems, which are more difficult to study. Nevertheless, afforestation is widely used as a measure of soil protection against soil erosion. Rainfall can be highly erosive particularly in the humid subtropics. Regarding climate change, also precipitation regime may change in direction to even more severe storms and higher rainfall intensities; it is a research field of growing importance. Key mechanisms of a vegetation cover in reducing or enhancing erosion are modifications of drop-size distribution, retention of raindrop impact on the soil and changes in amount and spatial distribution of rainfall at the ground surface. Controlling determinants are rainfall intensity, drop size distribution, drop fall velocity, height of the canopy as well as density of the canopy, crown and leaf traits, LAI and coverage by a litter layer. Large drops are supposed to be significant sources of splash detachment in forests (Brandt 1989; Vis 1986). However, the mechanisms of reducing (or enhancing?) splash detachment under forest in relation to species richness and species composition are not well understood. Some studies indicate that raindrop impact is species specific (Calder 2001; Nanko et al. 2006) and some neglect the effects of species specific impacts (Foot & Morgan 2005). Our research uses different methods of rainfall characterization (splash cups, tipping-bucket rain gauge, laser distrometer) to reveal the described mechanisms from the canopy through different vegetation layers to the ground. First results of splash cup measurements (revised after Ellison 1947) show that sand loss under vegetation

  10. Oxidative-stress: comparison of species specific and tissue specific effects in the marine bivalves Mytilus edulis (L.) and Dosinia lupinus (L.).

    PubMed

    Walker, S T; Mantle, D; Bythell, J C; Thomason, J C

    2000-11-01

    This study describes a novel approach to the objective of identifying a suitable biomarker of oxidative-stress in marine animals and evaluates an established assay under controlled experimental conditions in vivo and in vitro. Live animals and tissue homogenates of the euryoxic blue mussel Mytilus edulis (L.), and the stenoxic smooth artemis Dosinia lupinus (L.), were exposed to oxidative-stress generated using a 60Co gamma-radiation source. In live organisms, mortality-rates were significantly different between species. M. edulis showed zero mortality and D. lupinus 30% mortality over 18 h. Protein-carbonyl (PC=O) content was determined by colourimetric assay (total protein-carbonyl) or immunodetection (for individual proteins) in four tissue types: digestive gland, mantle, adductor muscle and foot. In tissue homogenates, digestive gland and adductor muscle of both species showed significant increases (greater for D. lupinus) in PC=O content following irradiation in vitro. All tissues from live animals (with the exception of M. edulis mantle and adductor muscle of D. lupinus which died under irradiation) showed significantly different levels of PC Os following irradiation; D. lupinus PC=O levels were increased whilst in M. edulis PC=O content decreased. In D. lupinus which died during irradiation, PC=O content was greater than in those D. lupinus which survived, particularly in the adductor muscle, the former were inceased by 74% above controls. The findings support the hypothesis that species-specific adaptations to euryoxic and stenoxic environments, and metabolic requirements of different tissues, should result in differing ROS defences. PMID:11126765

  11. In-Depth N-Glycosylation Reveals Species-Specific Modifications and Functions of the Royal Jelly Protein from Western (Apis mellifera) and Eastern Honeybees (Apis cerana).

    PubMed

    Feng, Mao; Fang, Yu; Han, Bin; Xu, Xiang; Fan, Pei; Hao, Yue; Qi, Yuping; Hu, Han; Huo, Xinmei; Meng, Lifeng; Wu, Bin; Li, Jianke

    2015-12-01

    Royal jelly (RJ), secreted by honeybee workers, plays diverse roles as nutrients and defense agents for honeybee biology and human health. Despite being reported to be glycoproteins, the glycosylation characterization and functionality of RJ proteins in different honeybee species are largely unknown. An in-depth N-glycoproteome analysis and functional assay of RJ produced by Apis mellifera lingustica (Aml) and Apis cerana cerana (Acc) were conducted. RJ produced by Aml yielded 80 nonredundant N-glycoproteins carrying 190 glycosites, of which 23 novel proteins harboring 35 glycosites were identified. For Acc, all 43 proteins glycosylated at 138 glycosites were reported for the first time. Proteins with distinct N-glycoproteomic characteristics in terms of glycoprotein species, number of N-glycosylated sites, glycosylation motif, abundance level of glycoproteins, and N-glycosites were observed in this two RJ samples. The fact that the low inhibitory efficiency of N-glycosylated major royal jelly protein 2 (MRJP2) against Paenibacillus larvae (P. larvae) and the absence of antibacterial related glycosylated apidaecin, hymenoptaecin, and peritrophic matrix in the Aml RJ compared to Acc reveal the mechanism for why the Aml larvae are susceptible to P. larvae, the causative agent of a fatal brood disease (American foulbrood, AFB). The observed antihypertension activity of N-glycosylated MRJP1 in two RJ samples and a stronger activity found in Acc than in Aml reveal that specific RJ protein and modification are potentially useful for the treatment of hypertensive disease for humans. Our data gain novel understanding that the western and eastern bees have evolved species-specific strategies of glycosylation to fine-tune protein activity for optimizing molecular function as nutrients and immune agents for the good of honeybee and influence on the health promoting activity for human as well. This serves as a valuable resource for the targeted probing of the biological

  12. Species-specific diagnostics of Apis mellifera trypanosomatids: A nine-year survey (2007-2015) for trypanosomatids and microsporidians in Serbian honey bees.

    PubMed

    Stevanovic, Jevrosima; Schwarz, Ryan S; Vejnovic, Branislav; Evans, Jay D; Irwin, Rebecca E; Glavinic, Uros; Stanimirovic, Zoran

    2016-09-01

    In this study, honey bees collected in Serbia over 9 consecutive years (2007-2015) were retrospectively surveyed to determine the prevalence of eukaryotic gut parasites by molecular screening of archival DNA samples. We developed species-specific primers for PCR to detect the two known honey bee trypanosomatid species, Crithidia mellificae and the recently described Lotmaria passim. These primers were validated for target specificity under single and mixed-species conditions as well as against the bumblebee trypanosomatid Crithidia bombi. Infections by Nosema apis and Nosema ceranae (Microsporidia) were also determined using PCR. Samples from 162 colonies (18 from each year) originating from 57 different localities were surveyed. L. passim was detected in every year with an overall frequency of 62.3% and annual frequencies ranging from 38.9% to 83.3%. This provides the earliest confirmed record to date for L. passim and the first report of this species in Serbia. N. ceranae was ubiquitous, occurring in every year and at 95.7% overall frequency, ranging annually from 83.3% to 100%. The majority of colonies (60.5%) were co-infected with L. passim and N. ceranae, but colony infections by each species were statistically independent of one another over the nine years. Although C. mellificae and N. apis have both been reported recently at low frequency in Europe, neither of these species was detected in Serbia. These results support the hypothesis that L. passim has predominated over C. mellificae in A. mellifera during the past decade. PMID:27392956

  13. A spontaneous genomic deletion in Listeria ivanovii identifies LIPI-2, a species-specific pathogenicity island encoding sphingomyelinase and numerous internalins.

    PubMed

    Domínguez-Bernal, Gustavo; Müller-Altrock, Stefanie; González-Zorn, Bruno; Scortti, Mariela; Herrmann, Petra; Monzó, Héctor J; Lacharme, Lizeth; Kreft, Jürgen; Vázquez-Boland, José A

    2006-01-01

    Listeria ivanovii differs from the human pathogen Listeria monocytogenes in that it specifically affects ruminants, causing septicaemia and abortion but not meningo-encephalitis. The genetic characterization of spontaneous L. ivanovii mutants lacking the virulence factor SmcL (sphingomyelinase) led us to identify LIPI-2, the first species-specific pathogenicity island from Listeria. Besides SmcL, this 22 kb chromosomal locus encodes 10 internalin (Inl) proteins: i-InlB1 and -B2 are large/surface-associated Inls similar to L. monocytogenes InlB; i-InlE to -L are small/excreted (SE)-Inls, i-InlG being a tandem fusion of two SE-Inls. Except i-inlB1, all LIPI-2 inl genes are controlled by the virulence regulator, PrfA. LIPI-2 is inserted into a tRNA locus and is unstable - half of it deleting at approximately 10(-4) frequency with a portion of contiguous DNA. The spontaneous mutants were attenuated in vivo in mice and lambs and showed impaired intracellular growth and apoptosis induction in bovine MDBK cells. Targeted knock-out mutations associated the virulence defect with LIPI-2 genes. The region between the core genome loci ysnB-tRNA(arg) and ydeI flanking LIPI-2 contained different gene complements in the different Listeria spp. and even serovars of L. monocytogenes, including remnants of the PSA bacteriophage int gene in serovar 4b, indicating it is a hot spot for horizontal genome diversification. LIPI-2 is conserved in L. ivanovii ssp. ivanovii and londoniensis, suggesting an early acquisition during the species' evolution. LIPI-2 is likely to play an important role in the pathogenic and host tropism of L. ivanovii. PMID:16390439

  14. Assessment of total and organic vanadium levels and their bioaccumulation in edible sea cucumbers: tissues distribution, inter-species-specific, locational differences and seasonal variations.

    PubMed

    Liu, Yanjun; Zhou, Qingxin; Xu, Jie; Xue, Yong; Liu, Xiaofang; Wang, Jingfeng; Xue, Changhu

    2016-02-01

    The objective of this study is to investigate the levels, inter-species-specific, locational differences and seasonal variations of vanadium in sea cucumbers and to validate further several potential factors controlling the distribution of metals in sea cucumbers. Vanadium levels were evaluated in samples of edible sea cucumbers and were demonstrated exhibit differences in different seasons, species and sampling sites. High vanadium concentrations were measured in the sea cucumbers, and all of the vanadium detected was in an organic form. Mean vanadium concentrations were considerably higher in the blood (sea cucumber) than in the other studied tissues. The highest concentration of vanadium (2.56 μg g(-1)), as well as a higher degree of organic vanadium (85.5 %), was observed in the Holothuria scabra samples compared with all other samples. Vanadium levels in Apostichopus japonicus from Bohai Bay and Yellow Sea have marked seasonal variations. Average values of 1.09 μg g(-1) of total vanadium and 0.79 μg g(-1) of organic vanadium were obtained in various species of sea cucumbers. Significant positive correlations between vanadium in the seawater and V org in the sea cucumber (r = 81.67 %, p = 0.00), as well as between vanadium in the sediment and V org in the sea cucumber (r = 77.98 %, p = 0.00), were observed. Vanadium concentrations depend on the seasons (salinity, temperature), species, sampling sites and seawater environment (seawater, sediment). Given the adverse toxicological effects of inorganic vanadium and positive roles in controlling the development of diabetes in humans, a regular monitoring programme of vanadium content in edible sea cucumbers can be recommended. PMID:25732906

  15. Vasculature analysis of patient derived tumor xenografts using species-specific PCR assays: evidence of tumor endothelial cells and atypical VEGFA-VEGFR1/2 signalings

    PubMed Central

    2014-01-01

    Background Tumor endothelial transdifferentiation and VEGFR1/2 expression by cancer cells have been reported in glioblastoma but remain poorly documented for many other cancer types. Methods To characterize vasculature of patient-derived tumor xenografts (PDXs), largely used in preclinical anti-angiogenic assays, we designed here species-specific real-time quantitative RT-PCR assays. Human and mouse PECAM1/CD31, ENG/CD105, FLT1/VEGFR1, KDR/VEGFR2 and VEGFA transcripts were analyzed in a large series of 150 PDXs established from 8 different tumor types (53 colorectal, 14 ovarian, 39 breast and 15 renal cell cancers, 6 small cell and 5 non small cell lung carcinomas, 13 cutaneous melanomas and 5 glioblastomas) and in two bevacizumab-treated non small cell lung carcinomas xenografts. Results As expected, mouse cell proportion in PDXs -evaluated by quantifying expression of the housekeeping gene TBP- correlated with all mouse endothelial markers and human VEGFA RNA levels. More interestingly, we observed human PECAM1/CD31 and ENG/CD105 expression in all tumor types, with higher rate in glioblastoma and renal cancer xenografts. Human VEGFR expression profile varied widely depending on tumor types with particularly high levels of human FLT1/VEGFR1 transcripts in colon cancers and non small cell lung carcinomas, and upper levels of human KDR/VEGFR2 transcripts in non small cell lung carcinomas. Bevacizumab treatment induced significant low expression of mouse Pecam1/Cd31, Eng/Cd105, Flt1/Vegfr1 and Kdr/Vefr2 while the human PECAM1/CD31 and VEGFA were upregulated. Conclusions Taken together, our results strongly suggest existence of human tumor endothelial cells in all tumor types tested and of both stromal and tumoral autocrine VEGFA-VEGFR1/2 signalings. These findings should be considered when evaluating molecular mechanisms of preclinical response and resistance to tumor anti-angiogenic strategies. PMID:24625025

  16. Molecular Characterization and Chromosomal Distribution of a Species-Specific Transcribed Centromeric Satellite Repeat from the Olive Fruit Fly, Bactrocera oleae

    PubMed Central

    Tsoumani, Konstantina T.; Drosopoulou, Elena; Mavragani-Tsipidou, Penelope; Mathiopoulos, Kostas D.

    2013-01-01

    Satellite repetitive sequences that accumulate in the heterochromatin consist a large fraction of a genome and due to their properties are suggested to be implicated in centromere function. Current knowledge of heterochromatic regions of Bactrocera oleae genome, the major pest of the olive tree, is practically nonexistent. In our effort to explore the repetitive DNA portion of B. oleae genome, a novel satellite sequence designated BoR300 was isolated and cloned. The present study describes the genomic organization, abundance and chromosomal distribution of BoR300 which is organized in tandem, forming arrays of 298 bp-long monomers. Sequence analysis showed an AT content of 60.4%, a CENP-B like-motif and a high curvature value based on predictive models. Comparative analysis among randomly selected monomers demonstrated a high degree of sequence homogeneity (88% – 97%) of BoR300 repeats, which are present at approximately 3,000 copies per haploid genome accounting for about 0.28% of the total genomic DNA, based on two independent qPCR approaches. In addition, expression of the repeat was also confirmed through RT-PCR, by which BoR300 transcripts were detected in both sexes. Fluorescence in situ hybridization (FISH) of BoR300 on mitotic metaphases and polytene chromosomes revealed signals to the centromeres of two out of the six chromosomes which indicated a chromosome-specific centromeric localization. Moreover, BoR300 is not conserved in the closely related Bactrocera species tested and it is also absent in other dipterans, but it’s rather restricted to the B. oleae genome. This feature of species-specificity attributed to BoR300 satellite makes it a good candidate as an identification probe of the insect among its relatives at early development stages. PMID:24244494

  17. Structure of the Adenovirus Type 4 (Species E) E3-19K/HLA-A2 Complex Reveals Species-Specific Features in MHC Class I Recognition.

    PubMed

    Li, Lenong; Santarsiero, Bernard D; Bouvier, Marlene

    2016-08-15

    Adenoviruses (Ads) subvert MHC class I Ag presentation and impair host anti-Ad cellular activities. Specifically, the Ad-encoded E3-19K immunomodulatory protein targets MHC class I molecules for retention within the endoplasmic reticulum of infected cells. We report the x-ray crystal structure of the Ad type 4 (Ad4) E3-19K of species E bound to HLA-A2 at 2.64-Å resolution. Structural analysis shows that Ad4 E3-19K adopts a tertiary fold that is shared only with Ad2 E3-19K of species C. A comparative analysis of the Ad4 E3-19K/HLA-A2 structure with our x-ray structure of Ad2 E3-19K/HLA-A2 identifies species-specific features in HLA-A2 recognition. Our analysis also reveals common binding characteristics that explain the promiscuous, and yet high-affinity, association of E3-19K proteins with HLA-A and HLA-B molecules. We also provide structural insights into why E3-19K proteins do not associate with HLA-C molecules. Overall, our study provides new information about how E3-19K proteins selectively engage with MHC class I to abrogate Ag presentation and counteract activation of CD8(+) T cells. The significance of MHC class I Ag presentation for controlling viral infections, as well as the threats of viral infections in immunocompromised patients, underline our efforts to characterize viral immunoevasins, such as E3-19K. PMID:27385781

  18. Ah-receptor controlled luciferase expression: A novel species-specific bioassay for Ah-receptor active compounds in environmental matrices

    SciTech Connect

    Murk, A.J.; Aarts, J.M.M.J.G.; Koeman, J.H.; Brouwer, A.; Denison, M.S.

    1995-12-31

    Polyhalogenated aromatic hydrocarbons (PHAHs) such as polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and biphenyls (PCBs) are persistent lipophilic compounds that accumulate especially in sediments and in top predators of the aquatic foodchain. PHAHs elicit a number of common toxic responses, which are highly species-specific. The most toxic, planar, PHAHs share a common mechanism of action mediated by the aryl hydrocarbon receptor (AhR). Based on this mechanism, the toxic equivalency factor (TEF) concept has been developed, allowing hazard and risk assessment for mixtures of PHAHs. The TEF-approach assumes additive responses, but also synergistic and antagonistic interactions have been observed. In addition, the often large number of compounds in a mixture, low levels of individual congeners, possible presence of unknown AhR-active substances, and species differences in inducibility, ask for an comprehensive approach in hazard assessment. A number of recombinant cell lines, including Hepa1c1c7 mouse and H411E rat hepatoma cell lines, were developed, showing AhR-mediated firefly (Photinuspyralis) luciferase gene expression. The response by 2,3,7,8-TCDD in the CALUX (chemical activated luciferase expression) assay with these cell lines is dose-dependent, and not subjected to substrate inhibition at higher ligand concentrations. The detection limit for 2,3,7,8-TCDD is below 1 pM (0.2 fmol). The luciferase assay has been successfully applied for monitoring the amount of AhR-active compounds in small aliquots of blood plasma and in both sediment and pore-water samples, of which examples will be presented.

  19. Seasonal Variation in Shell Calcification of Planktonic Foraminifera in the NE Atlantic Reveals Species-Specific Response to Temperature, Productivity, and Optimum Growth Conditions.

    PubMed

    Weinkauf, Manuel F G; Kunze, José G; Waniek, Joanna J; Kučera, Michal

    2016-01-01

    Using shells collected from a sediment trap series in the Madeira Basin, we investigate the effects of seasonal variation of temperature, productivity, and optimum growth conditions on calcification in three species of planktonic Foraminifera. The series covers an entire seasonal cycle and reflects conditions at the edge of the distribution of the studied species, manifesting more suitable growth conditions during different parts of the year. The seasonal variation in seawater carbonate saturation at the studied site is negligible compared to other oceanic regions, allowing us to assess the effect of parameters other than carbonate saturation. Shell calcification is quantified using weight and size of individual shells. The size-weight scaling within each species is robust against changes in environmental parameters, but differs among species. An analysis of the variation in calcification intensity (size-normalized weight) reveals species-specific response patterns. In Globigerinoides ruber (white) and Globigerinoides elongatus, calcification intensity is correlated with temperature (positive) and productivity (negative), whilst in Globigerina bulloides no environmental forcing is observed. The size-weight scaling, calcification intensity, and response of calcification intensity to environmental change differed between G. ruber (white) and G. elongatus, implying that patterns extracted from pooled analyses of these species may reflect their changing proportions in the samples. Using shell flux as a measure of optimum growth conditions, we observe significant positive correlation with calcification intensity in G. elongatus, but negative correlation in G. bulloides. The lack of a consistent response of calcification intensity to optimum growth conditions is mirrored by the results of shell size analyses. We conclude that calcification intensity in planktonic Foraminifera is affected by factors other than carbonate saturation. These factors include temperature

  20. Condensed matter astrophysics: A prescription for determining the species-specific composition and quantity of interstellar dust using x-rays

    SciTech Connect

    Lee, Julia C.; Xiang, Jingen; Ravel, Bruce; Kortright, Jeffrey B; Flanagan, Kathryn

    2009-01-05

    We present a newtechnique for determining the quantity and composition of dust in astrophysical environments using<6 keV X-rays.We argue that high-resolution X-ray spectra as enabled by the Chandra and XMM-Newton gratings should be considered a powerful and viable new resource for delving into a relatively unexplored regime for directlydetermining dust properties: composition, quantity, and distribution.We present initial cross section measurements of astrophysically likely iron-based dust candidates taken at the Lawrence Berkeley National Laboratory Advanced Light Source synchrotron beamline, as an illustrative tool for the formulation of our technique for determining the quantity and composition of interstellar dust with X-rays. (Cross sections for the materials presented here will be made available for astrophysical modeling in the near future.) Focused at the 700 eV Fe LIII and LII photoelectric edges, we discuss a technique for modeling dust properties in the soft X-rays using L-edge data to complement K-edge X-ray absorption fine structure analysis techniques discussed by Lee& Ravel. The paper is intended to be a techniques paper of interest and useful to both condensed matter experimentalists andastrophysicists. For the experimentalists, we offer a new prescription for normalizing relatively low signal-to-noise ratio L-edge cross section measurements. For astrophysics interests, we discuss the use of X-ray absorption spectra for determining dust composition in cold and ionized astrophysical environments and a new method for determining species-specific gas and dust ratios. Possible astrophysical applications of interest, including relevance to Sagittarius A*, are offered. Prospects for improving on this work in future X-ray missions with higher throughput and spectral resolution are also presented in the context of spectral resolution goals for gratings and calorimeters, for proposed and planned missions such as Astro-H and the International X

  1. Using digital time-lapse cameras to monitor species-specific understorey and overstorey phenology in support of wildlife habitat assessment.

    PubMed

    Bater, Christopher W; Coops, Nicholas C; Wulder, Michael A; Hilker, Thomas; Nielsen, Scott E; McDermid, Greg; Stenhouse, Gordon B

    2011-09-01

    Critical to habitat management is the understanding of not only the location of animal food resources, but also the timing of their availability. Grizzly bear (Ursus arctos) diets, for example, shift seasonally as different vegetation species enter key phenological phases. In this paper, we describe the use of a network of seven ground-based digital camera systems to monitor understorey and overstorey vegetation within species-specific regions of interest. Established across an elevation gradient in western Alberta, Canada, the cameras collected true-colour (RGB) images daily from 13 April 2009 to 27 October 2009. Fourth-order polynomials were fit to an RGB-derived index, which was then compared to field-based observations of phenological phases. Using linear regression to statistically relate the camera and field data, results indicated that 61% (r (2) = 0.61, df = 1, F = 14.3, p = 0.0043) of the variance observed in the field phenological phase data is captured by the cameras for the start of the growing season and 72% (r (2) = 0.72, df = 1, F = 23.09, p = 0.0009) of the variance in length of growing season. Based on the linear regression models, the mean absolute differences in residuals between predicted and observed start of growing season and length of growing season were 4 and 6 days, respectively. This work extends upon previous research by demonstrating that specific understorey and overstorey species can be targeted for phenological monitoring in a forested environment, using readily available digital camera technology and RGB-based vegetation indices. PMID:21082343

  2. Seasonal Variation in Shell Calcification of Planktonic Foraminifera in the NE Atlantic Reveals Species-Specific Response to Temperature, Productivity, and Optimum Growth Conditions

    PubMed Central

    Weinkauf, Manuel F. G.; Kunze, José G.; Waniek, Joanna J.; Kučera, Michal

    2016-01-01

    Using shells collected from a sediment trap series in the Madeira Basin, we investigate the effects of seasonal variation of temperature, productivity, and optimum growth conditions on calcification in three species of planktonic Foraminifera. The series covers an entire seasonal cycle and reflects conditions at the edge of the distribution of the studied species, manifesting more suitable growth conditions during different parts of the year. The seasonal variation in seawater carbonate saturation at the studied site is negligible compared to other oceanic regions, allowing us to assess the effect of parameters other than carbonate saturation. Shell calcification is quantified using weight and size of individual shells. The size–weight scaling within each species is robust against changes in environmental parameters, but differs among species. An analysis of the variation in calcification intensity (size-normalized weight) reveals species-specific response patterns. In Globigerinoides ruber (white) and Globigerinoides elongatus, calcification intensity is correlated with temperature (positive) and productivity (negative), whilst in Globigerina bulloides no environmental forcing is observed. The size–weight scaling, calcification intensity, and response of calcification intensity to environmental change differed between G. ruber (white) and G. elongatus, implying that patterns extracted from pooled analyses of these species may reflect their changing proportions in the samples. Using shell flux as a measure of optimum growth conditions, we observe significant positive correlation with calcification intensity in G. elongatus, but negative correlation in G. bulloides. The lack of a consistent response of calcification intensity to optimum growth conditions is mirrored by the results of shell size analyses. We conclude that calcification intensity in planktonic Foraminifera is affected by factors other than carbonate saturation. These factors include temperature

  3. A framework for modelling species-specific site quality index based on data generated from remote sensing imagery and a process-based model

    NASA Astrophysics Data System (ADS)

    Hassan, Quazi Khalid

    This Thesis presents a framework for modelling species-specific site quality index (SQI) at a spatial resolution of 250 m by integrating biophysical variables of growing degree days (ODD), soil water content (SWC), and incident photosynthetically active radiation (PAR) in descriptions of potential tree growth. Development of ODD maps is based on processing and blending remotely-sensed data acquired with the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor on the Terra satellite and ETM+ sensor on Landsat-7 satellite at spatial resolutions of 250 m and 28.5 m. Descriptions of SWC are based on a temperature-vegetation wetness index (TVWI) that relies on MODIS-based optical and thermal image products. PAR is estimated with an existing solar-radiation distribution model. SQI is defined as a function of species vital attributes and species environmental response to ODD, TVWI, and PAR. The methods are applied to a balsam fir [bF; Abies balsamea (L.) Mill.] dominated region in northwest New Brunswick. Comparisons between SQI and field-based estimates of site index and enhanced vegetation index showed that about 66 and 88% of the values corresponding to a series of Forest Development Survey lines (691 in total) were within 16% of SQI values. On average 92.1% of high bF-content stands (> 50% composition) in the area fell on medium-to-very high SQI values (> 0.50). Based on these agreements, SQI can be perceived as a good predictor of potential tree-species growth in the selection of optimal sites for biomass and wood fibre production

  4. Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata

    PubMed Central

    Vieira, Christophe; Engelen, Aschwin H.; Guentas, Linda; Aires, Tânia; Houlbreque, Fanny; Gaubert, Julie; Serrão, Ester A.; De Clerck, Olivier; Payri, Claude E.

    2016-01-01

    While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing, and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae) species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria, and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from nine families, four classes, and three phyla), some of which are not known as, but are related to pathogens involved in coral diseases, and others are naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of these bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation. PMID:27047453

  5. Species-specific differences in the inhibition of human and zebrafish 11β-hydroxysteroid dehydrogenase 2 by thiram and organotins.

    PubMed

    Meyer, Arne; Strajhar, Petra; Murer, Céline; Da Cunha, Thierry; Odermatt, Alex

    2012-11-15

    Dithiocarbamates and organotins can inhibit enzymes by interacting with functionally essential sulfhydryl groups. Both classes of chemicals were shown to inhibit human 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2), which converts active cortisol into inactive cortisone and has a role in renal and intestinal electrolyte regulation and in the feto-placental barrier to maternal glucocorticoids. In fish, 11β-HSD2 has a dual role by inactivating glucocorticoids and generating the major androgen 11-ketotestosterone. Inhibition of this enzyme may enhance glucocorticoid and diminish androgen effects in fish. Here, we characterized 11β-HSD2 activity of the model species zebrafish. A comparison with human and mouse 11β-HSD2 revealed species-specific substrate preference. Unexpectedly, assessment of the effects of thiram and several organotins on the activity of zebrafish 11β-HSD2 showed weak inhibition by thiram and no inhibition by any of the organotins tested. Sequence comparison revealed the presence of an alanine at position 253 on zebrafish 11β-HSD2, corresponding to cysteine-264 in the substrate-binding pocket of the human enzyme. Substitution of alanine-253 by cysteine resulted in a more than 10-fold increased sensitivity of zebrafish 11β-HSD2 to thiram. Mutating cysteine-264 on human 11β-HSD2 to serine resulted in 100-fold lower inhibitory activity. Our results demonstrate significant species differences in the sensitivity of human and zebrafish 11β-HSD2 to inhibition by thiram and organotins. Site-directed mutagenesis revealed a key role of cysteine-264 in the substrate-binding pocket of human 11β-HSD2 for sensitivity to sulfhydryl modifying agents. PMID:22796344

  6. Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata.

    PubMed

    Vieira, Christophe; Engelen, Aschwin H; Guentas, Linda; Aires, Tânia; Houlbreque, Fanny; Gaubert, Julie; Serrão, Ester A; De Clerck, Olivier; Payri, Claude E

    2016-01-01

    While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing, and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae) species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria, and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from nine families, four classes, and three phyla), some of which are not known as, but are related to pathogens involved in coral diseases, and others are naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of these bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation. PMID:27047453

  7. Loss of memory CD4+ T-cells in semi-wild mandrills (Mandrillus sphinx) naturally infected with species-specific simian immunodeficiency virus SIVmnd-1.

    PubMed

    Greenwood, Edward J D; Schmidt, Fabian; Liégeois, Florian; Kondova, Ivanela; Herbert, Anaïs; Ngoubangoye, Barthelemy; Rouet, François; Heeney, Jonathan L

    2014-01-01

    Simian immunodeficiency virus (SIV) infection is found in a number of African primate species and is thought to be generally non-pathogenic. However, studies of wild primates are limited to two species, with SIV infection appearing to have a considerably different outcome in each. Further examination of SIV-infected primates exposed to their natural environment is therefore warranted. We performed a large cross-sectional study of a cohort of semi-wild mandrills with naturally occurring SIV infection, including 39 SIV-negative and 33 species-specific SIVmnd-1-infected animals. This study was distinguished from previous reports by considerably greater sample size, examination of exclusively naturally infected animals in semi-wild conditions and consideration of simian T-lymphotropic virus (STLV) status in addition to SIVmnd-1 infection. We found that SIVmnd-1 infection was associated with a significant and progressive loss of memory CD4(+) T-cells. Limited but significant increases in markers of immune activation in the T-cell populations, significant increases in plasma neopterin and changes to B-cell subsets were also observed in SIV-infected animals. However, no increase in plasma soluble CD14 was observed. Histological examination of peripheral lymph nodes suggested that SIVmnd-1 infection was not associated with a significant disruption of the lymph node architecture. Whilst this species has evolved numerous strategies to resist the development of AIDS, significant effects of SIV infection could be observed when examined in a natural environment. STLVmnd-1 infection also had significant effects on some markers relevant to understanding SIV infection and thus should be considered in studies of SIV infection of African primates where present. PMID:24214347

  8. Back-trajectory modelling and DNA-based species-specific detection methods allow tracking of fungal spore transport in air masses.

    PubMed

    Grinn-Gofroń, Agnieszka; Sadyś, Magdalena; Kaczmarek, Joanna; Bednarz, Aleksandra; Pawłowska, Sylwia; Jedryczka, Malgorzata

    2016-11-15

    Recent advances in molecular detection of living organisms facilitate the introduction of novel methods to studies of the transport of fungal spores over large distances. Monitoring the migration of airborne fungi using microscope based spore identification is limited when different species produce very similar spores. In our study, DNA-based monitoring with the use of species-specific probes allowed us to track the aerial movements of two important fungal pathogens of oilseed rape (Brassica napus L.), i.e., Leptosphaeria maculans and Leptosphaeria biglobosa, which have identical spore shape and size. The fungi were identified using dual-labelled fluorescent probes that were targeted to a β-tubulin gene fragment of either Leptosphaeria species. Spore identification by Real-Time PCR techniques capable of detecting minute amounts of DNA of selected fungal species was combined with back-trajectory analysis, allowing the tracking of past movements of air masses using the Hybrid Single Particle Lagrangian Integrated Trajectory model. Over a study period spanning the previous decade (2006-2015) we investigated two specific events relating to the long distance transport of Leptosphaeria spp. spores to Szczecin in North-West Poland. Based on the above mentioned methods and the results obtained with the additional spore sampler located in nearby Szczecin, and operating at the ground level in an oilseed rape field, we have demonstrated that on both occasions the L. biglobosa spores originated from the Jutland Peninsula. This is the first successful attempt to combine analysis of back-trajectories of air masses with DNA-based identification of economically important pathogens of oilseed rape in Europe. In our studies, the timing of L. biglobosa ascospore dispersal in the air was unlikely to result in the infection of winter oilseed rape grown as a crop plant. However, the fungus could infect other host plants, such as vegetable brassicas, cruciferous weeds, spring rapeseed

  9. Evaluation of a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for the identification of Campylobacter strains isolated from diarrheal patients in Japan.

    PubMed

    Kabir, S M Lutful; Kikuchi, Ken; Asakura, Masahiro; Shiramaru, Sachi; Tsuruoka, Naoki; Goto, Aeko; Hinenoya, Atsushi; Yamasaki, Shinji

    2011-01-01

    We have developed a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for the detection and identification of Campylobacter jejuni, C. coli, and C. fetus. The applicability of this assay was evaluated with 325 Campylobacter strains isolated from diarrheal patients in Japan and the results were compared with those obtained by other genetic methods, including hipO gene detection and 16S rRNA gene sequencing. Of the 325 strains analyzed, 314 and 11 were identified as C. jejuni and C. coli, respectively, by combination of hipO gene detection and 16S rRNA gene sequencing. When the multiplex PCR assay was employed, 309, 310, and 314 strains were identified as C. jejuni on the basis of cdtA, cdtB, and cdtC gene-specific primers, respectively. Similarly, 11, 11, and 10 strains were identified as C. coli on the basis of cdtA, cdtB, and cdtC gene-specific primers, respectively. Sequence analysis of the cdt gene region of 6 strains (5 C. jejuni and 1 C. coli) which did not yield specific PCR products in any of the cdt gene-based multiplex PCR assays revealed deletions or mutations of the cdt genes. Pulsed-field gel electrophoresis indicated that C. jejuni and C. coli strains were genetically diverse. Taken together, these findings suggest that the cdtC gene-based multiplex PCR seems to be a particularly simple and rapid method for differentiating between species of Campylobacter strains, such as C. jejuni and C. coli. However, combination of these multiplex PCR assays will allow more accurate identification. PMID:21266751

  10. Evaluation of a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for the identification of Campylobacter strains isolated from poultry in Thailand.

    PubMed

    Samosornsuk, Worada; Asakura, Masahiro; Yoshida, Emi; Taguchi, Takashi; Nishimura, Kazuhiko; Eampokalap, Boonchuay; Phongsisay, Vongsavanh; Chaicumpa, Wanpen; Yamasaki, Shinji

    2007-01-01

    We have recently developed a cytolethal distending toxin (cdt) gene-based species-specific multiplex PCR assay for identifying Campylobacter jejuni, C. coli and C. fetus. In the present study, the applicability of this assay was evaluated with 34 Campylobacter-like organisms isolated from poultry in Thailand for species identification and was compared with other assays including API Campy, 16S rRNA gene sequence, and hippuricase (hipO) gene detection. Of the 34 strains analyzed, 20, 10 and 1 were identified as C. jejuni, C. coli, and Arcobacter cryaerophilus, respectively, and 3 could not be identified by API Campy. However, 16S rRNA gene analysis, showed that all 34 strains are C. jejuni/coli. To discriminate between these 2 species, the hipO gene, which is specifically present in C. jejuni, was examined by PCR and was detected in 20 strains, which were identified as C. jejuni by API Campy but not in the remaining 14 strains. Collective results indicated that 20 strains were C. jejuni whereas the 14 strains were C. coli. When the cdt gene-based multiplex PCR was employed, however, 19, 20 and 19 strains were identified as C. jejuni while 13, 14 and 13 were identified as C. coli by the cdtA, cdtB and cdtC gene-based multiplex PCR, respectively. Pulsed-field gel electrophoresis revealed that C. jejuni and C. coli strains analyzed are genetically diverse. Taken together, these data suggest that the cdt gene-based multiplex PCR, particularly cdtB gene-based multiplex PCR, is a simple, rapid and reliable method for identifying the species of Campylobacter strains. PMID:17895609

  11. Species-specific sperm-egg interaction affects the utility of a heterologous bovine in vitro fertilization system for evaluating antelope sperm.

    PubMed

    Kouba, A J; Atkinson, M W; Gandolf, A R; Roth, T L

    2001-10-01

    The purpose of this study was to evaluate cryopreserved fringe-eared (FE) oryx (Oryx gazella callotis) sperm function using a heterologous in vitro fertilization (IVF) system previously developed to study scimitar-horned (SH) oryx (Oryx dammah) spermatozoa. Semen was collected by electroejaculation from FE oryx (n = 2) and SH oryx (n = 2), evaluated immediately postcollection, and cryopreserved. Thawed spermatozoa were evaluated for motility, forward progression, and acrosomal status immediately post-thaw, after Percoll-separation, and 1, 2, 3, and 8 h after culture in IVF medium. In vitro-matured cow oocytes (n = 924) were inseminated with either domestic bull, FE, or SH oryx spermatozoa and after an 8-h coincubation period, half the oocytes were fixed and examined for sperm penetration, polyspermy, and male pronuclear formation. The remaining oocytes were placed into in vitro culture and evaluated for cleavage after 48 h. Overall, there were no between-species differences in sperm motility and acrosome integrity. However, an effect of time (P < 0.05) and a species-by-time interaction (P < 0.05) were detected for both parameters. Penetration, male pronuclear formation, and embryo cleavage were high (>90%, >85%, and >70%, respectively) for oocytes inseminated with domestic bull and SH oryx spermatozoa and did not differ (P > 0.05) between species. In contrast, very few oocytes (2.8%, 4 of 141) inseminated with FE oryx sperm were penetrated. Cleavage was rare (8.0%, 16 of 200) in oocytes inseminated with FE oryx spermatozoa and did not differ (P > 0.05) from that in parthenogenetic controls (4.2%, 3 of 72). Furthermore, FE oryx spermatozoa were incapable of penetrating zona-free cow oocytes. These results indicate that species-specific differences in gamete interaction may exist even between very closely related nondomestic bovids. PMID:11566750

  12. Mercury methylation and demethylation in highly contaminated sediments from the Deûle River in Northern France using species-specific enriched stable isotopes.

    PubMed

    Ouddane, Baghdad; Monperrus, Mathilde; Kadlecova, Milada; Daye, Mirna; Amouroux, David

    2015-01-01

    The methylation-demethylation processes in sediments of the Deûle River were determined using well-established isotope experiments. For this purpose, species-specific isotopically enriched tracers in the form of inorganic mercury IHg ((199)Hg) and methylmercury MeHg (Me(201)Hg) were used to determine Hg dynamics in the Deûle River. Sediment cores were collected at two sampling locations chosen in the most polluted zone of the Deûle River (Northern France) in proximity of a Zn, Pb, Cu, and Ni smelter called "Metaleurop" that had closed in 2003. Site I was chosen in the vicinity of the historic smelter site and site II upstream of the Deûle River. The incubation was realized directly in the sediment cores during the 24 hour experiment under environmental conditions close to the real natural systems (the same temperature, pH, humidity, light/dark conditions, oxygen levels…). The enriched isotopes were injected by needle into different sections of the core. After incubation, the core was sliced and the concentration of Hg species was determined in each section. The highest methylation potentials were found at sediment depths away from the sediment-water-interface. At site I, the methylation potential varied between 0.02-0.9% and at site II between 0.001-0.2%. The demethylation potentials fluctuated between 0.001-60% at site I and between 4-53% at site II. In both sites, negative net methylation potentials were obtained in several sediment depths, representing a net sink for MeHg. The average net methylation potential in site I demonstrated a negative value of 1919 ng g(-1) day(-1). It seems that in site I the demethylation process predominates methylation. Whereas, in site II, the average net methylation potential was a positive value of 138 ng g(-1) day(-1), demonstrating the dominance of methylation over demethylation. PMID:25421488

  13. Four-locus phylogeny of Fusarium avenaceum and related species and their species-specific identification based on partial phosphate permease gene sequences.

    PubMed

    Stakheev, Alexander A; Khairulina, Dina R; Zavriev, Sergey K

    2016-05-16

    The fungus Fusarium avenaceum and its closest relatives are responsible for contamination of agricultural plants and their products by mycotoxins such as enniatins and moniliformin. Precise identification of mycotoxin producers is necessary for estimation of the accumulation risk of those compounds and for preventing the consumption of highly contaminated products. Nucleic acids amplification-based techniques proved to be the most rapid and reliable approach for pathogen diagnostics and identification. In this study partial phosphate permease gene (PHO) sequences were determined for Fusarium avenaceum (including one isolate identified as F. arthrosporioides), F. tricinctum, F. acuminatum and F. torulosum. Phylogenetic analysis of 40 isolates of those species from different climates and geographical regions of Russia and some neighboring countries based on sequences of PHO, translation elongation factor 1 alpha (TEF1α), beta-tubulin (β-TUB), enniatin synthetase (Esyn1) genes and combined data set demonstrated that the PHO gene possesses the highest rate of variability among them and can be considered as an informative marker for phylogenetic studies of these species. According to the combined data set phylogeny, the isolates of each species formed clusters with a high bootstrap support. Analysis of PHO sequences revealed a high intraspecific variability of F. avenaceum: there were 5 independent clusters on the dendrogram, including one cluster which was closer to F. torulosum than to other F. avenaceum isolates. Variable sites in PHO sequences have been used for the design of species-specific primers and a fluorescent hydrolysis probe. The specificity of the assay was shown for DNA samples extracted from 68 isolates of 23 Fusarium species. Quantitative PCR approach was applied to estimate the contamination rate of 17 naturally infected oat and barley samples, previously characterized by microbiological procedures. PMID:26974249

  14. Herpes Simplex Virus 1 (HSV-1) and HSV-2 Mediate Species-Specific Modulations of Programmed Necrosis through the Viral Ribonucleotide Reductase Large Subunit R1

    PubMed Central

    Yu, Xiaoliang; Li, Yun; Chen, Qin; Su, Chenhe; Zhang, Zili; Yang, Chengkui; Hu, Zhilin; Hou, Jue; Zhou, Jinying; Gong, Ling; Jiang, Xuejun

    2015-01-01

    ABSTRACT Receptor-interacting protein kinase 3 (RIP3) and its substrate mixed-lineage kinase domain-like protein (MLKL) are core regulators of programmed necrosis. The elimination of pathogen-infected cells by programmed necrosis acts as an important host defense mechanism. Here, we report that human herpes simplex virus 1 (HSV-1) and HSV-2 had opposite impacts on programmed necrosis in human cells versus their impacts in mouse cells. Similar to HSV-1, HSV-2 infection triggered programmed necrosis in mouse cells. However, neither HSV-1 nor HSV-2 infection was able to induce programmed necrosis in human cells. Moreover, HSV-1 or HSV-2 infection in human cells blocked tumor necrosis factor (TNF)-induced necrosis by preventing the induction of an RIP1/RIP3 necrosome. The HSV ribonucleotide reductase large subunit R1 was sufficient to suppress TNF-induced necrosis, and its RIP homotypic interaction motif (RHIM) domain was required to disrupt the RIP1/RIP3 complex in human cells. Therefore, this study provides evidence that HSV has likely evolved strategies to evade the host defense mechanism of programmed necrosis in human cells. IMPORTANCE This study demonstrated that infection with HSV-1 and HSV-2 blocked TNF-induced necrosis in human cells while these viruses directly activated programmed necrosis in mouse cells. Expression of HSV R1 suppressed TNF-induced necrosis of human cells. The RHIM domain of R1 was essential for its association with human RIP3 and RIP1, leading to disruption of the RIP1/RIP3 complex. This study provides new insights into the species-specific modulation of programmed necrosis by HSV. PMID:26559832

  15. Potential Mediator of Inflammation

    PubMed Central

    Carp, Harvey; Janoff, Aaron

    1980-01-01

    microenvironment of inflammatory cells, at sites of acute or chronic inflammation, may allow proteases released from these cells to damage adjacent connective tissue components more readily. Images PMID:6253528

  16. Sirtuins Link Inflammation and Metabolism

    PubMed Central

    Vachharajani, Vidula T.; Liu, Tiefu; Wang, Xianfeng; Hoth, Jason J.; Yoza, Barbara K.; McCall, Charles E.

    2016-01-01

    Sirtuins (SIRT), first discovered in yeast as NAD+ dependent epigenetic and metabolic regulators, have comparable activities in human physiology and disease. Mounting evidence supports that the seven-member mammalian sirtuin family (SIRT1–7) guard homeostasis by sensing bioenergy needs and responding by making alterations in the cell nutrients. Sirtuins play a critical role in restoring homeostasis during stress responses. Inflammation is designed to “defend and mend” against the invading organisms. Emerging evidence supports that metabolism and bioenergy reprogramming direct the sequential course of inflammation; failure of homeostasis retrieval results in many chronic and acute inflammatory diseases. Anabolic glycolysis quickly induced (compared to oxidative phosphorylation) for ROS and ATP generation is needed for immune activation to “defend” against invading microorganisms. Lipolysis/fatty acid oxidation, essential for cellular protection/hibernation and cell survival in order to “mend,” leads to immune repression. Acute/chronic inflammations are linked to altered glycolysis and fatty acid oxidation, at least in part, by NAD+ dependent function of sirtuins. Therapeutically targeting sirtuins may provide a new class of inflammation and immune regulators. This review discusses how sirtuins integrate metabolism, bioenergetics, and immunity during inflammation and how sirtuin-directed treatment improves outcome in chronic inflammatory diseases and in the extreme stress response of sepsis. PMID:26904696

  17. Pancreatic Cancer, Inflammation and Microbiome

    PubMed Central

    Zambirinis, Constantinos P.; Pushalkar, Smruti; Saxena, Deepak; Miller, George

    2014-01-01

    Pancreatic cancer is one of the most lethal cancers worldwide. No effective screening methods exist and available treatment modalities do not effectively treat the disease. Inflammatory conditions such as pancreatitis represent a well-known risk for pancreatic cancer development. Yet only in the past two decades has pancreatic cancer been recognized as an inflammation-driven cancer, and the precise mechanisms underlying the pathogenic role of inflammation are beginning to be explored in detail. A substantial amount of preclinical and clinical evidence suggests that bacteria are likely to influence this process by activating immune receptors and perpetuating cancer-associated inflammation. The recent explosion of investigations into the human microbiome have highlighted how perturbations of commensal bacterial populations can promote inflammation and promote disease processes, including carcinogenesis. The elucidation of the interplay between inflammation and microbiome in the context of pancreatic carcinogenesis will provide novel targets for intervention in order to both prevent and treat pancreatic cancer more efficiently. Further studies towards this direction are urgently needed. PMID:24855007

  18. Sirtuins Link Inflammation and Metabolism.

    PubMed

    Vachharajani, Vidula T; Liu, Tiefu; Wang, Xianfeng; Hoth, Jason J; Yoza, Barbara K; McCall, Charles E

    2016-01-01

    Sirtuins (SIRT), first discovered in yeast as NAD+ dependent epigenetic and metabolic regulators, have comparable activities in human physiology and disease. Mounting evidence supports that the seven-member mammalian sirtuin family (SIRT1-7) guard homeostasis by sensing bioenergy needs and responding by making alterations in the cell nutrients. Sirtuins play a critical role in restoring homeostasis during stress responses. Inflammation is designed to "defend and mend" against the invading organisms. Emerging evidence supports that metabolism and bioenergy reprogramming direct the sequential course of inflammation; failure of homeostasis retrieval results in many chronic and acute inflammatory diseases. Anabolic glycolysis quickly induced (compared to oxidative phosphorylation) for ROS and ATP generation is needed for immune activation to "defend" against invading microorganisms. Lipolysis/fatty acid oxidation, essential for cellular protection/hibernation and cell survival in order to "mend," leads to immune repression. Acute/chronic inflammations are linked to altered glycolysis and fatty acid oxidation, at least in part, by NAD+ dependent function of sirtuins. Therapeutically targeting sirtuins may provide a new class of inflammation and immune regulators. This review discusses how sirtuins integrate metabolism, bioenergetics, and immunity during inflammation and how sirtuin-directed treatment improves outcome in chronic inflammatory diseases and in the extreme stress response of sepsis. PMID:26904696

  19. Bioactive Egg Components and Inflammation

    PubMed Central

    Andersen, Catherine J.

    2015-01-01

    Inflammation is a normal acute response of the immune system to pathogens and tissue injury. However, chronic inflammation is known to play a significant role in the pathophysiology of numerous chronic diseases, such as cardiovascular disease, type 2 diabetes mellitus, and cancer. Thus, the impact of dietary factors on inflammation may provide key insight into mitigating chronic disease risk. Eggs are recognized as a functional food that contain a variety of bioactive compounds that can influence pro- and anti-inflammatory pathways. Interestingly, the effects of egg consumption on inflammation varies across different populations, including those that are classified as healthy, overweight, metabolic syndrome, and type 2 diabetic. The following review will discuss the pro- and anti-inflammatory properties of egg components, with a focus on egg phospholipids, cholesterol, the carotenoids lutein and zeaxanthin, and bioactive proteins. The effects of egg consumption of inflammation across human populations will additionally be presented. Together, these findings have implications for population-specific dietary recommendations and chronic disease risk. PMID:26389951

  20. Mutant p97 exhibits species-specific changes of its ATPase activity and compromises the UBXD9-mediated monomerisation of p97 hexamers.

    PubMed

    Rijal, Ramesh; Arhzaouy, Khalid; Strucksberg, Karl-Heinz; Cross, Megan; Hofmann, Andreas; Schröder, Rolf; Clemen, Christoph S; Eichinger, Ludwig

    2016-01-01

    p97 (VCP) is a homo-hexameric triple-A ATPase that exerts a plethora of cellular processes. Heterozygous missense mutations of p97 cause at least five human neurodegenerative disorders. However, the specific molecular consequences of p97 mutations are hitherto widely unknown. Our in silico structural models of human and Dictyostelium p97 showed that the disease-causing human R93C, R155H, and R155C as well as Dictyostelium R154C, E219K, R154C/E219K p97 mutations constitute variations in surface-exposed locations. In-gel ATPase activity measurements of p97 monomers and hexamers revealed significant mutation- and species-specific differences. While all human p97 mutations led to an increase in ATPase activity, no changes could be detected for the Dictyostelium R154C mutant, which is orthologous to human R155C. The E219K mutation led to an almost complete loss of activity, which was partially recuperated in the R154C/E219K double-mutant indicating p97 inter-domain communication. By means of co-immunoprecipitation experiments we identified an UBX-domain containing Dictyostelium protein as a novel p97 interaction partner. We categorized all UBX-domain containing Dictyostelium proteins and named the interaction partner UBXD9. Pull-down assays and surface plasmon resonance analyses of Dictyostelium UBXD9 or the human orthologue TUG/ASPL/UBXD9 demonstrated direct interactions with p97 as well as species-, mutation- and ATP-dependent differences in the binding affinities. Sucrose density gradient assays revealed that both human and Dictyostelium UBXD9 proteins very efficiently disassembled wild-type, but to a lesser extent mutant p97 hexamers into monomers. Our results are consistent with a scenario in which p97 point mutations lead to differences in enzymatic activities and molecular interactions, which in the long-term result in a late-onset and progressive multisystem disease. PMID:27132113

  1. Reference measurements for total mercury and methyl mercury content in marine biota samples using direct or species-specific isotope dilution inductively coupled plasma mass spectrometry.

    PubMed

    Krata, Agnieszka; Vassileva, Emilia; Bulska, Ewa

    2016-11-01

    The analytical procedures for reference measurements of the total Hg and methyl mercury (MeHg) mass fractions at various concentration levels in marine biota samples, candidates for certified reference materials (oyster and clam Gafrarium tumidum), were evaluated. Two modes of application of isotope dilution inductively coupled plasma mass spectrometry method (ID ICP-MS), namely direct isotope dilution and species-specific isotope dilution analysis with the use of two different quantification mass spectrometry techniques were compared. The entire ID ICP-MS measurement procedure was described by mathematical modelling and the combined uncertainty of measurement results was estimated. All factors influencing the final results as well as isotopic equilibrium were syste