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Sample records for c-repeat region molecular

  1. Molecular absorption in transition region spectral lines

    CERN Document Server

    Schmit, Donald; Ayres, Thomas; Peter, Hardi; Curdt, Werner; Jaeggli, Sarah

    2014-01-01

    Aims: We present observations from the Interface Region Imaging Spectrograph (IRIS) of absorption features from a multitude of cool atomic and molecular lines within the profiles of Si IV transition region lines. Many of these spectral lines have not previously been detected in solar spectra. Methods: We examined spectra taken from deep exposures of plage on 12 October 2013. We observed unique absorption spectra over a magnetic element which is bright in transition region line emission and the ultraviolet continuum. We compared the absorption spectra with emission spectra that is likely related to fluorescence. Results: The absorption features require a population of sub-5000 K plasma to exist above the transition region. This peculiar stratification is an extreme deviation from the canonical structure of the chromosphere-corona boundary . The cool material is not associated with a filament or discernible coronal rain. This suggests that molecules may form in the upper solar atmosphere on small spatial scales...

  2. Low-temperature-induced expression of rice ureidoglycolate amidohydrolase is mediated by a C-repeat/dehydration-responsive element that specifically interacts with rice C-repeat-binding factor 3

    Directory of Open Access Journals (Sweden)

    Juan eLi

    2015-11-01

    Full Text Available Nitrogen recycling and redistribution are important for the environmental stress response of plants. In non nitrogen-fixing plants, ureide metabolism is crucial to nitrogen recycling from organic sources. Various studies have suggested that the rate-limiting components of ureide metabolism respond to environmental stresses. However, the underlying regulation mechanism is not well understood. In this report, rice ureidoglycolate amidohydrolase (OsUAH, which is a recently identified enzyme catalyzing the final step of ureide degradation, was identified as low-temperature- (LT but not abscisic acid- (ABA regulated. To elucidate the LT regulatory mechanism at the transcriptional level, we isolated and characterized the promoter region of OsUAH (POsUAH. Series deletions revealed that a minimal region between -522 and -420 relative to the transcriptional start site was sufficient for the cold induction of POsUAH. Detailed analyses of this 103-bp fragment indicated that a C-repeat/dehydration-responsive (CRT/DRE element localized at position -434 was essential for LT-responsive expression. A rice C-repeat-binding factors/DRE-binding proteins 1 (CBFs/DREB1s subfamily member, OsCBF3, was screened to specifically bind to the CRT/DRE element in the minimal region both in yeast one-hybrid assays and in in vitro gel-shift analysis. Moreover, the promoter could be exclusively trans-activated by the interaction between the CRT/DRE element and OsCBF3 in vivo. These findings may help to elucidate the regulation mechanism of stress-responsive ureide metabolism genes and provide an example of the member-specific manipulation of the CBF/DREB1 subfamily.

  3. Molecular line tracers of high-mass star forming regions

    NARCIS (Netherlands)

    Nagy, Zsofia; Van der Tak, Floris; Ossenkopf, Volker; Bergin, Edwin; Black, John; Faure, Alexandre; Fuller, Gary; Gerin, Maryvonne; Goicoechea, Javier; Joblin, Christine; Le Bourlot, Jacques; Le Petit, Franck; Makai, Zoltan; Plume, Rene; Roellig, Markus; Spaans, Marco; Tolls, Volker

    2013-01-01

    High-mass stars influence their environment in different ways including feedback via their FUV radiation. The penetration of FUV photons into molecular clouds creates Photon Dominated Regions (PDRs) with different chemical layers where the mainly ionized medium changes into mainly molecular. Differe

  4. Rotation of the Warm Molecular Gas Surrounding Ultracompact HII Regions

    CERN Document Server

    Klaassen, P D; Keto, E R; Zhang, Q

    2009-01-01

    We present molecular line and 1.4 mm continuum observations towards five massive star forming regions at arcsecond resolution using the Submillimeter Array (SMA). We find that the warm molecular gas surrounding each HII region (as traced by SO_2 and OCS) appears to be undergoing bulk rotation. From the molecular line emission and thermal component of the continuum emission, we independently derived gas masses for each region which are consistent with each other. From the free-free component of the continuum emission we estimate the minimum stellar mass required to power the HII region and find that this mass, when added to the derived gas mass, is a significant fraction of the dynamical mass for that region.

  5. The Equilibrium State of Molecular Regions in the Outer Galaxy

    CERN Document Server

    Heyer, M H; Snell, R L

    2001-01-01

    A summary of global properties and an evaluation of the equilibrium state of molecular regions in the outer Galaxy are presented from the decomposition of the FCRAO Outer Galaxy Survey and targeted 12CO and 13CO observations of four giant molecular cloud complexes. The ensemble of identified objects includes both small, isolated clouds and clumps within larger cloud complexes. 12CO velocity dispersions show little variation with cloud sizes for radii less than 10 pc. It is demonstrated that the internal motions of regions with molecular masses greater than 10**4 msuns are bound by self gravity, yet, the constituent clumps of cloud complexes and isolated molecular clouds with M < 10**3 msuns are not in self gravitational equilibrium. The required external pressures to maintain the equilibrium of this population are (1-2)x10**4 cm-3-K.

  6. Molecular Counterparts of Ultracompact HII Regions with Extended Envelopes

    CERN Document Server

    Kim, K T; Kim, Kee-Tae; Koo, Bon-Chul

    2003-01-01

    We carried out 13CO J=1-0, CS, and C34S J=2-1 and J=3-2 line observations of molecular clouds associated with 16 ultracompact (UC) HII regions with extended envelopes. The molecular clouds are the ones that give birth to rich stellar clusters and/or very massive (O7-O4) stars. Our data show that the clouds are very clumpy and of irregular morphology. They usually have much larger masses, velocity dispersions, and fractions of dense gas than molecular clouds that form early B or late O stars. This is compatible with earlier findings that more massive stars form in more massive cores. 13CO cores are in general associated with compact HII regions regardless of the presence of UC HII regions therein. In contrast, CS cores are preferentially associated with compact HII regions that contain UC HII regions. As with the fact that the compact HII regions containing UC HII regions are more compact than those not associated with UC HII regions, these indicate that the former may be in an earlier evolutionary phase than ...

  7. Molecular Lines of 13 Glactic Infrared Bubble Regions

    CERN Document Server

    Yan, Q Z; Zhang, B; Lu, D R; Chen, X; Tang, Z H

    2016-01-01

    We investigated the physical properties of molecular clouds and star formation processes around infrared bubbles which are essentially expanding HII regions. We performed observations of 13 galactic infrared bubble fields containing 18 bubbles. Five molecular lines, 12CO (J=1-0), 13CO (J=1-0), C18O(J=1-0), HCN (J=1-0), and HCO+ (J=1-0), were observed, and several publicly available surveys, GLIMPSE, MIPSGAL, ATLASGAL, BGPS, VGPS, MAGPIS, and NVSS, were used for comparison. We find that these bubbles are generally connected with molecular clouds, most of which are giant. Several bubble regions display velocity gradients and broad shifted profiles, which could be due to the expansion of bubbles. The masses of molecular clouds within bubbles range from 100 to 19,000 solar mass, and their dynamic ages are about 0.3-3.7 Myr, which takes into account the internal turbulence pressure of surrounding molecular clouds. Clumps are found in the vicinity of all 18 bubbles, and molecular clouds near four of these bubbles w...

  8. The Molecular Cloud Associated with the HII Region RCW:34

    Science.gov (United States)

    Pagani, L.; Heydari-Malayeri, M.; Castets, A.

    1993-08-01

    We present millimetric multi-line observations of the molecular cloud associated with the H II region RCW 34. We believe we are able to present a coherent description of the cloud: a molecular bar on top of the H II region is divided into three elements: a dense, heated part situated in the post-shock trail, a cold, less dense part besides, left unperturbed and a diffuse component either in front of the dense parts or possibly mixed with them if the dense parts are clumpy. This diffuse component has a density of a few hundreds per cm-3, a temperature in the range 30-60 K and its opacity in 12CO is close to or less than unity. We show that this diffuse component, the existence of which is controversial, is the best explanation to the large 12CO (J: 1 → 0)/(J: 2 → 1) ratio we have observed. A simple-minded model is presented to approach its properties. The cloud is on top and partly in front of the H II region and can explain the 4.2 mag of visual extinction measured by one of us (Heydari-Malayeri 1988). The very high velocity flow detected in Hα by Heydari-Malayeri has no counterpart in radio but could be a direct visualisation of the so-called "Champagne effect" (Tonorio-Tagle 1979).

  9. Molecular characterization of a strong candidate region for schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Karayiorgou, M. [MIT, Cambridge, MA (United States)]|[Fred Hutchinson Cancer Research Center, Seattle, WA (United States); Housman, D.E. [MIT, Cambridge, MA (United States); Morrow, B. [Albert Einstein College of Medicine, Bronx, NY (United States)] [and others

    1994-09-01

    Two lines of evidence point to a region on chromosome 22 as potentially involved in the etiology of schizophrenia: First, our own linkage data and second, observations that a greater than expected number of cases with the VCF (velo-cardio-facial) syndrome, a developmental syndrome due to microdeletions of the same genetic region, develop psychotic illness during adolescence. On the molecular genetic level, we are testing the hypothesis that the partial phenotypic overlap between schizophrenia and VCF may be due to overlapping genetic abnormalities. To that end, we have generated somatic cell hybrids from an initial group of nine VCF patients over the age of 15 who underwent psychiatric evaluation. Three were assigned a DSM-III-R diagnosis of schizophrenia. Several hybrid cell lines were generated from each patient carrying either the deleted chromosome, or the intact chromosome, or both. We have analyzed these hybrids and the extent of their chromosome 22 deletions with 41 markers so far (21 polymorphic microsatellite markers and 20 STSs). One of these markers is COMT (catechol-O-methyltransferase) that could be considered a candidate for schizophrenia. We are searching for potential molecular genetic differences between the subgroup of VCF patients that do develop schizophrenia and the subgroup that do not. Our initial efforts concentrate on the possibility of correlation between the extent of the deletion and the schizophrenic phenotype. Results from our analysis so far will be presented. Our goal is to narrow and define more accurately the region potentially involved in the etiology of schizophrenia and successfully identify any gene(s) that may play a role.

  10. Molecular evolution of the cacophony IVS6 region in sandflies.

    Science.gov (United States)

    Lins, R M M A; Oliveira, S G; Souza, N A; de Queiroz, R G; Justiniano, S C B; Ward, R D; Kyriacou, C P; Peixoto, A A

    2002-04-01

    A number of insects produce acoustic signals during courtship. Genes involved in the control of the courtship song are particularly interesting from an evolutionary viewpoint because interspecific variation in this signal is potentially important as a reproductive isolation mechanism and, as a consequence, in the speciation process. The cacophony gene was identified by a mutation affecting the "lovesong" in Drosophila melanogaster. Phlebotomine sandflies (Diptera: Psychodidae) also produce acoustic stimuli during courtship and therefore cacophony can be used as an interesting molecular marker in evolutionary studies in these important disease vectors. In this paper we have studied the molecular evolution of the IVS6 region of cacophony in sandflies. We compared the level of divergence in the exon sequences encoding this conserved domain in Drosophila and Phlebotomines. We also analysed the high level of variation in an intron that is present in sandflies but that was lost in Drosophila during evolution. The available cacophony sequences were also used for a phylogenetic analysis of some species of the Neotropical genus Lutzomyia.

  11. Molecular gas in the Galactic center region. III. Probing shocks in molecular cores

    Science.gov (United States)

    Huettemeister, S.; Dahmen, G.; Mauersberger, R.; Henkel, C.; Wilson, T. L.; Martin-Pintado, J.

    1998-06-01

    Multiline observations of C(18) O and SiO isotopomers toward 33 molecular peaks in the Galactic center region, taken at the SEST, JCMT and HHT telescopes, are presented. The C(18) O presumably traces the total H_2 column density, while the SiO traces gas affected by shocks and high temperature chemistry. The J =2-> 1 line of SiO is seen only in few regions of the Galactic disk. This line is easily detected in all Galactic center sources observed. A comparison of the strength of the rare isotopomers (29) SiO and (30) SiO to the strength of the main isotopomer (28) SiO implies that the J = 2 -> 1 transition of (28) SiO is optically thick. The (29) Si/(30) Si isotope ratio of 1.6 in the Galactic center clouds is consistent with the terrestrial value. Large Velocity Gradient models show that the dense component (n_H_2 >= 10(4) \\percc) in typical molecular cores in the Galactic center is cool (\\TKIN ~ 25 K), contrary to what is usually found in Giant Molecular Clouds in the disk, where the densest cores are the hottest. High kinetic temperatures, > 100 K, known to exist from NH_3 studies, are only present at lower gas densities of a few 10(3) cm(-3) , where SiO is highly subthermally excited. Assuming that \\CEIO\\ traces all of the molecular gas, it is found that in all cases but one, SiO emission is compatible with arising in gas at higher density that is (presently) relatively cool. The relative abundance of SiO is typically 10(-9) , but differs significantly between individual sources. It shows a dependence on the position of the source within the Galactic center region. High abundances are found in those regions for which bar potential models predict a high likelihood for cloud-cloud collisions. These results can be used to relate the amount of gas that has encountered shocks within the last ~ 10(6) years to the large scale kinematics in the inner ~ 500 pc of the Galaxy. Based on observations obtained at the Swedish-ESO Submillimeter Telescope (SEST, Project C

  12. Molecular Hydrogen in the Ionized Region of Planetary Nebulae

    CERN Document Server

    Aleman, I

    2004-01-01

    This paper presents an analysis of the concentration of the hydrogen molecule inside the ionized region of planetary nebulae. The equations corresponding to the ionization and chemical equilibria of H, H+, H-, H2, H2+, and H3+ are coupled with the equations of ionization and thermal balance for a photoionized atomic gas. Forty different reactions related to the formation or the destruction of these species are included. The presence of dust is taken into account, since grains act as catalysts for the production of H2, as well as shield the molecules against the stellar ionizing radiation. We analyze the effect of the stellar ionizing continuum, as well as of the gas and grain properties on the calculated H2 mass. It is shown that a significant concentration of H2 can survive inside the ionized region of planetary nebulae, mostly in the inner region of the recombination zone. The total H2 to total hydrogen mass ratio inside the ionized region increases with the central star temperature, and, depending on the P...

  13. A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region

    Directory of Open Access Journals (Sweden)

    Choudhary K.

    2015-09-01

    Full Text Available The rDNA region of eukaryotes has the immense potential to resolve the evolutionary and phylogeny problems using molecular markers. As evident from the present review, ITS region data is considered for interpretation of inter and intra-specific variations of 136 studies of 33 families including 78 genus and 114 species affecting individuals worldwide. Along with ITS-1 and ITS-2 region in 29 studies 18S region, in 38 studies 28S region and in 43 studies mitochondrial genes (COI and NDI were also analyzed. Three new genera (Allobilharzia gen. nov., Caulanus gen. nov., and Latuterus gen. nov. and 49 new species were discovered. Only 47 studies expressed variations at intra-specific and inter-specific level in complete ITS region, ITS-1 and ITS-2 rDNA sequences due to differences in nucleotide positions. According to the findings ITS region is more reliable and precise marker for demarcation and identification of species in combination of other DNA markers. Major studies were involved around the parasites of families Fasciolidae, Schistosomatidae, Opisthorchidae, Paragonimidae and Paramphistomidae, Clinostomidae, Diplostomidae, Haploporidae, among others infecting humans, farm animals, birds, fishes, reptiles and amphibians on the clinical basis. In future, molecular and bioinformatics aspects based on genetic variations will lead to explore the untouched areas of trematodes.

  14. Molecular profiling of midbrain dopamine regions in cocaine overdose victims.

    Science.gov (United States)

    Tang, Wen-Xue; Fasulo, Wendy H; Mash, Deborah C; Hemby, Scott E

    2003-05-01

    Chronic cocaine use in humans and animal models is known to lead to pronounced alterations in neuronal function in brain regions associated with drug reinforcement. To evaluate whether the alterations in gene expression in cocaine overdose victims are associated with specific dopamine populations in the midbrain, cDNA arrays and western blotting were used to compare gene and protein expression patterns between cocaine overdose victims and age-matched controls in the ventral tegmental area (VTA) and lateral substantia nigra (l-SN). Array analysis revealed significant up-regulation of numerous transcripts in the VTA, but not in the l-SN, of cocaine overdose victims including NMDAR1, GluR2, GluR5 and KA2 receptor mRNA (p overdose victims and controls were observed for GluR1, R3 or R4 mRNA levels. Correspondingly, western blot analysis revealed VTA-selective up-regulation of CREB (p cocaine overdose victims. The present results indicate that selective alterations of CREB and certain ionotropic glutamate receptor (iGluR) subtypes appear to be associated with chronic cocaine use in humans in a region-specific manner. Moreover, as subunit composition determines the functional properties of iGluRs, the observed changes may indicate alterations in the excitability of dopamine transmission underlying long-term biochemical and behavioral effects of cocaine in humans.

  15. Molecular gas in the star-forming region IRAS 08589-4714

    Science.gov (United States)

    Saldaño, Hugo P.; Vásquez, J.; Cappa, C. E.; Gómez, M.; Duronea, N.; Rubio, M.

    2016-10-01

    Aims: We present an analysis of the region IRAS 08589-4714 with the aim of characterizing the molecular environment. Methods: We observed the 12CO(3 -2), 13CO(3 -2), C18O(3 -2), HCO+(3 -2), and HCN(3 -2) molecular lines in a region of 150''× 150'', centered on the IRAS source, to analyze the distribution and characteristics of the molecular gas linked to the IRAS source. Results: The molecular gas distribution reveals a molecular clump that is coincident with IRAS 08589-4714 and with a dust clump detected at 1.2 mm. The molecular clump is 0.45 pc in radius and its mass and H2 volume density are 310 M⊙ and 1.2 × 104 cm-3, respectively. Two overdensities were identified within the clump in HCN(3-2) and HCO+(3-2) lines. A comparison of the LTE and virial masses suggests that the clump is collapsing in regions that harbor young stellar objects. An analysis of the molecular lines suggests that they are driving molecular outflows. Final reduced APEX data are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/594/A115

  16. Molecular gas in the star-forming region IRAS 08589-4714

    CERN Document Server

    Saldaño, Hugo P; Cappa, C E; Gómez, M; Duronea, N U; Rubio, M

    2016-01-01

    We present an analysis of the region IRAS 08589-4714 with the aim of characterizing the molecular environment. We observed the CO(3-2), ^{13}CO(3-2), C^{18}O(3-2), HCO+(3-2), and HCN(3-2) molecular lines in a region of 150" x 150", centered on the IRAS source, to analyze the distribution and characteristics of the molecular gas linked to the IRAS source. The molecular gas distribution reveals a molecular clump that is coincident with IRAS 08589-4714 and with a dust clump detected at 1.2 mm. The molecular clump is 0.45 pc in radius and its mass and H_2 volume density are 310 Mo and 1.2 x 10^4 cm^{-3}, respectively. Two overdensities were identified within the clump in HCN and HCO lines. A comparison of the LTE and virial masses suggests that the clump is collapsing in regions that harbor young stellar objects. An analysis of the molecular lines suggests that they are driving molecular outflows.

  17. Molecular methods for bacterial genotyping and analyzed gene regions

    Directory of Open Access Journals (Sweden)

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  18. The Orion Molecular Cloud 2/3 and NGC 1977 Regions

    OpenAIRE

    Peterson, Dawn E.; Megeath, Tom

    2008-01-01

    The Orion Molecular Cloud 2/3 region (hereafter, OMC-2/3) and the reflection nebula NGC 1977 encompass a section of the Orion A molecular cloud undergoing vigorous star forming activity. One of the richest assemblages of protostars in the nearest 500 pc is seen in OMC-2/3, while NGC 1977 contains a cluster of over 100 young stars. In this review, we present a census of the protostars, pre-main sequence stars, and young brown dwarfs in these regions. These are identified through sub-millimeter...

  19. ALMA high spatial resolution observations of the dense molecular region of NGC 6302

    Science.gov (United States)

    Santander-García, M.; Bujarrabal, V.; Alcolea, J.; Castro-Carrizo, A.; Sánchez Contreras, C.; Quintana-Lacaci, G.; Corradi, R. L. M.; Neri, R.

    2017-01-01

    Context. The mechanism behind the shaping of bipolar planetary nebulae is still poorly understood. It is becoming increasingly clear that the main agents must operate at their innermost regions, where a significant equatorial density enhancement should be present and related to the collimation of light and jet launching from the central star preferentially towards the polar directions. Most of the material in this equatorial condensation must be lost during the asymptotic giant branch as stellar wind and later released from the surface of dust grains to the gas phase in molecular form. Accurately tracing the molecule-rich regions of these objects can give valuable insight into the ejection mechanisms themselves. Aims: We investigate the physical conditions, structure and velocity field of the dense molecular region of the planetary nebula NGC 6302 by means of ALMA band 7 interferometric maps. Methods: The high spatial resolution of the 12CO and 13CO J = 3-2 ALMA data allows for an analysis of the geometry of the ejecta in unprecedented detail. We built a spatio-kinematical model of the molecular region with the software SHAPE and performed detailed non-LTE calculations of excitation and radiative transfer with the shapemol plug-in. Results: We find that the molecular region consists of a massive ring out of which a system of fragments of lobe walls emerge and enclose the base of the lobes visible in the optical. The general properties of this region are in agreement with previous works, although the much greater spatial resolution of the data allows for a very detailed description. We confirm that the mass of the molecular region is 0.1 M⊙. Additionally, we report a previously undetected component at the nebular equator, an inner, younger ring inclined 60° with respect to the main ring, showing a characteristic radius of 7.5 × 1016 cm, a mass of 2.7 × 10-3M⊙, and a counterpart in optical images of the nebula. This inner ring has the same kinematical age as

  20. A Study of Molecular Cloud Associated with the HII Region Sh156

    Science.gov (United States)

    Kang, Meejoo; Lee, Youngung

    2005-06-01

    We have conducted observations toward the molecular cloud associated with the HII region Sh 156 in tcocom (J=1-0), ȩocom(J=1-0), and CS(J=2-1) using the TRAO 14 m telescope. Combining with existing \\cocom(J=1-0) data of the Outer Galaxy Survey, we delineated the physical properties of the cloud. We found that there is a significant sign of interaction between the HII region and the molecular gas. We estimated the masses of the molecular cloud, using three different techniques; the most plausible mass is estimated to be 1.37 × 105 M⊙, using a conversion factor of X=1.9 × 1020 \\conf, and this is similar to virial mass estimate. This implies that the cloud is gravitationally bound and in virial equilibrium even though it is closely associated with the HII region. In addition to existing outflow, we found several MSX and IRAS point sources associated with dense core regions. Thus, more star forming activities other than the existing HII region are also going on in this region.

  1. Interstitial duplications of chromosome region 15q11q13 : Clinical and molecular characterization

    NARCIS (Netherlands)

    Repetto, GR; White, LM; Bader, PJ; Johnson, D; Knoll, JHM

    1998-01-01

    Duplications of chromosome region 15q11q13 often occur as a supernumerary chromosome 15. Less frequently they occur as interstitial duplications [dup(15)]. We describe the clinical and molecular characteristics of three patients with de novo dup(15). The patients, two males and one female (ages 3-21

  2. H2 formation on PAHs in photodissociation regions: a high-temperature pathway to molecular hydrogen

    NARCIS (Netherlands)

    Boschman, L.; Cazaux, S.; Spaans, M.; Hoekstra, R.; Schlathölter, T.

    2015-01-01

    Aims: Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H2 formation rates in photodissociation regions (PDRs) and asses

  3. H-2 formation on PAHs in photodissociation regions : a high-temperature pathway to molecular hydrogen

    NARCIS (Netherlands)

    Boschman, L.; Cazaux, S.; Spaans, M.; Hoekstra, R.; Schlatholter, T.

    2015-01-01

    Aims. Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H-2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H-2 formation rates in photodissociation regions (PDRs) and ass

  4. Interstitial duplications of chromosome region 15q11q13 : Clinical and molecular characterization

    NARCIS (Netherlands)

    Repetto, GR; White, LM; Bader, PJ; Johnson, D; Knoll, JHM

    1998-01-01

    Duplications of chromosome region 15q11q13 often occur as a supernumerary chromosome 15. Less frequently they occur as interstitial duplications [dup(15)]. We describe the clinical and molecular characteristics of three patients with de novo dup(15). The patients, two males and one female (ages 3-21

  5. ALMA high spatial resolution observations of the dense molecular region of NGC 6302

    CERN Document Server

    Santander-García, M; Alcolea, J; Castro-Carrizo, A; Sánchez-Contreras, C; Quintana-Lacaci, G; Corradi, R L M; Neri, R

    2016-01-01

    The mechanism behind the shaping of bipolar planetary nebulae is still poorly understood. Accurately tracing the molecule-rich equatorial regions of post-AGB stars can give valuable insight into the ejection mechanisms at work. We investigate the physical conditions, structure and velocity field of the dense molecular region of the planetary nebula NGC 6302 by means of ALMA band 7 interferometric maps. The high spatial resolution of the $^{12}$CO and $^{13}$CO J=3-2 ALMA data allows for an analysis of the geometry of the ejecta in unprecedented detail. We built a spatio-kinematical model of the molecular region with the software SHAPE and performed detailed non-LTE calculations of excitation and radiative transfer with the SHAPEMOL plug-in. We find that the molecular region consists of a massive ring out of which a system of fragments of lobe walls emerge and enclose the base of the lobes visible in the optical. The general properties of this region are in agreement with previous works, although the much grea...

  6. The Orion Molecular Cloud 2/3 and NGC 1977 Regions

    CERN Document Server

    Peterson, Dawn E

    2008-01-01

    The Orion Molecular Cloud 2/3 region (hereafter, OMC-2/3) and the reflection nebula NGC 1977 encompass a section of the Orion A molecular cloud undergoing vigorous star forming activity. One of the richest assemblages of protostars in the nearest 500 pc is seen in OMC-2/3, while NGC 1977 contains a cluster of over 100 young stars. In this review, we present a census of the protostars, pre-main sequence stars, and young brown dwarfs in these regions. These are identified through sub-millimeter surveys, far-red to near-infrared imaging and spectroscopy with ground-based telescopes, mid-infrared photometry from the Spitzer Space Telescope, and X-ray observations made with the Chandra X-ray Observatory. We present an overview of the distribution of molecular gas associated with these regions and the rich complex of shock heated nebulae created by the young stars interacting with the molecular gas. Finally, we discuss the relationship of OMC-2/3 and NGC 1977 to the neighboring Orion Nebula Cluster and the Orion OB...

  7. MOLECULAR GAS AND STAR-FORMATION PROPERTIES IN THE CENTRAL AND BAR REGIONS OF NGC 6946

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Hsi-An; Sorai, Kazuo [Department of Physics, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810 (Japan); Kuno, Nario [Division of Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305-8571 (Japan); Koda, Jin [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States); Hirota, Akihiko [Joint ALMA Observatory, Alonso de Cordova 3107, Vitacura, Santiago (Chile); Kaneko, Hiroyuki, E-mail: hapan@astro1.sci.hokudai.ac.jp [Nobeyama Radio Observatory, NAOJ, Minamimaki, Minamisaku, Nagano 384-1305 (Japan)

    2015-12-10

    In this work, we investigate the molecular gas and star-formation properties in the barred spiral galaxy NGC 6946 using multiple molecular lines and star-formation tracers. A high-resolution image (100 pc) of {sup 13}CO (1–0) is created for the inner 2 kpc disk by the single-dish Nobeyama Radio Observatory 45 m telescope and interferometer Combined Array for Research in Millimeter-wave Astronomy, including the central region (nuclear ring and bar) and the offset ridges of the primary bar. Single-dish HCN (1–0) observations were also made to constrain the amount of dense gas. The physical properties of molecular gas are inferred from (1) the large velocity gradient calculations using our observations and archival {sup 12}CO (1–0), {sup 12}CO(2–1) data, (2) the dense gas fraction suggested by the luminosity ratio of HCN to {sup 12}CO (1–0), and (3) the infrared color. The results show that the molecular gas in the central region is warmer and denser than that of the offset ridges. The dense gas fraction of the central region is similar to that of luminous infrared galaxies/ultraluminous infrared galaxies, whereas the offset ridges are close to the global average of normal galaxies. The coolest and least-dense region is found in a spiral-like structure, which was misunderstood to be part of the southern primary bar in previous low-resolution observations. The star-formation efficiency (SFE) changes by about five times in the inner disk. The variation of SFE agrees with the prediction in terms of star formation regulated by the galactic bar. We find a consistency between the star-forming region and the temperature inferred by the infrared color, suggesting that the distribution of subkiloparsec-scale temperature is driven by star formation.

  8. CO (v = 1-0) emission in the molecular shock regions of OMC-1

    Science.gov (United States)

    Grasdalen, G. L.; Hackwell, John A.; Lynch, David K.; Russell, Ray W.

    1992-01-01

    Using the new Aerospace spectrometer on the Kuiper Airborne Observatory, we have obtained observations of the molecular shocks associated with OMC-1. Unexpectedly these observations reveal (b = 1-0) emission from CO at 4.6 microns superposed on a strong continuum. Our observations strongly suggest that both the emission feature and the continuum are produced in molecular shocks. Since the (v = 1-0) band of CO is only excited in high-velocity shocks, we may be observing for the first time the primary driving mechanism in these regions. Even if these features are produced by scattering, the characteristics will provide new constraints on the conditions in and the geometry of the shock regions.

  9. CO (v = 1-0) emission in the molecular shock regions of OMC-1

    Science.gov (United States)

    Grasdalen, G. L.; Hackwell, John A.; Lynch, David K.; Russell, Ray W.

    1992-01-01

    Using the new Aerospace spectrometer on the Kuiper Airborne Observatory, we have obtained observations of the molecular shocks associated with OMC-1. Unexpectedly these observations reveal (b = 1-0) emission from CO at 4.6 microns superposed on a strong continuum. Our observations strongly suggest that both the emission feature and the continuum are produced in molecular shocks. Since the (v = 1-0) band of CO is only excited in high-velocity shocks, we may be observing for the first time the primary driving mechanism in these regions. Even if these features are produced by scattering, the characteristics will provide new constraints on the conditions in and the geometry of the shock regions.

  10. A dense molecular cloud in the OMC-1/OMC-2 region

    Science.gov (United States)

    Kutner, M. L.; Evans, N. J., II; Tucker, K. D.

    1976-01-01

    H2CO emission at 2 mm is seen over a region 30 arcmin in extent which includes OMC-1 and OMC-2. The mass of this cloud, estimated from H2CO and CO observations, is about 7000 solar masses. The velocity pattern is one of rotation, with evidence for fragmentation into two or three distinct condensations. A sharp boundary to the molecular cloud is observed at the edge of the H II region in NGC 1977. It appears likely that NGC 1977 is a condensation at the northern end of the cloud, complementary to the Orion Nebula at the southern end.

  11. A dense molecular cloud in the OMC-1/OMC-2 region

    Science.gov (United States)

    Kutner, M. L.; Evans, N. J., II; Tucker, K. D.

    1976-01-01

    H2CO emission at 2 mm is seen over a region 30 arcmin in extent which includes OMC-1 and OMC-2. The mass of this cloud, estimated from H2CO and CO observations, is about 7000 solar masses. The velocity pattern is one of rotation, with evidence for fragmentation into two or three distinct condensations. A sharp boundary to the molecular cloud is observed at the edge of the H II region in NGC 1977. It appears likely that NGC 1977 is a condensation at the northern end of the cloud, complementary to the Orion Nebula at the southern end.

  12. MOLECULAR PHYLOGENETIC ANALYSIS OF MONASCUS FUNGI BASED ON INTERNAL TRANSCRIBED SPACER REGION

    OpenAIRE

    Kikuchi, Y.; N. SUHARNA; Fukatsu, T

    2005-01-01

    A molecular analysis of internal transcribed spacer region has been carried out to reveal the relationship among 16 strains of Monascus spp. A primer set comprised primer ITS1 and ITS4 was used to amplify this region in which they were cloned and scqucnccd. We also compared the sequence result with M. purpureus AF458473, M.ruber AF458470, M. kaoliang AF451859, M. araneous AF458471 and M. pilosus AF451856 and one outgroup species Thermoascus crustaceus U18353. The result showed that 16 M...

  13. Tetrasomy 21 pter {yields} q22.1 and Down syndrome: Molecular definition of the region

    Energy Technology Data Exchange (ETDEWEB)

    Daumer-Haas, C.; Schuffenhauer, S.; Walther, J.U. [Universitaet Muenchen (Germany); Portsmann, T. [Humboldt Universitaet, Berlin (Germany); Korenberg, J.R.; Schipper, R.D. [Univ. of California, Los Angeles, CA (United States)

    1994-12-01

    Down syndrome is usually caused by complete trisomy 21. Rarely, it is due to partial trisomy of the segment 21q22. We report on a 33-month-old girl with tetrasomy 21 pter {yields} q22.1 resulting from an extra chromosome idic(21)(q22.1). She has craniofacial traits typical of Down syndrome, including brachycephaly, third fontanel, upward slanting palpebral fissures, round face, and protruding tongue. Speech development is quite delayed whereas motor development is only mildly retarded. The molecular content of the extra isodicentric chromosome was defined by molecular genetic investigations using 13 single copy probes unique to chromosome 21, and SOD1 expression studies. The child was found to have 4 copies of the region defined by D21S16 (21cen) through D21S93 on 21q22.1 and two copies of the remaining region defined by SOD1 {yields} D21S55 {yields} D21S123. In view of the recent assignment of Down syndrome facial characters to the 21q22 region, defined in part by D21S55, it is significant that this child shows a subset of Down syndrome facial manifestations, without duplication of this region. These results suggest that genes contributing to the facial and some of the hand manifestations of Down syndrome also exist in the chromosomal region proximal to D21S55 in band 21q22.1. 34 refs., 6 figs., 3 tabs.

  14. The molecular cloud-H II region complexes associated with SH 90 and SH 235

    Science.gov (United States)

    Lafon, G.; Baudry, A.; de La Noe, J.; Deharveng, L.

    1983-07-01

    The Sharpless regions Sh 90 and Sh 235 are characterized on the basis of monochromatic photographs (at H-alpha, N III, and O III) and H-alpha photographic interferograms made at the Observatoire de Haute-Provence and of molecular-cloud maps (at 110.201 and 89.189 GHz) made at the Observatoire de Bordeaux. Sh 90, at a distance of 2.4 kpc, is found to have an evolved-H II-region shell structure, with ionized gas flowing both away from and toward a neutral molecular cloud with a mass of about 60,000 solar mass which lies partly in front of the H II region. Sh 235, at 1.6 kpc, has two extended 100,000-300,000-solar-mass neutral clouds which partly overlap. The northern cloud, identified at -20 km/s, is related to the optical nebula; the southern cloud (at -17 km/s) contains three compact H II regions (A, B, and C) and exhibits recent star-formation processes. The 'champagne' model of H II regions proposed by Tenorio-Tagle (1979) is considered applicable to Sh 90 and to Sh 235C.

  15. Molecular Emission in Dense Massive Clumps from the Star-Forming Regions S231-S235

    CERN Document Server

    Ladeyschikov, D A; Tsivilev, A P; Sobolev, A M

    2016-01-01

    The article deals with observations of star-forming regions S231-S235 in 'quasi-thermal' lines of ammonia (NH$_3$), cyanoacetylene (HC$_3$N) and maser lines of methanol (CH$_3$OH) and water vapor (H$_2$O). S231-S235 regions is situated in the giant molecular cloud G174+2.5. We selected all massive molecular clumps in G174+2.5 using archive CO data. For the each clump we determined mass, size and CO column density. After that we performed observations of these clumps. We report about first detections of NH$_3$ and HC$_3$N lines toward the molecular clumps WB89 673 and WB89 668. This means that high-density gas is present there. Physical parameters of molecular gas in the clumps were estimated using the data on ammonia emission. We found that the gas temperature and the hydrogen number density are in the ranges 16-30 K and 2.8-7.2$\\times10^3$ cm$^{-3}$, respectively. The shock-tracing line of CH$_3$OH molecule at 36.2 GHz is newly detected toward WB89 673.

  16. Discovery of radiatively excited molecular hydrogen in the giant extragalactic HII region complex NGC 604

    NARCIS (Netherlands)

    Israel, F.P.; Hawarden, T.G.; Wade, R.S.; Geballe, T.R.; Dishoeck, van E.F.

    1989-01-01

    The 1-0S(1), 2-1S(1), 1-0S(0) and 1-0Q branch transitions of molecular hydrogen (H2) towards the giant emission nebula (HII region) NGC 604 in M33 have been detected. The line ratios are incompatible with shock-excited H2, but indicate the widespread presence of fluorescent H2 at a mean temperature

  17. Assessing the Value of DNA Barcodes and Other Priority Gene Regions for Molecular Phylogenetics of Lepidoptera

    Science.gov (United States)

    Wilson, John James

    2010-01-01

    Background Despite apparently abundant amounts of observable variation and species diversity, the order Lepidoptera exhibits a morphological homogeneity that has provided only a limited number of taxonomic characters and led to widespread use of nucleotides for inferring relationships. This study aims to characterize and develop methods to quantify the value of priority gene regions designated for Lepidoptera molecular systematics. In particular, I assess how the DNA barcode segment of the mitochondrial COI gene performs across a broad temporal range given its number one position of priority, most sequenced status, and the conflicting opinions on its phylogenetic performance. Methodology/Principal Findings Gene regions commonly sequenced for Lepidoptera phylogenetics were scored using multiple measures across three categories: practicality, which includes universality of primers and sequence quality; phylogenetic utility; and phylogenetic signal. I found that alternative measures within a category often appeared correlated, but high scores in one category did not necessarily translate into high scores in another. The DNA barcode was easier to sequence than other genes, and had high scores for utility but low signal above the genus level. Conclusions/Significance Given limited financial resources and time constraints, careful selection of gene regions for molecular phylogenetics is crucial to avoid wasted effort producing partially informative data. This study introduces an approach to assessing the value of gene regions prior to the initiation of new studies and presents empirical results to help guide future selections. PMID:20479871

  18. Assessing the value of DNA barcodes and other priority gene regions for molecular phylogenetics of Lepidoptera.

    Directory of Open Access Journals (Sweden)

    John James Wilson

    Full Text Available BACKGROUND: Despite apparently abundant amounts of observable variation and species diversity, the order Lepidoptera exhibits a morphological homogeneity that has provided only a limited number of taxonomic characters and led to widespread use of nucleotides for inferring relationships. This study aims to characterize and develop methods to quantify the value of priority gene regions designated for Lepidoptera molecular systematics. In particular, I assess how the DNA barcode segment of the mitochondrial COI gene performs across a broad temporal range given its number one position of priority, most sequenced status, and the conflicting opinions on its phylogenetic performance. METHODOLOGY/PRINCIPAL FINDINGS: Gene regions commonly sequenced for lepidoptera phylogenetics were scored using multiple measures across three categories: practicality, which includes universality of primers and sequence quality; phylogenetic utility; and phylogenetic signal. I found that alternative measures within a category often appeared correlated, but high scores in one category did not necessarily translate into high scores in another. The DNA barcode was easier to sequence than other genes, and had high scores for utility but low signal above the genus level. CONCLUSIONS/SIGNIFICANCE: Given limited financial resources and time constraints, careful selection of gene regions for molecular phylogenetics is crucial to avoid wasted effort producing partially informative data. This study introduces an approach to assessing the value of gene regions prior to the initiation of new studies and presents empirical results to help guide future selections.

  19. A CATALOG OF METHANOL MASERS IN MASSIVE STAR-FORMING REGIONS. III. THE MOLECULAR OUTFLOW SAMPLE

    Energy Technology Data Exchange (ETDEWEB)

    Gómez-Ruiz, A. I. [Instituto Nacional de Astrofísica, Óptica y Electrónica, Luis E. Erro 1, Tonantzintla, Puebla, C.P. 72840, México (Mexico); Kurtz, S. E.; Loinard, L. [Instituto de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Apartado Postal 3-72, Morelia 58089, México (Mexico); Araya, E. D. [Physics Department, Western Illinois University, 1 University Circle, Macomb, IL 61455 (United States); Hofner, P. [New Mexico Institute of Mining and Technology, Socorro, NM 87801 (United States)

    2016-02-15

    We present an interferometric survey of the 44 GHz class I methanol maser transition toward a sample of 69 sources consisting of high-mass protostellar object (HMPO) candidates and ultracompact (UC) H ii regions. We found a 38% detection rate (16 of 42) in the HMPO candidates and a 54% detection rate (13 of 24) for the regions with ionized gas. This result indicates that class I methanol maser emission is more common toward the more evolved young stellar objects of our sample. Comparing with similar interferometric data sets, our observations show narrower linewidths, likely due to our higher spatial resolution. Based on a comparison between molecular outflow tracers and the maser positions, we find several cases where the masers appear to be located at the outflow interface with the surrounding core. Unlike previous surveys, we also find several cases where the masers appear to be located close to the base of the molecular outflow, although we cannot discard projection effects. This and other surveys of class I methanol masers not only suggest that these masers may trace shocks at different stages, but also that they may even trace shocks arising from a number of different phenomena occurring in star-forming regions: young/old outflows, cloud–cloud collisions, expanding H ii regions, among others.

  20. Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae

    Directory of Open Access Journals (Sweden)

    Alexandra Kerbl

    2016-08-01

    Full Text Available Abstract Background Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain. Despite this heterogeneity of neural arrangements, the molecular profiles related to central nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy. Results We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct-developing meiofaunal annelid Dinophilus gyrociliatus. The small, compact brain shows expression of dimmed, foxg, goosecoid, homeobrain, nk2.1, orthodenticle, orthopedia, pax6, six3/6 and synaptotagmin-1. Although most of the studied markers localize to specific brain areas, the genes six3/6 and synaptotagmin-1 are expressed in nearly all perikarya of the brain. All genes except for goosecoid, pax6 and nk2.2 overlap in the anterior brain region, while the respective expression domains are more separated in the posterior brain. Conclusions Our findings reveal that the expression patterns of the genes foxg, orthodenticle, orthopedia and six3/6 correlate with those described in Platynereis dumerilii larvae, and homeobrain, nk2.1, orthodenticle and synaptotagmin-1 resemble the pattern of late larvae of Capitella teleta. Although data on other annelids are limited, molecular similarities between adult Dinophilus and larval Platynereis and Capitella suggest an overall conservation of molecular mechanisms patterning the anterior neural regions, independent

  1. Molecular characterization of a serine/threonine kinase in the DiGeorge minimal critical region.

    Science.gov (United States)

    Goldmuntz, E; Fedon, J; Roe, B; Budarf, M L

    1997-10-01

    The majority of patients with DiGeorge, velocardiofacial or conotruncal anomaly facial syndromes share a common genetic etiology, deletion of chromosomal region 22q11.2. This report describes a computational approach toward the identification and molecular characterization of a newly identified serine/threonine kinase from the minimal critical deleted region (MDGCR). A cosmid contig of the minimal critical region has been assembled and sequenced in its entirety. Database searches and computer analysis of one cosmid (111f11) for coding sequences identified two regions with high similarity to the mouse serine/threonine kinase, Tsk1. Our investigations demonstrate that one of these regions contains a testis-specific gene that undergoes differential splicing, while the other region is most likely a pseudogene. Northern blot analysis and cDNA cloning demonstrate that there is alternate processing of the 3'UTR without altering the conserved kinase domains within the open reading frame. Serine/threonine kinases can play a regulatory role and have been found to be expressed during early embryogenesis. Based on its position in the MDGCR and possible function, the gene reported here is a candidate for the features seen in the 22q11 deletion syndrome.

  2. Formation of Pillars at the Boundaries between HII Regions and Molecular Clouds

    Energy Technology Data Exchange (ETDEWEB)

    Mizuta, A; Kane, J O; Pound, M W; Remington, B A; Ryutov, D D; Takabe, H

    2006-04-20

    We investigate numerically the hydrodynamic instability of an ionization front (IF) accelerating into a molecular cloud, with imposed initial perturbations of different amplitudes. When the initial amplitude is small, the imposed perturbation is completely stabilized and does not grow. When the initial perturbation amplitude is large enough, roughly the ratio of the initial amplitude to wavelength is greater than 0.02, portions of the IF temporarily separate from the molecular cloud surface, locally decreasing the ablation pressure. This causes the appearance of a large, warm HI region and triggers nonlinear dynamics of the IF. The local difference of the ablation pressure and acceleration enhances the appearance and growth of a multimode perturbation. The stabilization usually seen at the IF in the linear regimes does not work due to the mismatch of the modes of the perturbations at the cloud surface and in density in HII region above the cloud surface. Molecular pillars are observed in the late stages of the large amplitude perturbation case. The velocity gradient in the pillars is in reasonably good agreement with that observed in the Eagle Nebula. The initial perturbation is imposed in three different ways: in density, in incident photon number flux, and in the surface shape. All cases show both stabilization for a small initial perturbation and large growth of the second harmonic by increasing amplitude of the initial perturbation above a critical value.

  3. The molecular environment of the Galactic star forming region G19.61-0.23

    CERN Document Server

    Santangelo, G; Leurini, S; Walmsley, C M; Cesaroni, R; Bronfman, L; Carey, S; Gregorini, L; Menten, K M; Molinari, S; Noriega-Crespo, A; Olmi, L; Schuller, F

    2010-01-01

    We present single-dish (sub)millimeter observations of gas and dust in the Galactic high-mass star-forming region G19.61-0.23, with the aim of studying the large-scale properties and physical conditions of the molecular gas across the region. The final aim is to compare the large-scale (about 100 pc) properties with the small-scale (about 3 pc) properties and to consider possible implications for extragalactic studies. We have mapped CO isotopologues in the J=1-0 transition using the FCRAO-14m telescope and the J=2-1 transition using the IRAM-30m telescope. We have also used data from the ATLASGAL survey and from the BU-FCRAO Galactic Ring Survey, as well as the Spitzer infrared Galactic plane surveys GLIMPSE and MIPSGAL to characterize the star-formation activity within the molecular clouds. We reveal a population of molecular clumps in the 13CO(1-0) emission. Our analysis of the 13CO suggests that the virial parameter (ratio of kinetic to gravitational energy) varies over an order of magnitude between clump...

  4. Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae)

    DEFF Research Database (Denmark)

    Kerbl, Alexandra; Martín-Durán, José M.; Worsaae, Katrine;

    2016-01-01

    BACKGROUND: Annelida is a morphologically diverse animal group that exhibits a remarkable variety in nervous system architecture (e.g., number and location of longitudinal cords, architecture of the brain). Despite this heterogeneity of neural arrangements, the molecular profiles related to central...... nervous system patterning seem to be conserved even between distantly related annelids. In particular, comparative molecular studies on brain and anterior neural region patterning genes have focused so far mainly on indirect-developing macrofaunal taxa. Therefore, analyses on microscopic, direct......-developing annelids are important to attain a general picture of the evolutionary events underlying the vast diversity of annelid neuroanatomy. RESULTS: We have analyzed the expression domains of 11 evolutionarily conserved genes involved in brain and anterior neural patterning in adult females of the direct...

  5. Molecular Cross-Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions.

    Science.gov (United States)

    Harden, Bradley J; Frueh, Dominique P

    2017-01-24

    Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N-terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post-translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.

  6. Molecular phylogeny of Burkholderia pseudomallei from a remote region of Papua New Guinea.

    Directory of Open Access Journals (Sweden)

    Anthony Baker

    Full Text Available BACKGROUND: The island of New Guinea is located midway between the world's two major melioidosis endemic regions of Australia and Southeast Asia. Previous studies in Papua New Guinea have demonstrated autochthonous melioidosis in Balimo, Western province. In contrast to other regions of endemicity, isolates recovered from both environmental and clinical sources demonstrate narrow genetic diversity over large spatial and temporal scales. METHODOLOGY/PRINCIPAL FINDINGS: We employed molecular typing techniques to determine the phylogenetic relationships of these isolates to each other and to others worldwide to aid in understanding the origins of the Papua New Guinean isolates. Multi-locus sequence typing of the 39 isolates resolved three unique sequence types. Phylogenetic reconstruction and Structure analysis determined that all isolates were genetically closer to those from Australia than those from Southeast Asia. Gene cluster analysis however, identified a Yersinia-like fimbrial gene cluster predominantly found among Burkholderia pseudomallei derived from Southeast Asia. Higher resolution VNTR typing and phylogenetic reconstruction of the Balimo isolates resolved 24 genotypes with long branch lengths. These findings are congruent with long term persistence in the region and a high level of environmental stability. CONCLUSIONS/SIGNIFICANCE: Given that anthropogenic influence has been hypothesized as a mechanism for the dispersal of B. pseudomallei, these findings correlate with limited movement of the indigenous people in the region. The palaeogeographical and anthropogenic history of Australasia and the results from this study indicate that New Guinea is an important region for the further study of B. pseudomallei origins and dissemination.

  7. Spectroscopic Studies of Atomic and Molecular Processes in the Edge Region of Magnetically Confined Fusion Plasmas

    Science.gov (United States)

    Hey, J. D.; Brezinsek, S.; Mertens, Ph.; Unterberg, B.

    2006-12-01

    Edge plasma studies are of vital importance for understanding plasma-wall interactions in magnetically confined fusion devices. These interactions determine the transport of neutrals into the plasma, and the properties of the plasma discharge. This presentation deals with optical spectroscopic studies of the plasma boundary, and their rôle in elucidating the prevailing physical conditions. Recorded spectra are of four types: emission spectra of ions and atoms, produced by electron impact excitation and by charge-exchange recombination, atomic spectra arising from electron impact-induced molecular dissociation and ionisation, visible spectra of molecular hydrogen and its isotopic combinations, and laser-induced fluorescence (LIF) spectra. The atomic spectra are strongly influenced by the confining magnetic field (Zeeman and Paschen-Back effects), which produces characteristic features useful for species identification, temperature determination by Doppler broadening, and studies of chemical and physical sputtering. Detailed analysis of the Zeeman components in both optical and LIF spectra shows that atomic hydrogen is produced in various velocity classes, some related to the relevant molecular Franck-Condon energies. The latter reflect the dominant electron collision processes responsible for production of atoms from molecules. This assignment has been verified by gas-puffing experiments through special test limiters. The higher-energy flanks of hydrogen line profiles probably also show the influence of charge-exchange reactions with molecular ions accelerated in the plasma sheath (`scrape-off layer') separating limiter surfaces from the edge plasma, in analogy to acceleration in the cathode-fall region of gas discharges. While electron collisions play a vital rôle in generating the spectra, ion collisions with excited atomic radiators act through re-distribution of population among the atomic fine-structure sublevels, and momentum transfer to the atomic nuclei

  8. A Molecular Brake in the Kinase Hinge Region Regulates the Activity of Receptor Tyrosine Kinases

    Energy Technology Data Exchange (ETDEWEB)

    Chen,H.; Ma, J.; Li, W.; Eliseenkova, A.; Xu, C.; Neubert, T.; Miller, W.; Mohammadi, M.

    2007-01-01

    Activating mutations in the tyrosine kinase domain of receptor tyrosine kinases (RTKs) cause cancer and skeletal disorders. Comparison of the crystal structures of unphosphorylated and phosphorylated wild-type FGFR2 kinase domains with those of seven unphosphorylated pathogenic mutants reveals an autoinhibitory 'molecular brake' mediated by a triad of residues in the kinase hinge region of all FGFRs. Structural analysis shows that many other RTKs, including PDGFRs, VEGFRs, KIT, CSF1R, FLT3, TEK, and TIE, are also subject to regulation by this brake. Pathogenic mutations activate FGFRs and other RTKs by disengaging the brake either directly or indirectly.

  9. A molecular model of proton neutralization at solid surface: the intermediate velocity region

    Energy Technology Data Exchange (ETDEWEB)

    Nedeljkovic, N.N.; Nedeljkovic, L.D. (Faculty of Physics, Belgrade Univ. (Yugoslavia)); Janev, R.K. (Inst. of Physics, Belgrade (Yugoslavia)); Miskovic, Z.L. (Boris Kidric Inst. of Nuclear Sciences, Belgrade (Yugoslavia))

    1991-06-01

    The proton neutralization (into ground hydrogen state) at solid surface is treated in the normal emergence geometry. For the intermediate proton velocity region (between v{approx equal}1 and 4 a.u.) a new, molecular-type dynamic model of the process is proposed. Evaluation of the electron transition amplitude is based on an elaboration of the Demkov-Ostrovsky method. The calculation showed that the electron transitions have a nonresonant character. Comparison with experiments leads to the conclusion that the electron capture into ground state is almost sufficient to explain the experiment data. (orig.).

  10. Molecular epidemiology of avian leukosis virus subgroup J and evolutionary history of its 3' untranslated region.

    Science.gov (United States)

    Zavala, G; Cheng, S; Jackwood, M W

    2007-12-01

    Avian leukosis subgroup J (ALV-J) causes a variety of tumors and mortality in meat-type chickens. Since its discovery in the late 1980s, ALV-J has spread to breeding stock produced by most primary breeding companies of North America, the European Union, and Asia. ALV-J seems to have been eradicated from elite breeding stock produced by most primary breeders, albeit ALV-J still circulates in some commercial poultry. This study was undertaken to examine the molecular epidemiology and evolution of ALV-J detected in breeding stock and broiler chickens representing eight primary breeding companies over a period of approximately 20 yr (1988-2007). The redundant transmembrane region of the envelope gene has been deleted in some isolates, suggesting that this region is dispensable for viral fitness. Within the 3' untranslated region (3' UTR), the direct repeat 1 was present in 100% of the ALV-J isolates studied. In contrast, the E element has undergone substantial deletions in >50% of the ALV-J proviruses studied. Overall, the unique region 3 was the least conserved within the 3' long terminal repeat (LTR), albeit the transcriptional regulatory elements typical of avian retroviruses (CAAT, CArG, PRE, TATA, and Y boxes) were highly conserved. The direct repeat region of the LTR was identical in all of the proviruses, and the 3' unique region 5 was relatively well conserved. Thus, the 3' UTR of ALV-J has evolved rapidly, reflecting significant instability of this region. Some of the mutations in the 3' UTR have resulted in the emergence of moderately distinct genetic lineages representing each primary breeding company from which ALV-J was isolated.

  11. High resolution ALMA observations of dense molecular medium in the central regions of active galaxies

    CERN Document Server

    Kohno, Kotaro; Taniguchi, Akio; Izumi, Takuma; Tosaki, Tomoka

    2016-01-01

    In the central regions of active galaxies, dense molecular medium are exposed to various types of radiation and energy injections, such as UV, X-ray, cosmic ray, and shock dissipation. With the rapid progress of chemical models and implementation of new-generation mm/submm interferometry, we are now able to use molecules as powerful diagnostics of the physical and chemical processes in galaxies. Here we give a brief overview on the recent ALMA results to demonstrate how molecules can reveal underlying physical and chemical processes in galaxies. First, new detections of Galactic molecular absorption systems with elevated HCO/H$^{13}$CO$^+$ column density ratios are reported, indicating that these molecular media are irradiated by intense UV fields. Second, we discuss the spatial distributions of various types of shock tracers including HNCO, CH$_3$OH and SiO in NGC 253 and NGC 1068. Lastly, we provide an overview of proposed diagnostic methods of nuclear energy sources using ALMA, with an emphasis on the syne...

  12. Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms.

    Directory of Open Access Journals (Sweden)

    Alessandra Cenci

    Full Text Available The role of variable regions of HIV-1 gp120 in immune escape of HIV has been investigated. However, there is scant information on how conserved gp120 regions contribute to virus escaping. Here we have studied how molecular sequence characteristics of conserved C3, C4 and V3 regions of clade C HIV-1 gp120 that are involved in HIV entry and are target of the immune response, are modulated during the disease course. We found an increase of "shifting" putative N-glycosylation sites (PNGSs in the α2 helix (in C3 and in C4 and an increase of sites under positive selection pressure in the α2 helix during the chronic stage of disease. These sites are close to CD4 and to co-receptor binding sites. We also found a negative correlation between electric charges of C3 and V4 during the late stage of disease counteracted by a positive correlation of electric charges of α2 helix and V5 during the same stage. These data allow us to hypothesize possible mechanisms of virus escape involving constant and variable regions of gp120. In particular, new mutations, including new PNGSs occurring near the CD4 and CCR5 binding sites could potentially affect receptor binding affinity and shield the virus from the immune response.

  13. The molecular composition of the planet-forming regions of protoplanetary disks across the luminosity regime

    Science.gov (United States)

    Walsh, Catherine; Nomura, Hideko; van Dishoeck, Ewine

    2015-10-01

    Context. Near- to mid-infrared observations of molecular emission from protoplanetary disks show that the inner regions are rich in small organic volatiles (e.g., C2H2 and HCN). Trends in the data suggest that disks around cooler stars (Teff ≈ 3000 K) are potentially (i) more carbon-rich; and (ii) more molecule-rich than their hotter counterparts (Teff ≳ 4000 K). Aims: We explore the chemical composition of the planet-forming region (gas-grain chemical network to map the molecular abundances in the planet-forming zone. The effects of (i) N2 self shielding; (ii) X-ray-induced chemistry; and (iii) initial abundances, are investigated. The chemical composition in the "observable" atmosphere is compared with that in the disk midplane where the bulk of the planet-building reservoir resides. Results: M dwarf disk atmospheres are relatively more molecule rich than those for T Tauri or Herbig Ae disks. The weak far-UV flux helps retain this complexity which is enhanced by X-ray-induced ion-molecule chemistry. N2 self shielding has only a small effect in the disk molecular layer and does not explain the higher C2H2/HCN ratios observed towards cooler stars. The models underproduce the OH/H2O column density ratios constrained in Herbig Ae disks, despite reproducing (within an order of magnitude) the absolute value for OH: the inclusion of self shielding for H2O photodissociation only increases this discrepancy. One possible explanation is the adopted disk structure. Alternatively, the "hot" H2O (T ≳ 300 K) chemistry may be more complex than assumed. The results for the atmosphere are independent of the assumed initial abundances; however, the composition of the disk midplane is sensitive to the initial main elemental reservoirs. The models show that the gas in the inner disk is generally more carbon rich than the midplane ices. This effect is most significant for disks around cooler stars. Furthermore, the atmospheric C/O ratio appears larger than it actually is when

  14. Molecular characterization of the genomic region linked with apomixis in Pennisetum/Cenchrus.

    Science.gov (United States)

    Ozias-Akins, Peggy; Akiyama, Yukio; Hanna, Wayne W

    2003-07-01

    Apomixis is defined as asexual reproduction through seeds, although this outcome can be achieved by multiple pathways. Since little is known about the molecular control of these pathways, how they might intersect is also a mystery. Two of these pathways in the grass family, diplospory and apospory, are receiving attention from molecular biologists. Apospory in Pennisetum/Cenchrus, two genera of panicoid grasses, results in the formation of four-nucleate embryo sacs that lack antipodals. Sexual reproduction frequently aborts so that the resulting seed is composed of (1) a parthenogenetically derived embryo that is genetically identical to the mother and (2) endosperm formed through pseudogamy. The transmission of apomixis is associated with the transfer of a linkage block on a single chromosome. This linkage block contains repetitive sequences as well as hemizygous, low-copy DNA sequences. Fluorescence in situ hybridization has demonstrated that these DNA regions occur on only a single chromosome, but not its homologs, in the polyploid apomicts studied. Features of the apomixis-associated region resemble those of other chromosomal segments isolated from recombination and replete with "selfish" DNAs.

  15. A far-infrared molecular and atomic line survey of the Orion KL region

    CERN Document Server

    Lerate, M R; Swinyard, B M; Goicoechea, J R; Cernicharo, J; Grundy, T W; Lim, T L; Polehampton, E T; Baluteau, J P; Viti, S; Yates, J

    2006-01-01

    We have carried out a high spectral resolution line survey towards the Orion Kleinmann-Low (KL) cluster from 44-188 um. The observations were taken with the Long Wavelength Spectrometer (LWS) in Fabry-Perot mode, on board the Infrared Space Observatory (ISO). A total of 152 lines are clearly detected and a further 34 features are present as possible detections. The spectrum is dominated by the molecular species H2O, OH and CO, along with [OI] and [CII] lines from PDR or shocked gas and [OIII], [NIII] lines from the foreground M42 HII region. Several isotopic species, as well as NH3, are also detected. HDO and H3O+ are tentatively detected for the first time in the far-infrared range towards Orion-KL. A basic analysis of the line observations is carried out, by comparing with previous measurements and published models and deriving rotational temperatures and column densities in the case of the molecular species. The complexity of the region requires more sophisticated models for the interpretation of all the l...

  16. A Catalog of Methanol Masers in Massive Star-forming Regions. III. The Molecular Outflow Sample

    CERN Document Server

    Gómez-Ruiz, A I; Araya, E D; Hofner, P; Loinard, L

    2016-01-01

    We present an interferometric survey of the 44 GHz class I methanol maser transition toward a sample of 69 sources consisting of High Mass Protostellar Object candidates and Ultracompact (UC) H II regions. We found a 38% detection rate (16 of 42) in the HMPO candidates and a 54% detection rate (13 of 24) for the regions with ionized gas. This result indicates that class I methanol maser emission is more common toward more evolved young stellar objects of our sample. Comparing with similar interferometric data sets, our observations show narrower linewidths, likely due to our higher spatial resolution. Based on a comparison between molecular outflow tracers and the maser positions, we find several cases where the masers appear to be located at the outflow interface with the surrounding core. Unlike previous surveys, we also find several cases where the masers appear to be located close to the base of the molecular outflow, although we can not discard projection effects. This and other surveys of class I methan...

  17. Molecular structural and functional characterization of STAT1 gene regulatory region in teleost Channa argus.

    Science.gov (United States)

    Jia, Weizhang; Zhou, Xiuxia

    2010-05-15

    The transcription factor STAT1 is involved in signal transduction of type I and II interferons (IFNs). However, the molecular characteristics of the STAT1 regulatory region still remain to be elucidated in teleosts. In the present study, the complete cDNA and the regulatory region of the STAT1 gene were isolated from snakehead (Channa argus). More than 2.4kb 5'-flanking region of STAT1 shares the regulatory elements of IFN-stimulated response element (ISRE) and IFN-gamma activation site (GAS). Consensus ISRE and GAS were located from -373 to -361 and -716 to -724 in the promoter region, respectively. Moreover, it is noticeable that the crucial elements of ISRE (+698 to +710) and GAS (+294 and +301) are present in the first intron of snakehead STAT1. Comparisons of six vertebrate STAT1 5'-flanking regions all present the common sequence characteristics of IFN-induced gene promoter, which include ISRE, GAS and Sp1 sites. In order to further characterize the snakehead STAT1 regulatory region, six reporter constructs of snakehead STAT1 promoter and first intron were generated to examine the specificity to human interferon-gamma (hIFN-gamma). Only those constructs containing the ISRE element showed notable reporter activity after stimulation of Hela cells with hIFN-gamma. However, sequential deletions of putative transcription factor binding sites indicated that GAS elements have little effect on the promoter and intronic activity in response to hIFN-gamma. Taken together, these results suggest that the regulatory mechanisms of IFN-signalling appear to be mediated in a similar manner in fish and mammals.

  18. Molecular characterization of monoclonal antibodies that inhibit acetylcholinesterase by targeting the peripheral site and backdoor region.

    Directory of Open Access Journals (Sweden)

    Yves Bourne

    Full Text Available The inhibition properties and target sites of monoclonal antibodies (mAbs Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE, have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis.

  19. Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia

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    Gharbi Jawhar

    2010-11-01

    Full Text Available Abstract Background In Tunisia, country of intermediate endemicity for Hepatitis B virus (HBV infection, most molecular studies on the virus have been carried out in the North of the country and little is known about other regions. The aim of this study was to determine HBV genotype and subgenotypes in Central-East Tunisia. A total of 217 HBs antigen positive patients were enrolled and determination of genotype was investigated in 130 patients with detectable HBV DNA. HBV genotyping methods were: PCR-RFLP on the pre-S region, a PCR using type-specific primers in the S region (TSP-PCR and partial sequencing in the pre-S region. Results Three genotypes (D, B and A were detected by the PCR-RFLP method and two (D and A with the TSP-PCR method, the concordance between the two methods was 93%. Sequencing and phylogenetic analysis of 32 strains, retrieved the same genotype (D and A for samples with concordant results and genotype D for samples with discordant results. The sequences of discordant genotypes had a restriction site in the pre-S gene which led to erroneous result by the PCR-RFLP method. Thus, prevalence of genotype D and A was 96% and 4%, respectively. Phylogenetic analysis showed the predominance of two subgenotypes D1 (55% and D7 (41%. Only one strain clustered with D3 subgenotype (3%. Conclusions Predominance of subgenotype D7 appears to occur in northern regions of Africa with transition to subgenotype D1 in the East of the continent. HBV genetic variability may lead to wrong results in rapid genotyping methods and sequence analysis is needed to clarify atypical results.

  20. MOLECULAR EPIDEMIOLOGY FEATURES OF HEPATITIS C VIRUS ISOLATES FROM DIFFERENT REGIONS OF THE REPUBLIC SAKHA (YAKUTIA

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    A. V. Semenov

    2015-01-01

    Full Text Available According to WHO data about 3% of population are infected by hepatitic C virus (HCV worldwide. Chronic hepatitis C is the leading cause of cirrhosis and hepatocellular carcinoma, thus it becoming one of the global public health problems. Clinical manifestations are varied and depend mainly of the virus biological properties and its interaction with the host immune system. Determination of virus genotype and subtype is important for a better understanding of the epidemiological and virological features of the disease. The prevalence genotypes hepatitis C virus is varies in different geographical regions of the world. The data about HCV genotypes distribution in some Russian Federation regions are very limited, especially about HCV genotypes prevalence in Siberia, Far East and some rural regions. One of such regions is Yakutia. In our study we identified genetic variants of HCV in chronic hepatitis C patients with moderate and high viral load from Yakutia by direct sequencing of HCV RNA NS5B region. Based on phylogenetic analysis we found the prevalent genotype 1 (88.3%, than genotype 2 (6.7% and 3 (3.2% among HCV patients with moderate and high viral load. Our results on the prevalence of subtype 1b are consistent with the data on the connection between this subtype with high levels of viremia, greater duration and severity of liver disease, as well as the development of chronic hepatits C in patients infected by HCV subtype 1b, compared with those infected with other subtypes of hepatitis virus C. The similarity of some Yakutian isolates with isolates from the United States, Brazil and Ireland was found. We discuss HCV subtype 2a isolates identified origin from isolates found in China. First in the territory of the Russian Federation HCV subtype 3g was identified, presumably imported from South Asia. Interconnected use of molecular, virological, demographic and epidemiological methods and information to monitor the infections will contribute to

  1. Disruption of Molecular Clouds by Expansion of Dusty H II Regions

    CERN Document Server

    Kim, Jeong-Gyu; Ostriker, Eve C

    2016-01-01

    Dynamical expansion of H II regions around star clusters plays a key role in dispersing the surrounding dense gas and therefore in limiting the efficiency of star formation in molecular clouds. We use a semi-analytic method and numerical simulations to explore expansion of spherical dusty H II regions and surrounding neutral shells and the resulting cloud disruption. Our model for shell expansion adopts the static solutions of Draine (2011) for dusty H II regions and considers the contact outward forces on the shell due to radiation and thermal pressures as well as the inward gravity from the central star and the shell itself. We show that the internal structure we adopt and the shell evolution from the semi-analytic approach are in good agreement with the results of numerical simulations. Strong radiation pressure in the interior controls the shell expansion indirectly by enhancing the density and pressure at the ionization front. We calculate the minimum star formation efficiency $\\epsilon_{min}$ required f...

  2. THE INNER GALACTIC STRUCTURE TRACED BY MOLECULAR CLOUDS ASSOCIATED WITH ULTRA-COMPACT HII REGIONS

    Directory of Open Access Journals (Sweden)

    A. Luna

    2008-01-01

    Full Text Available Estamos sometiendo a pruebas un método para determinar las distancias para una muestra de regiones HII ultracompactas con colores en IRAS y con detección de CS(J=2-1. La ambigüedad de las distancias cinem aticas se resuelve mediante simulaciones Monte Carlo. Utilizando nubes moleculares sintéticas simulamos las distribuciones longitud heliocéntrica-radio (l-R sobre el plano galáctico, y las proyecciones asociadas longitudvelocidad LSR (l-VLSR. Se escoge la mejor distribución galáctica por comparación con los mapas observados de CO. Se presentan resultados preliminares para el IV cuadrante galáctico.

  3. Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.

    Science.gov (United States)

    Albuixech-Crespo, Beatriz; López-Blanch, Laura; Burguera, Demian; Maeso, Ignacio; Sánchez-Arrones, Luisa; Moreno-Bravo, Juan Antonio; Somorjai, Ildiko; Pascual-Anaya, Juan; Puelles, Eduardo; Bovolenta, Paola; Garcia-Fernàndez, Jordi; Puelles, Luis; Irimia, Manuel; Ferran, José Luis

    2017-04-01

    All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice.

  4. Molecular Epidemiology and Characterization of Genotypes of Acinetobacter baumannii Isolates from Regions of South China.

    Science.gov (United States)

    Ying, Jun; Lu, Junwan; Zong, Li; Li, Ailing; Pan, Ruowang; Cheng, Cong; Li, Kunpeng; Chen, Liqiang; Ying, Jianchao; Tou, Huifen; Zhu, Chuanxin; Xu, Teng; Yi, Huiguang; Li, Jinsong; Ni, Liyan; Xu, Zuyuan; Bao, Qiyu; Li, Peizhen

    2016-05-20

    The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistant strains (resistant to more than 7 drugs) were identified, representing 36.7% of all isolates. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for molecular subtyping. According to the PFGE results (with a cutoff of 70% similarity for the DNA electrophoretic bands), 146 strains were subdivided into 15 clusters, with cluster A being the largest (33.6%, distributed in all districts except Jiaxing). Cluster B was also widespread and included 14.4% of all strains. In addition, MLST results revealed 11 sequence types (ST), with ST208 being the most prevalent, followed by ST191 and ST729. Furthermore, 4 novel alleles and 6 novel STs were identified. Our results showed that multi-drug-resistant A. baumannii in South China shares the origin with other widespread strains in other countries. The nosocomial infections caused by A. baumannii have been severe in South China. Continuous monitoring and judicious antibiotic use are required.

  5. The molecular environment of the massive star forming region NGC 2024: Multi CO transition analysis

    CERN Document Server

    Emprechtinger, M; Simon, R; Wieching, G; Volgenau, N H; Bielau, F; Graf, U U; Guesten, R; Honingh, C E; Jacobs, K; Rabanus, D; Stutzki, J; Wyrowski, F

    2009-01-01

    NGC 2024, a sites of massive star formation, have complex internal structures caused by cal heating by young stars, outflows, and stellar winds. These complex cloud structures lead to intricate emission line shapes. The goal of this paper is to show that the complex line shapes of 12 CO lines in NGC 2024 can be explained consistently with a model, whose temperature and velocity structure are based on the well-established scenario of a PDR and the Blister model. We present velocity-resolved spectra of seven CO lines ranging from J=3 to J=13, and we combined these data with CO high-frequency data from the ISO satellite. We find that the bulk of the molecular cloud associated with NGC 2024 consists of warm (75 K) and dense (9e5 cm-3) gas. An additional hot (~ 300 K) component, located at the interface of the HII region and the molecular cloud, is needed to explain the emission of the high-J CO lines. Deep absorption notches indicate that very cold material (20 K) exists in front of the warm material, too. A temp...

  6. LABOCA observations of giant molecular clouds in the south west region of the Small Magellanic Cloud

    CERN Document Server

    Bot, Caroline; Boulanger, Francois; Albrecht, Marcus; Leroy, Adam; Bolatto, Alberto D; Bertoldi, Frank; Gordon, Karl; Engelbracht, Chad; Block, Miwa; Misselt, Karl

    2010-01-01

    The amount of molecular gas is a key for understanding the future star formation in a galaxy. Because H2 is difficult to observe directly in dense and cold clouds, tracers like CO are used. However, at low metallicities especially, CO only traces the shielded interiors of the clouds. mm dust emission can be used as a tracer to unveil the total dense gas masses. The comparison of masses deduced from the continuum SIMBA 1.2 mm emission and virial masses in a sample of giant molecular clouds (GMCs), in the SW region of the Small Magellanic Cloud (SMC), showed a discrepancy that is in need of an explanation. This study aims at better assessing possible uncertainties on the dust emission observed in the sample of GMCs from the SMC and focuses on the densest parts of the GMCs where CO is detected. New observations were obtained with the LABOCA camera on the APEX telescope. All GMCs previously observed in CO are detected and their emission at 870microns is compared to ancillary data. The different contributions to t...

  7. Regional and accelerated molecular evolution in group I snake venom gland phospholipase A2 isozymes.

    Science.gov (United States)

    Chuman, Y; Nobuhisa, I; Ogawa, T; Deshimaru, M; Chijiwa, T; Tan, N H; Fukumaki, Y; Shimohigashi, Y; Ducancel, F; Boulain, J C; Ménez, A; Ohno, M

    2000-03-01

    In accordance with detection of a few phospholipase A2 (PLA2) isozyme genes by Southern blot analysis, only two cDNAs, named NnkPLA-I , and NnkPLA-II, encoding group I PLA2s, NnkPLA-I and NnkPLA-II, respectively, were isolated from the venom gland cDNA library of Elapinae Naja naja kaouthia of Malaysia. NnkPLA-I and NnkPLA-II showed four amino acid substitutions, all of which were brought about by single nucleotide substitution. No existence of clones encoding CM-II and CM-III, PLA2 isozymes which had been isolated from the venom of N. naja kaouthia of Thailand, in Malaysian N. naja kaouthia venom gland cDNA library was verified by dot blot hybridization analysis with particular probes. NnkPLA-I and NnkPLA-II differed from CM-II and CM-III with four and two amino acid substitutions, respectively, suggesting that their molecular evolution is regional. The comparison of NnkPLA-I, NnkPLA-II and cDNAs encoding other group I snake venom gland PLA2s indicated that the 5'- and 3'-untranslated regions are more conserved than the mature protein-coding region and that the number of nucleotide substitutions per nonsynonymous site is almost equal to that per synonymous site in the protein-coding region, suggesting that accelerated evolution has occurred in group I venom gland PLA2s possibly to acquire new physiological functions.

  8. New Young Brown Dwarfs in the Orion Molecular Cloud 2/3 Region

    CERN Document Server

    Peterson, Dawn E; Luhman, K L; Pipher, J L; Stauffer, J R; Navascues, D Barrado y; Wilson, J C; Skrutskie, M F; Nelson, M J; Smith, J D

    2008-01-01

    Forty new low mass members with spectral types ranging from M4-M9 have been confirmed in the Orion Molecular Cloud 2/3 region. Through deep, I, z', J, H, K photometry of a 20' x 20' field in OMC 2/3, we selected brown dwarf candidates for follow-up spectroscopy. Low resolution far-red and near-infrared spectra were obtained for the candidates, and 19 young brown dwarfs in the OMC 2/3 region are confirmed. They exhibit spectral types of M6.5-M9, corresponding to approximate masses of 0.075-0.015 M_solar using the evolutionary models of Baraffe et al. (1998). At least one of these bona fide young brown dwarfs has strong Halpha emission, indicating that it is actively accreting. In addition, we confirm 21 new low mass members with spectral types of M4-M6, corresponding to approximate masses of 0.35-0.10 M_solar in OMC 2/3. By comparing pre-main sequence tracks to the positions of the members in the H-R diagram, we find that most of the brown dwarfs are less than 1 Myr, but find a number of low mass stars with in...

  9. An organelle-exclusion envelope assists mitosis and underlies distinct molecular crowding in the spindle region.

    Science.gov (United States)

    Schweizer, Nina; Pawar, Nisha; Weiss, Matthias; Maiato, Helder

    2015-08-31

    The mitotic spindle is a microtubular assembly required for chromosome segregation during mitosis. Additionally, a spindle matrix has long been proposed to assist this process, but its nature has remained elusive. By combining live-cell imaging with laser microsurgery, fluorescence recovery after photobleaching, and fluorescence correlation spectroscopy in Drosophila melanogaster S2 cells, we uncovered a microtubule-independent mechanism that underlies the accumulation of molecules in the spindle region. This mechanism relies on a membranous system surrounding the mitotic spindle that defines an organelle-exclusion zone that is conserved in human cells. Supported by mathematical modeling, we demonstrate that organelle exclusion by a membrane system causes spatio-temporal differences in molecular crowding states that are sufficient to drive accumulation of mitotic regulators, such as Mad2 and Megator/Tpr, as well as soluble tubulin, in the spindle region. This membranous "spindle envelope" confined spindle assembly, and its mechanical disruption compromised faithful chromosome segregation. Thus, cytoplasmic compartmentalization persists during early mitosis to promote spindle assembly and function.

  10. Two physical regimes for the Giant HII Regions and Giant Molecular Clouds in the Antennae Galaxies

    CERN Document Server

    Zaragoza-Cardiel, Javier; Beckman, John E; García-Lorenzo, Begoña; Erroz-Ferrer, Santiago; Gutiérrez, Leonel

    2014-01-01

    We have combined observations of the Antennae galaxies from the radio interferometer ALMA (Atacama Large Millimetre/submillimetre Array) and from the optical interferometer GH$\\alpha$FaS (Galaxy Halpha Fabry-Perot System). The two sets of observations have comparable angular and spectral resolutions, enabling us to identify 142 giant molecular clouds and 303 HII regions. We have measured, and compare, their basic physical properties (radius, velocity dispersion, luminosity). For the HII regions we find two physical regimes, one for masses $>10^{5.4} \\mathrm{M_{\\odot}}$ of ionized gas, which the gas density increases with gas mass, the other for masses $<10^{5.4} \\mathrm{M_{\\odot}}$ of ionized gas where the gas density decreases with gas mass. For the GMCs we find, in contrast to previous studies in other galaxies over a generally lower mass range of clouds, that the gas density increases with the total gas mass, hinting at two regimes for these clouds if we consider both sources of data. We also find that ...

  11. H2 formation on PAHs in photodissociation regions: a high-temperature pathway to molecular hydrogen

    CERN Document Server

    Boschman, Leon; Spaans, Marco; Hoekstra, Ronnie; Schlathölter, Thomas

    2015-01-01

    Molecular hydrogen is the most abundant molecule in the Universe. It is thought that a large portion of H2 forms by association of hydrogen atoms to polycyclic aromatic hydrocarbons (PAHs). We model the influence of PAHs on total H2 formation rates in photodissociation regions (PDRs) and assess the effect of these formation rates on the total cloud structure. We set up a chemical kinetic model at steady state in a PDR environment and included adiative transfer to calculate the chemistry at different depths in the PDR. This model includes known dust grain chemistry for the formation of H2 and a H2 formation mechanism on PAHs. Since H2 formation on PAHs is impeded by thermal barriers, this pathway is only efficient at higher temperatures (T > 200 K). At these temperatures the conventional route of H2 formation via H atoms physisorbed on dust grains is no longer feasible, so the PAH mechanism enlarges the region where H2 formation is possible. We find that PAHs have a significant influence on the structure of PD...

  12. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    Science.gov (United States)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  13. A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins

    CERN Document Server

    Zhang, Jiapu

    2014-01-01

    Prion diseases are invariably fatal neurodegenerative diseases that affect humans and animals. Unlike most other amyloid forming neurodegenerative diseases, these can be highly infectious. Prion diseases occur in a variety of species. They include the fatal human neurodegenerative diseases Creutzfeldt-Jakob Disease (CJD), Fatal Familial Insomnia (FFI), Gerstmann-Straussler-Scheinker syndrome (GSS), Kuru, the bovine spongiform encephalopathy (BSE or 'mad-cow' disease) in cattle, the chronic wasting disease (CWD) in deer and elk, and scrapie in sheep and goats, etc. Transmission across the species barrier to humans, especially in the case of BSE in Europe, CWD in North America, and variant CJDs (vCJDs) in young people of UK, is a major public health concern. Fortunately, scientists reported that the (central) hydrophobic region of prion proteins (PrP) controls the formation of diseased prions. This article gives a detailed survey on PrP hydrophobic region and does molecular dynamics studies of human PrP(110-136...

  14. MOLECULAR PHYLOGENETIC ANALYSIS OF MONASCUS FUNGI BASED ON INTERNAL TRANSCRIBED SPACER REGION

    Directory of Open Access Journals (Sweden)

    Y. KIKUCHI

    2005-01-01

    Full Text Available A molecular analysis of internal transcribed spacer region has been carried out to reveal the relationship among 16 strains of Monascus spp. A primer set comprised primer ITS1 and ITS4 was used to amplify this region in which they were cloned and scqucnccd. We also compared the sequence result with M. purpureus AF458473, M.ruber AF458470, M. kaoliang AF451859, M. araneous AF458471 and M. pilosus AF451856 and one outgroup species Thermoascus crustaceus U18353. The result showed that 16 Monascus spp. were divided into two large clades while M. ruber AF458470 was basically separated from all those Monascus. One of the two large clades included the seven M. purpureus strains, M. purpureus AF458473, M. araneosus AF458471 and M. kaoliang AF451859. Another large cladc included the six Monascus sp. strains which typically have whitish colonies, the three M. ruber strains and M.pilosus AF451856. However, even outstanding morphological differences possessed by several white Monascus and one whitish M. purpureus strain, all Monascus strains were suggested to be very closely related with similarity >99% almost 100%. Although this ITS analysis could not discriminate cultural and morphological differentiation of Monascus strains studied, yet there is still little genetic va riation within these strains.

  15. Atmospheric molecular hydrogen (H2) at the Shangdianzi regional background station in China

    Science.gov (United States)

    Luan, Tian; Fang, Shuangxi; Yao, Bo; Wang, Hongyang; Dong, Fan; Shi, Qingfeng; Zhou, Liyan; Zhou, Huaigang

    2016-11-01

    Atmospheric molecular hydrogen (H2) mole fractions have been continuously measured at the Shangdianzi regional station in China. In this study, we present the atmospheric H2 time series from January 2015 to April 2016, and investigate the diurnal and seasonal cycles, and the impact of meteorological factors on the observed values. Atmospheric H2 mole fractions at Shangdianzi vary from a minimum of 381 ppb (parts per billion, 10-9 dry air mole fraction) to a maximum of 1535 ppb, with a median of 510 ppb and a mean (± standard deviation) of 555 ± 113 ppb during the observation period. The results indicate that H2 mole fractions at Shangdianzi are frequently influenced by local sources and sinks. Regionally representative conditions account for 44.7% of the total records with a mean mole fraction of 488 ± 20 ppb. The highest regionally representative H2 mole fraction is observed in July, while the lowest is observed in October. Peak-to-trough amplitude in the seasonal cycle is 63 ± 3 ppb. H2 mole fractions show nighttime depletion in all seasons, with the lowest values in the morning (7:00-10:00 local time). The H2 mole fractions are also influenced by local surface wind direction at Shangdianzi. Winds from NW-NNW-N-NNE-NE-ENE-E directions are always associated with negative contribution to atmospheric H2 loading, whereas winds from SSW-SW-WSW-W directions generally enhance the H2 values. The results of trajectory clustering analysis demonstrate that air masses from a southerly direction induce high H2 mole fractions. Conversely, mean H2 mole fractions are low when air masses are from the north, northwest, and east directions.

  16. Molecular cloning of rhamnose-binding lectin gene and its promoter region from snakehead Channa argus.

    Science.gov (United States)

    Jia, W Z; Shang, N; Guo, Q L

    2010-09-01

    Lectins are sugar-binding proteins that mediate pathogen recognition and cell-cell interactions. A rhamnose-binding lectin (RBL) gene and its promoter region have been cloned and characterized from snakehead Channa argus. From the transcription initiation site, snakehead rhamnose-binding lectin (SHL) gene extends 2,382 bp to the end of the 3' untranslated region (UTR), and contains nine exons and eight introns. The open reading frame (ORF) of the SHL transcript has 675 bp which encodes 224 amino acids. The molecular structure of SHL is composed of two tandem repeat carbohydrate recognition domains (CRD) with 35% internal identity. Analysis of the gene organization of SHL indicates that the ancestral gene of RBL may diverge and evolve by exon shuffling and gene duplication, producing new forms to play their own roles in various organisms. The characteristics of SHL gene 5' flanking region are the presence of consensus nuclear factor of interleukin 6 (NF-IL6) and IFN-gamma activation (GAS) sites. The results provide indirect evidence that up-regulation of SHL expression may be induced in response to inflammatory stimuli, such as lipopolysaccharide (LPS), interleukin 6 (IL-6), and interferon gamma (IFN-gamma). The transcript of SHL mRNA was expressed in the head kidney, posterior kidney, spleen, liver, intestine, heart, muscle, and ovary. No tissue-specific expressive pattern is different from reported STLs, WCLs, and PFLs, suggesting that different types of RBLs exist in species-specific fish that have evolved and adapted to their surroundings.

  17. Molecular epidemiology of enterovirus 71 infection in the central region of Taiwan from 2002 to 2012.

    Directory of Open Access Journals (Sweden)

    Wen-Hao Wu

    Full Text Available Enterovirus 71 (EV71, a causative agent of hand, foot, and mouth disease can be classified into three genotypes and many subtypes. The objectives of this study were to conduct a molecular epidemiological study of EV71 in the central region of Taiwan from 2002-2012 and to test the hypothesis that whether the alternative appearance of different EV71 subtypes in Taiwan is due to transmission from neighboring countries or from re-emergence of pre-existing local strains. We selected 174 EV71 isolates and used reverse transcription-polymerase chain reaction to amplify their VP1 region for DNA sequencing. Phylogenetic analyses were conducted using Neighbor-Joining, Maximum Likelihood and Bayesian methods. We found that the major subtypes of EV71 in Taiwan were B4 for 2002 epidemic, C4 for 2004-2005 epidemic, B5 for 2008-2009 epidemic, C4 for 2010 epidemic and B5 for 2011-2012 epidemic. Phylogenetic analysis demonstrated that the 2002 and 2008 epidemics were associated with EV71 from Malaysia and Singapore; while both 2010 and 2011-2012 epidemics originated from different regions of mainland China including Shanghai, Henan, Xiamen and Gong-Dong. Furthermore, minor strains have been identified in each epidemic and some of them were correlated with the subsequent outbreaks. Therefore, the EV71 infection in Taiwan may originate from pre-existing minor strains or from other regions in Asia including mainland China. In addition, 101 EV71 isolates were selected for the detection of new recombinant strains using the nucleotide sequences spanning the VP1-2A-2B region. No new recombinant strain was found. Analysis of clinical manifestations showed that patients infected with C4 had significantly higher rates of pharyngeal vesicles or ulcers than patients infected with B5. This is the first study demonstrating that different EV 71 genotypes may have different clinical manifestations and the association of EV71 infections between Taiwan and mainland China.

  18. Molecular and phenotypic characterisation of Phaeomoniella chlamydospora isolates from the demarcated wine region of Dão (Portugal

    Directory of Open Access Journals (Sweden)

    Jorge SOFIA

    2015-09-01

    Full Text Available Sixty-eight isolates of Phaeomoniella chlamydospora obtained from symptomatic esca and Petri disease grapevines, obtained mostly within the Portuguese Dão appellation, were investigated regarding their phenotypic and molecular diversity, in order to determine intraspecific variability and population structure. Phenotypic features such as texture, colour, growing margin zonation, hyphal morphology and diameter growth were evaluated. Molecular characterization was performed through the sequencing of the total ITS region and molecular analyses were used to infer phylogenetic relationships, using the Maximum Likelihood approach. Isolates were divided into two groups, by both phenotypic and molecular analysis, but no clear correspondence was found between the two approaches. Nevertheless, both phenotypic and molecular analysis revealed a strong homogeneity among all isolates, despite their geographical origin, year of isolation and scion/rootstock combination, therefore supporting the clonal reproduction strategy described for this species.

  19. The molecular environment of the pillar-like features in the H ii region G46.5-0.2

    Science.gov (United States)

    Paron, S.; Celis Peña, M.; Ortega, M. E.; Fariña, C.; Petriella, A.; Rubio, M.; Ashley, R. P.

    2017-10-01

    At the interface of H ii regions and molecular gas, peculiar structures appear, some of them with pillar-like shapes. Understanding their origin is important for characterizing triggered star formation and the impact of massive stars on the interstellar medium. In order to study the molecular environment and influence of radiation on two pillar-like features related to the H ii region G46.5-0.2, we performed molecular line observations with the Atacama Submillimeter Telescope Experiment and spectroscopic optical observations with the Isaac Newton Telescope. From the optical observations, we identified the star that is exciting the H ii region as spectral type O4-6. The molecular data allowed us to study the structure of the pillars and an HCO+ cloud lying between them. In this HCO+ cloud, which has no well-defined 12CO counterpart, we found direct evidence of star formation: two molecular outflows and two associated near-IR nebulosities. The outflow axis orientation is perpendicular to the direction of the radiation flow from the H ii region. Several Class I sources are also embedded in this HCO+ cloud, showing that it is usual that young stellar objects (YSOs) form large associations occupying a cavity bounded by pillars. On the other hand, it was confirmed that the radiation-driven implosion (RDI) process is not occurring in one of the pillar tips.

  20. Hemoglobinopathy: molecular epidemiological characteristics and health effects on Hakka people in the Meizhou region, southern China.

    Directory of Open Access Journals (Sweden)

    Min Lin

    Full Text Available BACKGROUND: Hemoglobinopathies are the most common inherited diseases in southern China. However, there have been only a few epidemiological studies of hemoglobinopathies in Guangdong province. MATERIALS AND METHODS: Peripheral blood samples were collected from 15299 "healthy" unrelated subjects of dominantly ethnic Hakka in the Meizhou region, on which hemoglobin electrophoresis and routine blood tests were performed. Suspected cases with hemoglobin variants and hereditary persistence of fetal hemoglobin (HPFH were further characterized by PCR, DNA sequencing, reverse dot blot (RDB or multiplex ligation-dependent probe amplification (MLPA. In addition, 1743 samples were randomly selected from the 15299 subjects for thalassemia screening, and suspected thalassemia carriers were identified by PCR and RDB. RESULTS: The gene frequency of hemoglobin variants was 0.477% (73/15299. The five main subgroups of the ten hemoglobin variants were Hb E, Hb G-Chinese, Hb Q-Tahiland, Hb New York and Hb J-Bangkok. 277 cases (15.89%, 277/1743 of suspected thalassemia carriers with microcytosis (MCV<82 fl were found by thalassemia screening, and were tested by a RDB gene chip to reveal a total of 196 mutant chromosomes: including 124 α-thalassemia mutant chromosomes and 72 β-thalassemia mutant chromosomes. These results give a heterozygote frequency of 11.24% for common α and β thalassemia in the Hakka population in the Meizhou region. 3 cases of HPFH/δβ-thalassemia were found, including 2 cases of Vietnamese HPFH (FPFH-7 and a rare Belgian( Gγ((Aγδβ⁰-thalassemia identified in Chinese. CONCLUSIONS: Our results provide a detailed prevalence and molecular characterization of hemoglobinopathies in Hakka people of the Meizhou region. The estimated numbers of pregnancies each year in the Meizhou region, in which the fetus would be at risk for β thalassemia major or intermedia, Bart's hydrops fetalis, and Hb H disease, are 25 (95% CI, 15 to 38, 40 (95% CI

  1. Physical characteristics of G331.5-0.1: The luminous central region of a Giant Molecular Cloud

    CERN Document Server

    Merello, Manuel; Garay, Guido; Nyman, Lars-Ake; Evans, Neal J; Walmsley, C Malcolm

    2013-01-01

    We report molecular line and dust continuum observations toward the high-mass star forming region G331.5-0.1, one of the most luminous regions of massive star-formation in the Milky Way, located at the tangent region of the Norma spiral arm, at a distance of 7.5 kpc. Molecular emission was mapped toward the G331.5-0.1 GMC in the CO (J=1-0) and C18O (J=1-0) lines with NANTEN, while its central region was mapped in CS (J=2-1 and J=5-4) with SEST, and in CS (J=7-6) and 13CO (J=3-2) with ASTE. Continuum emission mapped at 1.2 mm with SIMBA and at 0.87 mm with LABOCA reveal the presence of six compact and luminous dust clumps, making this source one of the most densely populated central regions of a GMC in the Galaxy. The dust clumps are associated with molecular gas and they have the following average properties: size of 1.6 pc, mass of 3.2x10^3 Msun, molecular hydrogen density of 3.7x10^4 cm^{-3}, dust temperature of 32 K, and integrated luminosity of 5.7x10^5 Lsun, consistent with values found toward other mass...

  2. Molecular analysis of fungal populations in patients with oral candidiasis using internal transcribed spacer region.

    Science.gov (United States)

    Ieda, Shinsuke; Moriyama, Masafumi; Takeshita, Toru; Takashita, Toru; Maehara, Takashi; Imabayashi, Yumi; Shinozaki, Shoichi; Tanaka, Akihiko; Hayashida, Jun-Nosuke; Furukawa, Sachiko; Ohta, Miho; Yamashita, Yoshihisa; Nakamura, Seiji

    2014-01-01

    Oral candidiasis is closely associated with changes in the oral fungal flora and is caused primarily by Candida albicans. Conventional methods of fungal culture are time-consuming and not always conclusive. However, molecular genetic analysis of internal transcribed spacer (ITS) regions of fungal rRNA is rapid, reproducible and simple to perform. In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions. Fifty-two patients with pseudomembranous oral candidiasis (POC) and 30 healthy controls were included in the study. Fungal DNA from oral rinse was examined for fungal species diversity by LH-PCR. Fungal populations were quantified by real-time PCR and previously-unidentified signals were confirmed by nucleotide sequencing. Relationships between the oral fungal flora and treatment-resistant factors were also examined. POC patients showed significantly more fungal species and a greater density of fungi than control individuals. Sixteen fungi were newly identified. The fungal populations from both groups were composed predominantly of C. albicans, though the ratio of C. dubliniensis was significantly higher in POC patients than in controls. The diversity and density of fungi were significantly reduced after treatment. Furthermore, fungal diversity and the proportion of C. dubliniensis were positively correlated with treatment duration. These results suggest that C. dubliniensis and high fungal flora diversity might be involved in the pathogenesis of oral candidiasis. We therefore conclude that LH-PCR is a useful technique for diagnosing and assessing the severity of oral candidal infection.

  3. Evolutionary Status of Brightest and Youngest Source in the Orion Molecular Cloud-3 Region

    CERN Document Server

    Takahashi, Satoko; Tang, Ya-Wen; Kawabe, Ryohei; Saito, Masao

    2009-01-01

    The brightest continuum source in the Orion Molecular Cloud-3 region (OMC-3), MMS 6, was observed with the Very Large Array (VLA), the Nobeyama Millimeter Array (NMA), and the Submillimeter Array (SMA). Our data were supplemented by near- to mid-infrared archival data taken by Spitzer Space Telescope. The compact continuum source, MMS 6-main, was detected with an H_2 mass of 3.0 Msun with a size of 510 AU. Despite its compact and well condensed appearance, neither clear CO outflow, radio jet, nor infrared sources (at a wave-length shorter than 8 um) were detected at MMS 6-main even with the present high-spatial resolution and high-sensitivity observations. The derived H_2 column density, 2.6x10^25 cm^-2, corresponds to a visual extinction of A_v~15000 mag., and the derived number density is at least two orders of magnitude higher than for the other OMC-2/3 continuum sources. The volume density profile of the source was estimated to have a power-law index of 2 or steeper down to a radius of ~450 AU. The time s...

  4. Examining molecular clouds in the Galactic Centre region using X-ray reflection spectra simulations

    Science.gov (United States)

    Walls, M.; Chernyakova, M.; Terrier, R.; Goldwurm, A.

    2016-12-01

    In the centre of our Galaxy lies a supermassive black hole, identified with the radio source Sagittarius A⋆. This black hole has an estimated mass of around 4 million solar masses. Although Sagittarius A⋆ is quite dim in terms of total radiated energy, having a luminosity that is a factor of 1010 lower than its Eddington luminosity, there is now compelling evidence that this source was far brighter in the past. Evidence derived from the detection of reflected X-ray emission from the giant molecular clouds in the Galactic Centre region. However, the interpretation of the reflected emission spectra cannot be done correctly without detailed modelling of the reflection process. Attempts to do so can lead to an incorrect interpretation of the data. In this paper, we present the results of a Monte Carlo simulation code we developed in order to fully model the complex processes involved in the emerging reflection spectra. The simulated spectra can be compared to real data in order to derive model parameters and constrain the past activity of the black hole. In particular, we apply our code to observations of Sagittarius B2, in order to constrain the position and density of the cloud and the incident luminosity of the central source. The results of the code have been adapted to be used in XSPEC by a large community of astronomers.

  5. Molecular fingerprinting of lacustrian cyanobacterial communities: regional patterns in summer diversity.

    Science.gov (United States)

    Touzet, Nicolas; McCarthy, David; Fleming, Gerard T A

    2013-12-01

    The assessment of lacustrian water quality is necessary to comply with environmental regulations. At the regional scale, difficulties reside in the selection of representative lakes. Given the risks towards water quality associated with phytoplankton blooms, a mesoscale survey was carried out in Irish lakes to identify patterns in the distribution and diversity of planktonic cyanobacteria. A stratified sampling strategy was carried out via geographic information systems (GIS) analysis of river catchment attributes due to the range of hydrogeomorphological features and the high number of lakes within the study area. 16S rRNA gene denaturing gradient gel electrophoresis analysis showed variation between the cyanobacterial communities sampled, with lower occurrence of cyanobacteria in August concomitant to increased wind and precipitation regimes. Multivariate analysis delineated three ecoregions based on land cover typology and revealed significant patterns in the distribution of cyanobacterial diversity. A majority of filamentous cyanobacteria genotypes occurred in larger lakes contained river catchments with substantial forest cover. In contrast, higher diversity of spherical cyanobacteria genotypes was observed in lakes of lesser trophic state. In the context of aquatic resource management, the combined use of GIS-based sampling strategy and molecular methods offers promising prospects for assessing microbial community structure at varying scales of space and time.

  6. Excitation of the molecular gas in the nuclear region of M82

    CERN Document Server

    Loenen, A F; Güsten, R; Meijerink, R; Israel, F P; Requena-Torres, M A; García-Burillo, S; Harris, A I; Klein, T; Kramer, C; Lord, S; Martín-Pintado, J; Röllig, M; Stutzki, J; Szczerba, R; Weiß, A; Philipp-May, S; Yorke, H; Caux, E; Delforge, B; Helmich, F; Lorenzani, A; Morris, P; Philips, T G; Risacher, C; Tielens, A G G M

    2010-01-01

    We present high resolution HIFI spectroscopy of the nucleus of the archetypical starburst galaxy M82. Six 12CO lines, 2 13CO lines and 4 fine-structure lines are detected. Besides showing the effects of the overall velocity structure of the nuclear region, the line profiles also indicate the presence of multiple components with different optical depths, temperatures and densities in the observing beam. The data have been interpreted using a grid of PDR models. It is found that the majority of the molecular gas is in low density (n=10^3.5 cm^-3) clouds, with column densities of N_H=10^21.5 cm^-2 and a relatively low UV radiation field (GO = 10^2). The remaining gas is predominantly found in clouds with higher densities (n=10^5 cm^-3) and radiation fields (GO = 10^2.75), but somewhat lower column densities (N_H=10^21.2 cm^-2). The highest J CO lines are dominated by a small (1% relative surface filling) component, with an even higher density (n=10^6 cm^-3) and UV field (GO = 10^3.25). These results show the str...

  7. Examining molecular clouds in the Galactic Centre region using X-ray reflection spectra simulations

    CERN Document Server

    Walls, Michael; Terrier, Regis; Goldwurm, Andrea

    2016-01-01

    In the centre of our galaxy lies a super-massive black hole, identified with the radio source Sagittarius A*. This black hole has an estimated mass of around 4 million solar masses. Although Sagittarius A* is quite dim in terms of total radiated energy, having a luminosity that is a factor of $10^{10}$ lower than its Eddington luminosity, there is now compelling evidence that this source was far brighter in the past. Evidence derived from the detection of reflected X-ray emission from the giant molecular clouds in the galactic centre region. However, the interpretation of the reflected emission spectra cannot be done correctly without detailed modelling of the reflection process. Attempts to do so can lead to an incorrect interpretation of the data. In this paper we present the results of a Monte Carlo simulation code we developed in order to fully model the complex processes involved in the emerging reflection spectra. The simulated spectra can be compared to real data in order to derive model parameters and...

  8. Using Homology Modeling, Molecular Dynamics and Molecular Docking Techniques to Identify Inhibitor Binding Regions of Somatostatin Receptor 1

    Institute of Scientific and Technical Information of China (English)

    LAN Hai-nan; WANG Yue-xi; ZHENG Ming-zhu; HAN Wei-wei; ZHENG Xin

    2013-01-01

    The G protein coupled receptor(GPCR),one of the members in the superfamily,which consists of thousands of integral membrane proteins,exerts a wide variety of physiological functions and responses to a large portion of the drug targets.The 3D structure of somatostatin receptor 1(SSTR1) was modeled and refined by means of homology modeling and molecular dynamics simulation.This model was assessed by Verify-3D and Vadar,which confirmed the reliability of the refined model.The interaction between the inhibitor cysteamine,somatostatin(SST) and SSTRI was investigated by a molecular docking program,Affinity.The binding module not only showed the crucial residues involved in the interaction,but also provided important information about the interaction between SSTR1 on the one hand and ligands on the other,which might be the significant evidence for the structure-based design.

  9. Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation.

    Directory of Open Access Journals (Sweden)

    Navin Elango

    2008-02-01

    Full Text Available Transitions at CpG dinucleotides, referred to as "CpG substitutions", are a major mutational input into vertebrate genomes and a leading cause of human genetic disease. The prevalence of CpG substitutions is due to their mutational origin, which is dependent on DNA methylation. In comparison, other single nucleotide substitutions (for example those occurring at GpC dinucleotides mainly arise from errors during DNA replication. Here we analyzed high quality BAC-based data from human, chimpanzee, and baboon to investigate regional variation of CpG substitution rates. We show that CpG substitutions occur approximately 15 times more frequently than other single nucleotide substitutions in primate genomes, and that they exhibit substantial regional variation. Patterns of CpG rate variation are consistent with differences in methylation level and susceptibility to subsequent deamination. In particular, we propose a "distance-decaying" hypothesis, positing that due to the molecular mechanism of a CpG substitution, rates are correlated with the stability of double-stranded DNA surrounding each CpG dinucleotide, and the effect of local DNA stability may decrease with distance from the CpG dinucleotide.Consistent with our "distance-decaying" hypothesis, rates of CpG substitution are strongly (negatively correlated with regional G+C content. The influence of G+C content decays as the distance from the target CpG site increases. We estimate that the influence of local G+C content extends up to 1,500 approximately 2,000 bps centered on each CpG site. We also show that the distance-decaying relationship persisted when we controlled for the effect of long-range homogeneity of nucleotide composition. GpC sites, in contrast, do not exhibit such "distance-decaying" relationship. Our results highlight an example of the distinctive properties of methylation-dependent substitutions versus substitutions mostly arising from errors during DNA replication. Furthermore

  10. Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics

    NARCIS (Netherlands)

    Pirie, M.D.; Vargas, M.P.B.; Botermans, M.; Bakker, F.T.; Chatrou, L.W.

    2007-01-01

    The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses c

  11. Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics

    NARCIS (Netherlands)

    Pirie, M.D.; Vargas, M.P.B.; Botermans, M.; Bakker, F.T.; Chatrou, L.W.

    2007-01-01

    The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses

  12. Molecular Gas and Dust in the Massive Star Forming Region S 233 IR

    Institute of Scientific and Technical Information of China (English)

    Rui-Qing Mao; Qin Zeng

    2004-01-01

    The massive star forming region S 233 IR is observed in the molecular lines CO J = 2-1, 3-2, NH3 (1,1), (2,2) and the 870μm dust continuum. Four submillimeter continuum sources, labelled SMM 1-4, are revealed in the 870μm dust emission. The main core, SMM1, is found to be associated with a deeply embedded near infrared cluster in the northeast; while the weaker source SMM2 coincides with a more evolved cluster in the southwest. The best fit spectral energy distribution of SMM1 gives an emissivity ofβ = 1.6, and temperatures of 32 K and 92 K for the cold- and hot-dust components. An SMM1 core mass of 246 M⊙ and a total mass of 445 M⊙ are estimated from the 870 μm dust continuum emission.SMM1 is found to have a temperature gradient decreasing from inside out, indicative of the presence of interior heating sources. The total outflow gas mass as traced by the CO J - 3-2 emission is estimated to be 35 M⊙. Low velocity outflows are also found in the NH3 (1,1) emission. The non-thermal dominant NH3 line width as well as the substantial core mass suggest that the SMM1 core is a "turbulent,massive dense core", in the process of forming a group or a cluster of stars. The much higher star formation efficiency found in the southwest cluster supports the suggestion that this cluster is more evolved than the northeast one. Large near infrared photometric variations found in the source PCS-IR93, a previously found highly polarized nebulosity, indicate an underlying star showing the FU Orionis type of behavior.

  13. MOLECULAR-EPIDEMIOLOGICAL INVESTIGATION OF THE OUTBREAK OF ASEPTIC MENINGITIS IN NOVOSIBIRSK REGION

    Directory of Open Access Journals (Sweden)

    A. V. Demina

    2016-01-01

    Full Text Available The aim of this study was to investigate the outbreak of aseptic meningitis in theNovosibirskregion in 2008–2009. We studied genetic diversity and molecular-epidemiological characteristics of human enteroviruses that caused aseptic meningitis. Materials and metods. In the present study we investigated samples of cerebrospinal fluid from 199 patients with a diagnosis “aseptic meningitis”, based on the clinical characteristics of the disease (headache, stiff neck, fever, nausea, vomiting, and confirmed by laboratory tests of spinal fluid (lymphocyte cell count > 10 cells/ml.All samples were tested by PCR for RNA of Enterovirus and Flavivirus and DNA Myc. tuberculosis, Borrelia spp., Neisseria spp. In the samples there were not found RNA Flavivirus, DNA Myc. tuberculosis, Borrelia spp., Neisseria spp., but in 73 samples (37% was identified RNA enterovirus (EV. Determination of nucleotide sequences of 5’UTR and VP1-region of EV revealed that they belong to the following genotypes: the highest percentage was presented by genotype ECHO 30 (62%; another genotypes were Cox A2 (8%, Cox A4 (5%, Cox A14 (3%, Cox A16 (5%, Cox B5 (8%, ECHO 6 (3%, ECHO 9 (3% and ECHO 25 (3%. In 2008 most of the EV that caused the symptoms of aseptic meningitis belonged to genotype ECHO 30 (76%. In 2009 the clinical specimens containing genotype ECHO 30 were not found, but the largest percentage of EV belonged to genotypes Cox A2 (33% and Cox A4 (22%. Thus, in 2008 we recorded outbreak of aseptic meningitis, the major etiological factor was enterovirus ECHO 30. And the rise of the incidence of aseptic meningitis in 2009 is related to the circulation of new genotypes of EV. The investigated strains were deposited in an international database GenBank under accession numbers KP258231-KP258235, HM559584.

  14. Pathology of camel tuberculosis and molecular characterization of its causative agents in pastoral regions of Ethiopia.

    Directory of Open Access Journals (Sweden)

    Gezahegne Mamo

    Full Text Available A cross sectional study was conducted on 906 apparently healthy camels slaughtered at Akaki and Metehara abattoirs to investigate the pathology of camel tuberculosis (TB and characterize its causative agents using postmortem examination, mycobacteriological culturing, and multiplex polymerase chain reaction (PCR, region of difference-4 (RD4-based PCR and spoligotyping. The prevalence of camel TB was 10.04% (91/906 on the basis of pathology and it was significantly higher in females (χ(2 = 4.789; P = 0.029. The tropism of TB lesions was significantly different among the lymph nodes (χ(2 = 22.697; P = 0.002 and lung lobes (χ(2 = 17.901; P = 0.006. Mycobacterial growth was observed in 34% (31/91 of camels with grossly suspicious TB lesions. Upon further molecular characterization using multiplex PCR, 68% (21/31 of the colonies showed a positive signal for the genus Mycobacterium, of which two were confirmed Mycobacterium bovis (M. bovis by RD4 deletion typing. Further characterization of the two M. bovis at strains level revealed that one of the strains was SB0133 while the other strain was new and had not been reported to the M. bovis database prior to this study. Hence, it has now been reported to the database, and designated as SB1953. In conclusion, the results of the present study have shown that the majority of camel TB lesions are caused by mycobacteria other than Mycobacterium tuberculosis complex. And hence further identification and characterization of these species would be useful towards the efforts made to control TB in camels.

  15. The Dynamics of Molecular Clouds in the Galactic Bar Region on the Near-Side of the CMZ

    Science.gov (United States)

    Tolls, Volker; Smith, Howard Alan; HIGGS Team

    2017-01-01

    The inner Galaxy, the area inside the 3-kpc arms, can be divided into two main regions, the Central Molecular Zone (CMZ; Morris and Serabyn 1996) and the Galactic Bar region. Gas and dust moves from the end points of the Galactic Bar on dust lanes towards the CMZ, where it merges with the gas and dust forming a 100-pc molecular ring or stream around the central black hole. The stream of gas and dust on the dust lanes is not continuous, but fragmented into irregularly separated clumps of varying sizes and clustering. On the near side of the CMZ the most prominent cloud clusters are the l=1.6o complex, Clump 2, and the molecular clouds around l=5.5o. We are analyzing Herschel, MOPRA, APEx, and other archival observations in order a) to identify molecular clouds that are part of the gas and dust stream in the Galactic Bar region near the CMZ, b) to determine the dynamics of the Galactic Bar clouds, and c) to derive a gas and dust mass flow rate to the CMZ. This poster will present our initial results.

  16. The Vitis vinifera C-repeat binding protein 4 (VvCBF4) transcriptional factor enhances freezing tolerance in wine grape

    Science.gov (United States)

    Tillett, Richard L.; Wheatley, Matthew D.; Tattersall, Elizabeth A.R.; Schlauch, Karen A.; Cramer, Grant R.; Cushman, John C.

    2014-01-01

    Summary Chilling and freezing can reduce significantly vine survival and fruit set in Vitis vinifera wine grape. To overcome such production losses, a recently identified grapevine C-repeat binding factor (CBF) gene, VvCBF4, was overexpressed in grape vine cv. “Freedom” and found to improve freezing survival and reduced freezing-induced electrolyte leakage by up to 2°C in non-cold-acclimated vines. In addition, overexpression of this transgene caused a reduced growth phenotype similar to that observed for CBF overexpression in Arabidopsis and other species. Both freezing tolerance and reduced growth phenotypes were manifested in a transgene dose-dependent manner. To understand the mechanistic basis of VvCBF4 transgene action, one transgenic line (9–12) was genotyped using microarray-based mRNA expression profiling. Forty-seven and 12 genes were identified in unstressed transgenic shoots with either a greater than 1.5-fold increase or decrease in mRNA abundance, respectively. Comparison of mRNA changes with characterized CBF regulons in woody and herbaceous species revealed partial overlaps suggesting that CBF-mediated cold acclimation responses are widely conserved. Putative VvCBF4-regulon targets included genes with functions in cell wall structure, lipid metabolism, epicuticular wax formation, and stress-responses suggesting that the observed cold tolerance and dwarf phenotypes are the result of a complex network of diverse functional determinants. PMID:21914113

  17. Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight.

    Science.gov (United States)

    Purohit, Rituraj

    2014-01-01

    KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805-850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.

  18. [The occurrence of fasciola hepatica in chosen regions of Poland based on molecular and serological methods].

    Science.gov (United States)

    Kozak-Cieszczyk, Monika

    2006-01-01

    Fasciolosis, caused by the liver fluke (Fasciola hepatica) is an important issue for both human and animal health. The disease evokes economic losses which are a consequence of impaired animal productivity leading to higher costs of meat and milk production, as well as liver condemnation. The goals of this thesis were to: (1) elaborate a molecular method--PCR for the detection of F. hepatica DNA in intermediate and definite hosts; (2) estimate the usefulness of a recombinated cysteine proteinase produced in E. coli in the form of inclusive bodies in serological diagnosis of F. hepatica infection in definite hosts, using an enzyme-linked immunosorbent assay (ELISA); (3) conduct field research on the prevalence of infection among intermediate and definitive hosts (cattle) in chosen regions of Poland, utilizing the elaborated methods. Based on the results obtained in this study, it was established that it is possible to detect F. hepatica DNA in the feces of definite hosts with the elaborated PCR method. The amplification of a 124 base pair tandem repeat allows the detection of fluke larval stages in intermediate hosts within 12 hours of exposure and F. hepatica infection in definite hosts (by the 5th week in rats, 8th week in sheep and 10th week in cattle). Therefore, the PCR test is more sensitive than traditional microscopic methods. Furthermore, it was determined that, the recombinated cysteine proteinase in the form of inclusive bodies, after solubillization exhibits antigenic properties of the native protein and the ELISA method based on this antigen may be useful as a tool for diagnosing fasciolosis in sheep and cattle, in both serum and milk samples. The test achieves a greater sensitivity and specificity than an ELISA based on native excretory-secretory antigens. The results of field research indicate that Fasciola hepatica is a frequent parasite of cattle in central and eastern Poland. The mean prevalence was 34.86% (+/- 16.95) in all studied areas. The

  19. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    Science.gov (United States)

    Batenburg, A. M.; Schuck, T. J.; Baker, A. K.; Zahn, A.; Brenninkmeijer, C. A. M.; Röckmann, T.

    2012-05-01

    More than 450 air samples that were collected in the upper troposphere - lower stratosphere (UTLS) region by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container) have been analyzed for molecular hydrogen (H2) mixing ratios (χ(H2)) and H2 isotopic composition (deuterium content, δD). More than 120 of the analyzed samples contained air from the lowermost stratosphere (LMS). These show that χ(H2) does not vary appreciably with O3-derived height above the thermal tropopause (TP), whereas δD does increase with height. The isotope enrichment is caused by H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D); the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (χ(CH4)) and nitrous oxide (χ(N2O)), as a result of the relatively long lifetimes of these three species. The correlations are described by δD[‰]=-0.35 · χ(CH4)[ppb]+768 and δD[‰]=-1.90· χ(N2O)[ppb]+745. These correlations are similar to previously published results and likely hold globally for the LMS. Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in χ(H2), but δD is up to 12.3‰ lower in the July, August and September monsoon samples. This δD decrease is correlated with the χ(CH4) increase in these samples. The significant correlation with χ(CH4) and the absence of a perceptible χ(H2) increase that accompanies the δD decrease indicates that microbial production of very D-depleted H2 in the wet season may contribute to this phenomenon. Some of the samples have very high χ(H2) and very low δD values, which indicates a pollution effect. Aircraft engine exhaust plumes are a suspected cause, since the effect mostly occurs in samples

  20. Small-scale structure and chemical differentiation in the central region of the Sagittarius B2 molecular cloud

    Energy Technology Data Exchange (ETDEWEB)

    Goldsmith, P.F.; Snell, R.L.; Hasegawa, T.; Ukita, N.

    1987-03-01

    Fifteen arcsec angular resolution observations of a number of molecular species in the center of the Sgr B2 molecular cloud, including HC3N in the ground and v7 = 1 vibrational states, SO, OCS,l and HNCO, have been performed. Emission from HC3N is fairly uniformly distributed over the region studied; SO and OCS have a spatially extended component but are strongly centrally peaked. HNCO and vibrationally excited HC/sub 3/N emission are essentially restricted to a very small region around the center of activity in the north. The difference between the spatial distributions are attributed to variation in the chemical abundances of the various clumps. The excitation requirements of the vibrationally excited HC/sub 3/N imply the presence of dust and gas at high temperatures. The results further heighten the apparent contradiction presented by the lack of infrared emission from this source. 53 references.

  1. Age, size, and position of H ii regions in the Galaxy. Expansion of ionized gas in turbulent molecular clouds

    CERN Document Server

    Tremblin, P; Didelon, P; Raga, A C; Minier, V; Ntormousi, E; Pettitt, A; Pinto, C; Samal, M; Schneider, N; Zavagno, A

    2014-01-01

    This work aims at improving the current understanding of the interaction between H ii regions and turbulent molecular clouds. We propose a new method to determine the age of a large sample of OB associations by investigating the development of their associated H ii regions in the surrounding turbulent medium. Using analytical solutions, one-dimensional (1D), and three-dimensional (3D) simulations, we constrained the expansion of the ionized bubble depending on the turbulent level of the parent molecular cloud. A grid of 1D simulations was then computed in order to build isochrone curves for H ii regions in a pressure-size diagram. This grid of models allowed to date large sample of OB associations and was used on the H ii Region Discovery Survey (HRDS). Analytical solutions and numerical simulations showed that the expansion of H ii regions is slowed down by the turbulence up to the point where the pressure of the ionized gas is in a quasi-equilibrium with the turbulent ram pressure. Based on this result, we ...

  2. Four highly luminous massive star forming regions in the Norma Spiral Arm.: I. Molecular gas and dust observations

    CERN Document Server

    Garay, Guido; Bronfman, Leonardo; May, Jorge; Chavarria, Luis; Nyman, Lars-Ake

    2009-01-01

    We report molecular line and dust continuum observations, made with the SEST telescope, towards four young high-mass star forming regions associated with highly luminous (L> 6x10^5 Lsun) IRAS sources (15290-5546, 15502-5302, 15567-5236 and 16060-5146). Molecular emission was mapped in lines of CS (J=2-1, 3-2 and 5-4), SiO (J=2-1 and 3-2), CH3OH (Jk=3k-2k and 2k-1k), and C34S (J=3-2). In addition, single spectra at the peak position were taken in the CO, 13CO and C18O (J=1-0) lines. We find that the luminous star forming regions are associated with molecular gas and dust structures with radii of typically 0.5 pc, masses of ~5x10^3 Msun, column densities of ~5x10^{23} cm^{-2}, molecular hydrogen densities of typically ~2x10^5 cm^{-3} and dust temperatures of ~40 K. The 1.2 mm dust continuum observations further indicate that the cores are centrally condensed, having radial density profiles with power-law indices in the range 1.6-1.9. We find that under these conditions dynamical friction by the gas plays an imp...

  3. A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

    Science.gov (United States)

    Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimarães

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

  4. The stable isotopic composition of molecular hydrogen in the tropopause region probed by the CARIBIC aircraft

    Directory of Open Access Journals (Sweden)

    A. M. Batenburg

    2012-05-01

    Full Text Available More than 450 air samples that were collected in the upper troposphere – lower stratosphere (UTLS region by the CARIBIC aircraft (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container have been analyzed for molecular hydrogen (H2 mixing ratios (χ(H2 and H2 isotopic composition (deuterium content, δD.

    More than 120 of the analyzed samples contained air from the lowermost stratosphere (LMS. These show that χ(H2 does not vary appreciably with O3-derived height above the thermal tropopause (TP, whereas δD does increase with height. The isotope enrichment is caused by H2 production and destruction processes that enrich the stratospheric H2 reservoir in deuterium (D; the exact shapes of the profiles are mainly determined by mixing of stratospheric with tropospheric air. Tight negative correlations are found between δD and the mixing ratios of methane (χ(CH4 and nitrous oxide (χ(N2O, as a result of the relatively long lifetimes of these three species. The correlations are described by δD[‰]=−0.35 · χ(CH4[ppb]+768 and δD[‰]=−1.90· χ(N2O[ppb]+745. These correlations are similar to previously published results and likely hold globally for the LMS.

    Samples that were collected from the Indian subcontinent up to 40° N before, during and after the summer monsoon season show no significant seasonal change in χ(H2, but δD is up to 12.3‰ lower in the July, August and September monsoon samples. This δD decrease is correlated with the χ(CH4 increase in these samples. The significant correlation with χ(CH4 and the absence of a perceptible χ(H2 increase that accompanies the δD decrease indicates that microbial production of

  5. The far-IR spectrum of Sagittarius B2 region: Extended molecular absorption, photodissociation and photoionization

    OpenAIRE

    Goicoechea, J. R.; Rodriguez-Fernandez, N. J.; Cernicharo, J.

    2003-01-01

    We present large scale 9'x 27'(25 pc x 70 pc) far-IR observations around Sgr B2 using the Long-wavelength spectrometer (LWS) on board the Infrared Space Observatory (ISO). The spectra are dominated by the strong continuum emission of dust, the widespread molecular absorption of light hydrides (OH, CH and H2O) and the fine structure lines of [NII], [NIII], [OIII], [CII] and [OI]. The molecular richness in the outer layers of Sgr B2 is probed by the ISO-LWS Fabry-Perot (35 km s^-1) detections t...

  6. A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions.

    Science.gov (United States)

    Cheng, Jijun; Roden, Christine A; Pan, Wen; Zhu, Shu; Baccei, Anna; Pan, Xinghua; Jiang, Tingting; Kluger, Yuval; Weissman, Sherman M; Guo, Shangqin; Flavell, Richard A; Ding, Ye; Lu, Jun

    2016-03-30

    Clustered regularly-interspaced palindromic repeats (CRISPR)-based genetic screens using single-guide-RNA (sgRNA) libraries have proven powerful to identify genetic regulators. Applying CRISPR screens to interrogate functional elements in noncoding regions requires generating sgRNA libraries that are densely covering, and ideally inexpensive, easy to implement and flexible for customization. Here we present a Molecular Chipper technology for generating dense sgRNA libraries for genomic regions of interest, and a proof-of-principle screen that identifies novel cis-regulatory domains for miR-142 biogenesis. The Molecular Chipper approach utilizes a combination of random fragmentation and a type III restriction enzyme to derive a densely covering sgRNA library from input DNA. Applying this approach to 17 microRNAs and their flanking regions and with a reporter for miR-142 activity, we identify both the pre-miR-142 region and two previously unrecognized cis-domains important for miR-142 biogenesis, with the latter regulating miR-142 processing. This strategy will be useful for identifying functional noncoding elements in mammalian genomes.

  7. Molecular studies of Callithrix pygmaea (Primates, Platyrrhini based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

    Directory of Open Access Journals (Sweden)

    Tagliaro Claudia Helena

    2000-01-01

    Full Text Available Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1 and a nuclear gene (intronic regions of the transferrin gene, suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.

  8. Molecular differentiation of Russian wild ginseng using mitochondrial nad7 intron 3 region

    Directory of Open Access Journals (Sweden)

    Guisheng Li

    2017-07-01

    Conclusion: An effective DNA method for molecular discrimination of Russian wild ginseng from Chinese and Korean cultivated ginseng was developed. The established real-time allele-specific PCR was simple and reliable, and the present method should be a crucial complement of chemical analysis for authentication of Russian wild ginseng.

  9. Molecular Dynamic Simulation of Lattice Distortion Region Produced by Rounded Grain Boundary in Nanocrystalline Materials

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The distortion structure in nanocrystalline NiAl is studied using molecular dynamics simulation. The rounded grain boundaries in these nanograins are a direct source for the observed lattice distortion. The change of grain size affects directly the volume fraction of the distorted lattice in the nanograin.

  10. 74 MHz Nonthermal Emission from Molecular Clouds: Evidence for a Cosmic Ray Dominated Region at the Galactic Center

    Science.gov (United States)

    Yusef-Zadeh, F.; Wardle, M.; Lis, D.; Viti, S.; Brogan, C.; Chambers, E.; Pound, M.; Rickert, M.

    2013-10-01

    We present 74 MHz radio continuum observations of the Galactic center region. These measurements show nonthermal radio emission arising from molecular clouds that is unaffected by free-free absorption along the line of sight. We focus on one cloud, G0.13-0.13, representative of the population of molecular clouds that are spatially correlated with steep spectrum (α327MHz74MHz = 1.3 ± 0.3) nonthermal emission from the Galactic center region. This cloud lies adjacent to the nonthermal radio filaments of the Arc near l - 0.2° and is a strong source of 74 MHz continuum, SiO (2-1), and Fe I Kα 6.4 keV line emission. This three-way correlation provides the most compelling evidence yet that relativistic electrons, here traced by 74 MHz emission, are physically associated with the G0.13-0.13 molecular cloud and that low-energy cosmic ray electrons are responsible for the Fe I Kα line emission. The high cosmic ray ionization rate -10-13 s-1 H-1 is responsible for heating the molecular gas to high temperatures and allows the disturbed gas to maintain a high-velocity dispersion. Large velocity gradient (LVG) modeling of multitransition SiO observations of this cloud implies H2 densities -104-5 cm-3 and high temperatures. The lower limit to the temperature of G0.13-0.13 is -100 K, whereas the upper limit is as high as 1000 K. Lastly, we used a time-dependent chemical model in which cosmic rays drive the chemistry of the gas to investigate for molecular line diagnostics of cosmic ray heating. When the cloud reaches chemical equilibrium, the abundance ratios of HCN/HNC and N2H+/HCO+ are consistent with measured values. In addition, significant abundance of SiO is predicted in the cosmic ray dominated region of the Galactic center. We discuss different possibilities to account for the origin of widespread SiO emission detected from Galactic center molecular clouds.

  11. H II Region G46.5-0.2: The Interplay between Ionizing Radiation, Molecular Gas, and Star Formation

    Science.gov (United States)

    Paron, S.; Ortega, M. E.; Dubner, G.; Yuan, Jing-Hua; Petriella, A.; Giacani, E.; Zeng Li, Jin; Wu, Yuefang; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju

    2015-06-01

    H ii regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing toward the ionizing sources, and cometary globules of dense gas where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic H ii region located at about 4 kpc, is an excellent target for performing this kind of study. Using public molecular data extracted from the Galactic Ring Survey (13CO J = 1-0) and from the James Clerk Maxwell Telescope data archive (12CO, 13CO, C18O J = 3-2, HCO+, and HCN J = 4-3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment, and the young stellar objects (YSOs) placed around it. We found that G46, probably excited by an O7V star, is located close to the edge of the GRSMC G046.34-00.21 molecular cloud. It presents a horse-shoe morphology opening in the direction of the cloud. We observed a filamentary structure in the molecular gas likely related to G46 and not considerable molecular emission toward its open border. We found that about 10‧ to the southwest of G46 there are some pillar-like features, shining at 8 μm and pointing toward the H ii region open border. We propose that the pillar-like features were carved and sculpted by the ionizing flux from G46. We found several YSOs likely embedded in the molecular cloud grouped in two main concentrations: one, closer to the G46 open border consisting of Class II type sources, and another mostly composed of Class I type YSOs located just ahead of the pillar-like features, strongly suggesting an age gradient in the YSO distribution.

  12. H ii REGION G46.5-0.2: THE INTERPLAY BETWEEN IONIZING RADIATION, MOLECULAR GAS, AND STAR FORMATION

    Energy Technology Data Exchange (ETDEWEB)

    Paron, S.; Ortega, M. E.; Dubner, G.; Petriella, A.; Giacani, E. [Instituto de Astronomía y Física del Espacio (IAFE, CONICET-UBA), CC 67, Suc. 28, 1428 Buenos Aires (Argentina); Yuan, Jing-Hua; Li, Jin Zeng; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju [National Astronomical Observatories, Chinese Academy of Sciences, 20 A Datun Road, Chaoyang District, Beijing 100012 (China); Wu, Yuefang, E-mail: sparon@iafe.uba.ar [Department of Astronomy, Peking University, 100871 Beijing (China)

    2015-06-15

    H ii regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing toward the ionizing sources, and cometary globules of dense gas where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic H ii region located at about 4 kpc, is an excellent target for performing this kind of study. Using public molecular data extracted from the Galactic Ring Survey ({sup 13}CO J = 1–0) and from the James Clerk Maxwell Telescope data archive ({sup 12}CO, {sup 13}CO, C{sup 18}O J = 3–2, HCO{sup +}, and HCN J = 4–3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment, and the young stellar objects (YSOs) placed around it. We found that G46, probably excited by an O7V star, is located close to the edge of the GRSMC G046.34-00.21 molecular cloud. It presents a horse-shoe morphology opening in the direction of the cloud. We observed a filamentary structure in the molecular gas likely related to G46 and not considerable molecular emission toward its open border. We found that about 10′ to the southwest of G46 there are some pillar-like features, shining at 8 μm and pointing toward the H ii region open border. We propose that the pillar-like features were carved and sculpted by the ionizing flux from G46. We found several YSOs likely embedded in the molecular cloud grouped in two main concentrations: one, closer to the G46 open border consisting of Class II type sources, and another mostly composed of Class I type YSOs located just ahead of the pillar-like features, strongly suggesting an age gradient in the YSO distribution.

  13. Molecular Identification of Dendrobium Species (Orchidaceae Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

    Directory of Open Access Journals (Sweden)

    Shangguo Feng

    2015-09-01

    Full Text Available The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae. For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium.

  14. X-ray Diagnostics of Giant Molecular Clouds in the Galactic Center Region and Past Activity of Sgr A*

    CERN Document Server

    Odaka, Hirokazu; Watanabe, Shin; Tanaka, Yasuyuki; Khangulyan, Dmitry; Takahashi, Tadayuki; 10.1088/0004-637X/740/2/103

    2011-01-01

    Strong iron fluorescence at 6.4 keV and hard-X-ray emissions from giant molecular clouds in the Galactic center region have been interpreted as reflections of a past outburst of the Sgr A* supermassive black hole. Careful treatment of multiple interactions of photons in a complicated geometry is essential to modeling the reprocessed emissions from the dense clouds. We develop a new calculation framework of X-ray reflection from molecular clouds based on Monte Carlo simulations for accurate interpretation of high-quality observational data. By utilizing this simulation framework, we present the first calculations of morphologies and spectra of the reflected X-ray emission for several realistic models of Sgr B2, which is the most massive molecular cloud in our Galaxy. The morphology of scattered hard X-rays above 20 keV is significantly different from that of iron fluorescence due to their large penetrating power into dense regions of the cloud, probing the structure of the cloud. High-resolution spectra provid...

  15. Molecular phylogeny of Acer monspessulanum L. subspecies from Iran inferred using the ITS region of nuclear ribosomal DNA

    Directory of Open Access Journals (Sweden)

    HANIF KHADEMI

    2016-04-01

    Full Text Available Abstract. Khademi H, Mehregan I, Assadi M, Nejadsatari T, Zarre S. 2015. Molecular phylogeny of Acer monspessulanum L. subspecies from Iran inferred using the ITS region of nuclear ribosomal DNA. Biodiversitas 17: 16-23. This study was carried out on the Acer monspessulanum complex growing wild in Iran. Internal transcribed spacer (ITS sequences for 75 samples representing five different subspecies of Acer monspessulanum were analyzed. Beside this, 86 previously published ITS sequences from GenBank were used to test the monophyly of the complex worldwide. Phylogenetic analyses were conducted using Bayesian inference and maximum parsimony. The results indicate that most samples of A. monspessulanum species from Iran were part of a monophyletic clade with 8 samples of A. ibericum from Georgia, A. hyrcanum from Iran and one of A. sempervirens from Greece (PP= 1; BS= 79%. Our results indicate that use of morphological characteristics coupled with molecular data will be most effective.

  16. Millimeter- and Submillimeter-Wave Observations of the OMC-2/3 Region. III. An Extensive Survey for Molecular Outflows

    CERN Document Server

    Takahashi, Satoko; Ohashi, Nagayoshi; Kusakabe, Nobuhiko; Takakuwa, Shigehisa; Shimajiri, Yoshito; Tamura, Motohide; Kawabe, Ryohei

    2008-01-01

    Using the ASTE 10 m submillimeter telescope and the 1.4 m Infrared Survey Facility (IRSF), we performed an extensive outflow survey in the Orion Molecular Cloud -2 and -3 region. Our survey, which includes 41 potential star-forming sites, has been newly compiled using multi-wavelength data based on millimeter- and submillimeter-continuum observations as well as radio continuum observations. From the CO (3-2) observations performed with the ASTE 10 m telescope, we detected 14 CO molecular outflows, seven of which were newly identified. This higher detection rate, as compared to previous CO (1-0) results in the same region, suggests that CO (3-2) may be a better outflow tracer. Physical properties of these outflows and their possible driving sources were derived. Derived parameters were compared with those of CO outflows in low- and high-mass starforming regions. We show that the CO outflow momentum correlates with the bolometric luminosity of the driving source and with the envelope mass, regardless of the mas...

  17. Molecular identification of cetaceans from the West Atlantic using the E3-I5 region of COI.

    Science.gov (United States)

    Falcão, L H O; Campos, A S; Freitas, J E P; Furtado-Neto, M A A; Faria, V V

    2017-04-20

    Molecular identification is very useful in cases where morphology-based species identification is not possible. Examples for its application in cetaceans include the identification of carcasses of stranded animals in advanced state of decomposition and body parts that are illegally traded. One DNA region that is often used for molecular identification is the Folmer region of the mitochondrial gene cytochrome c oxidase subunit I (COI) (locus 48 to 705 bp). This locus has been used for the identification of several animal species, including whales and dolphins. The goal of the present study was to evaluate the usefulness of another region of COI, the E3-I5 (locus 685 to locus 1179; 495 bp) as a marker for identification of cetaceans from northeastern Canada and northeastern Brazil. The identification markers were successfully obtained for seven cetacean species after performing percent identity and Basic Local Alignment Search Tool analyses. The obtained markers are now publicly available and are useful for the identification of the endangered blue whale (Balaenoptera musculus), common minke whale (B. acutorostrata), vulnerable sperm whale (Physeter macrocephalus), harbor porpoise (Phocoena phocoena), common bottlenose dolphin (Tursiops truncatus), Guiana dolphin (Sotalia guianensis), and melon-headed whale (Peponocephala electra).

  18. Molecular detection and phylogenetic analysis of tick-borne encephalitis virus in rodents captured in the transdanubian region of Hungary.

    Science.gov (United States)

    Pintér, Réka; Madai, Mónika; Horváth, Győző; Németh, Viktória; Oldal, Miklós; Kemenesi, Gábor; Dallos, Bianka; Bányai, Krisztián; Jakab, Ferenc

    2014-08-01

    Abstract Tick-borne encephalitis virus (TBEV) infection is a common zoonotic disease affecting humans in Europe and Asia. To determine whether TBEV is present in small mammalian hosts in Hungary, liver samples of wild rodents were tested for TBEV RNA. Over a period of 7 years, a total of 405 rodents were collected at five different geographic locations of the Transdanubian region. TBEV nucleic acid was identified in four rodent species: Apodemus agrarius, A. flavicollis, Microtus arvalis, and Myodes glareolus. Out of the 405 collected rodents, 17 small mammals (4.2%) were positive for TBEV. The present study provides molecular evidence and sequence data of TBEV from rodents in Hungary.

  19. MOLECULAR GENETIC ANALYSIS OF INTERLEUKIN 4 GENE POLYMORPHISM AMONG TELEUTIANS, SHORIANS, AND CAUCASIANS IN KEMEROVO REGION

    Directory of Open Access Journals (Sweden)

    A. V. Ostaptseva

    2006-01-01

    Full Text Available Abstract. An interleukin 4 polymorphism has been studied in Teleutians, Shorians, and Caucasoids living in the Kemerovo Region. The groups of Teleutians and Caucasoids are characterised with even or close-to-even distribution of the IL-4 alleles. The most widespread genotype in populations of Teleutians and Caucasoids was the 2R/3R heterozygosity, and 3R/3R proved to be the mostly rare. These data are indicative for mixing processes among Teleutians in the Kemerovo Region and Siberian Caucasoids. The major IL-4 genotype in Shorian population was 3R/3R, and the heterozygotic genotype 2R/3R took the second position.

  20. Chirped Grating Tunable Lasers for the Infrared Molecular Fingerprint Spectral Region

    Science.gov (United States)

    2013-09-01

    406-408 (2002). [20] M. Ito and T. Kimura, “Oscillation properties of AlGaAs DH Lasrs with an external grating,” IEEE J. Quant. Elec- tron. QE-16...Reed DTRA DTRA-TR-13-62 Approved for public release;distribution is unlimited. A new approach approach to tunable mid-infrared lasers, an optically ...Molecular Fingerprint Spectral Region” Abstract A new approach to tunable mid-infrared lasers, an optically pumped, type- II, InGaSb/InAs gain

  1. Ehrlichia canis in dogs in a semiarid region of Northeastern Brazil: serology, molecular detection and associated factors.

    Science.gov (United States)

    Tanikawa, A; Labruna, M B; Costa, A; Aguiar, D M; Justiniano, S V; Mendes, R S; Melo, A L T; Alves, C J; Azevedo, S S

    2013-06-01

    This study investigated infection by Ehrlichia spp. agents by PCR, immunofluorescence assay test (IFAT), and by Giemsa-stained blood smears in 108 dogs from a semiarid region of the state of Paraíba, Northeastern Brazil. Seventy-five (69.4%) of the 108 dogs were found to be seropositive to Ehrlichia canis, while only four dogs (3.7%) were positive in real-time PCR for E. canis. In six dogs (5.6%) E. canis-like morulae were observed in monocytes. Animals that stayed in environment whose floor was dried dirt, and dogs whose owners reported low frequency of cleaning the dog environment had higher (Pcanis. Increasing seropositivity was found in older dogs (P=0.012). This study provides the first molecular detection of E. canis in the semiarid region of Northeastern Brazil.

  2. Molecular characterisation of multidrug-resistant Salmonella enterica serovar Typhimurium isolates from Gomel region, Belarus

    DEFF Research Database (Denmark)

    Tapalski, D.; Hendriksen, Rene S.; Hasman, Henrik;

    2007-01-01

    an infection outside hospitals in the Gomel region of Belarus. Thirty-one isolates were highly similar according to PFGE and MLVA typing, were multidrug-resistant, including resistance to ceftiofur, and harboured the bla(CTX-M-5) gene. These results indicate that a common source may have been responsible...

  3. Detection and Molecular Characterization of Zoonotic Poxviruses Circulating in the Amazon Region of Colombia, 2014

    Science.gov (United States)

    Usme-Ciro, Jose A.; Paredes, Andrea; Walteros, Diana M.; Tolosa-Pérez, Erica Natalia; Laiton-Donato, Katherine; Pinzón, Maria del Carmen; Petersen, Brett W.; Gallardo-Romero, Nadia F.; Li, Yu; Wilkins, Kimberly; Davidson, Whitni; Gao, Jinxin; Patel, Nishi; Nakazawa, Yoshinori; Reynolds, Mary G.; Satheshkumar, P. S.; Emerson, Ginny L.

    2017-01-01

    During 2014, cutaneous lesions were reported in dairy cattle and farmworkers in the Amazon Region of western Colombia. Samples from 6 patients were analyzed by serologic and PCR testing, and results demonstrated the presence of vaccinia virus and pseudocowpox virus. These findings highlight the need for increased poxvirus surveillance in Colombia. PMID:28322708

  4. Molecular mapping of the Edwards syndrome phenotype to two noncontiguous regions on chromosome 18

    Energy Technology Data Exchange (ETDEWEB)

    Boghosian-Sell, L.; Mewar, R.; Harrison, W.; Shapiro, R.M.; Zackai, E.H.; Carey, J.; Davis-Keppen, L.; Hudgins, L.; Overhauser, J.

    1994-09-01

    In an effort to identify regions on chromosome 18 that may be critical in the appearance of the Edwards syndrome phenotype, the authors have analyzed six patients with partial duplication of chromosome 18. Four of the patients have duplications involving the distal half of 18q (18q21.1-qter) and are very mildly affected. The remaining two patients have most of 18q (18q12.1-qter) duplicated, are severely affected, and have been diagnosed with Edwards syndrome. The authors have employed FISH, using DNA probes from a chromosome 18-specific library, for the precise determination of the duplicated material in each of these patients. The clinical features and the extent of the chromosomal duplication in these patients were compared with four previously reported partial trisomy 18 patients, to identify regions of chromosome 18 that may be responsible for certain clinical features of trisomy 18. The comparative analysis confirmed that there is no single region on 18q that is sufficient to produce the trisomy 18 phenotype and identified two regions on 18q that may work in conjunction to produce the Edwards syndrome phenotype. In addition, correlative analysis indicates that duplication of 18q12.3-q22.1 may be associated with more severe mental retardation in trisomy 18 individuals. 25 refs., 3 figs., 1 tab.

  5. A low molecular weight artificial RNA of unique size with multiple probe target regions

    Science.gov (United States)

    Pitulle, C.; Dsouza, L.; Fox, G. E.

    1997-01-01

    Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

  6. A molecular cloud complex above the galactic plane.. I. Extended CO observations of the NGC 281 region

    Science.gov (United States)

    Lee, Youngung; Jung, Jae-Hoon

    2003-03-01

    We have mapped the entire extent of the molecular cloud complex associated with NGC 281, both in 12CO ( J=1-0) and 13CO ( J=1-0), using the Taeduk Radio Astronomy Observatory (TRAO) 14 m telescope. We also observed a few selected fields with bright 13CO emission, in CS ( J=2-1) and HCO + ( J=1-0). This region is distinguished by its vertical height of ˜320 pc above the midplane of the Perseus spiral arm, at a distance of 2.9 kpc. The molecular gas in the mapped region is found to extend far beyond the H II region NGC 281 (Sh 184). The southern boundary of the CO emission closely follows the southern boundary of the 100 μm dust emission. The molecular cloud complex consists of two main clouds bisected by the H II region, as well as several other clouds distributed over a range of 90 pc along the galactic longitude direction. Except for one cloud at VLSR=-43.9 km s -1, all these clouds occupy a small, contiguous velocity range centered at VLSR=-30 km s -1. Although these clouds are weakly connected, they clearly show distinct, knotted features along the galactic longitude direction. We assigned names to each cloud (A-H), derive their various physical parameters, and discuss their physical properties. These clouds do not show any specific, systematic behavior in their velocity field, except for a small gradient along galactic longitude (for A-E). The brightest 12CO and 13CO emissions are detected toward cloud A, which is located farthest from the two main clouds. We found star formation to be ongoing in clouds A and B, though these are not as active as D and E. The associated newborn stars have FIR properties similar to those of Herbig Ae/Be stars, and several outflows are also seen. We estimated the cloud masses in three different ways, and discuss the discrepancies between the resulting values. We estimate the total mass of the mapped region to be ˜3.7×10 4 M ⊙, using a conversion factor from CO luminosity to gas mass. About half of the clouds seem to be

  7. H II regions, infrared dark molecular clouds and the local geometry of the Milky Way's nuclear star-forming ring

    CERN Document Server

    Liszt, H S

    2009-01-01

    To interpret the galactic center H II region complexes as constituents of a barred galaxy's nuclear star-forming ring, we compare 18cm VLA radiocontinuumm, $8-22\\mu$ MSX IR and 2.6mm BTL and ARO12m CO emission in the inner few hundred pc. Galactic center H II regions are comparable in their IR appearance, luminosity and SED to M17 or N!0, but the IR light distribution is strongly modified by extinction at 8-22$\\mu$, locally and overall. In Sgr B2 at $l > 0.6$\\degr strong radio H II regions are invisible in the IR. In two favorable cases, extinction from individual galactic center molecular clouds is shown to have $\\tau \\ga 1$ at 8-22$\\mu$ independent of wavelength. The gas kinematics are mostly rotational but with systematic $\\pm 30-50$ \\kms non-circular motion. Sgr B and C both show the same shell and high-velocity cap structure. The H II regions lie in a slightly-inclined ring of radius $\\approx$ 180 pc (1.2\\degr) whose near side appears at higher latitude and lower velocity and contains Sgr B. Sgr C is on ...

  8. Sarcocystis neurona: molecular characterization of enolase domain I region and a comparison to other protozoa.

    Science.gov (United States)

    Bolten, K E; Marsh, A E; Reed, S M; Dubey, J P; Toribio, R E; Saville, W J A

    2008-09-01

    Sarcocystis neurona causes protozoal myeloencephalitis and has the ability to infect a wide host range in contrast to other Sarcocystis species. In the current study, five S. neurona isolates from a variety of sources, three Sarcocystis falcatula, one Sarcocystis dasypi/S. neurona-like isolate, and one Besnoitia darlingi isolate were used to compare the enolase 2 gene segment containing the domain I region to previously sequenced enolase genes from Neospora caninum, Neospora hughesi, Toxoplasma gondii, Plasmodium falciparum, and Trypanosoma cruzi; enolase 2 segment containing domain I region is highly conserved amongst these parasites of veterinary and medical importance. Immunohistochemistry results indicates reactivity of T. gondii enolase 1 and 2 antibodies to S. neurona merozoites and metrocytes, but no reactivity of anti-enolase 1 to the S. neurona bradyzoite stage despite reactivity to T. gondii bradyzoites, suggesting expression differences between organisms.

  9. The C-terminal region of E1A: a molecular tool for cellular cartography.

    Science.gov (United States)

    Yousef, Ahmed F; Fonseca, Gregory J; Cohen, Michael J; Mymryk, Joe S

    2012-04-01

    The adenovirus E1A proteins function via protein-protein interactions. By making many connections with the cellular protein network, individual modules of this virally encoded hub reprogram numerous aspects of cell function and behavior. Although many of these interactions have been thoroughly studied, those mediated by the C-terminal region of E1A are less well understood. This review focuses on how this region of E1A affects cell cycle progression, apoptosis, senescence, transformation, and conversion of cells to an epithelial state through interactions with CTBP1/2, DYRK1A/B, FOXK1/2, and importin-α. Furthermore, novel potential pathways that the C-terminus of E1A influences through these connections with the cellular interaction network are discussed.

  10. Dense gas and exciting sources of the molecular outflow in the AFGL 437 star-forming region

    CERN Document Server

    Manjarrez, G; de Gregorio-Monsalvo, I

    2011-01-01

    We present Very Large Array (VLA) high resolution observations of the NH3(1,1) and NH3(2,2) molecular transitions towards the high mass star forming region AFGL 437. Our aim was to investigate if the poorly collimated CO molecular outflow previously detected in the region is the result of a projection effect, with no intrinsic bipolarity, as suggested by Gomez et al. We complemented our observations with radio continuum archived data from the VLA at 2 and 3.6 cm, and with unpublished public data at 450 {\\mu}m taken with Submillimetre Common-User Bolometer Array at the James Clerk Maxwell Telescope. Ammonia emission was found mainly in three clumps located at the south and east of the position of the compact infrared cluster of AFGL 437, where the CO outflow seemed to have its origin. One of the NH3(1,1) clumps coincides with the maximum of NH3(2,2) and with a local peak of emission at 450 {\\mu}m. A near infrared source (s11) is also found at that position. Our continuum map at 2 cm shows extended elongated em...

  11. The molecular H2 emission and the stellar kinematics in the nuclear region of the Sombrero galaxy

    CERN Document Server

    Menezes, R B

    2015-01-01

    We analyze the molecular H$_2$ emission and the stellar kinematics in a data cube of the nuclear region of M104, the Sombrero galaxy, obtained with NIFS on the Gemini-north telescope. After a careful subtraction of the stellar continuum, the only emission line we detected in the data cube was H$_2 \\lambda 21218$. An analysis of this emission revealed the existence of a rotating molecular torus/disk, aproximately co-planar with a dusty structure detected by us in a previous work. We interpret these two structures as being associated with the same obscuring torus/disk. The kinematic maps provided by the Penalized Pixel Fitting method revealed that the stellar kinematics in the nuclear region of M104 appears to be the result of the superposition of a "cold" rotating disk and a "hot" bulge. Using a model of a thin eccentric disk, we reproduced the main properties of the maps of the stellar radial velocity and of the stellar velocity dispersion, specially within a distance of 0.2" from the kinematic axis (in regio...

  12. Interaction Effects between Cellulose and Water in Nanocrystalline and Amorphous Regions: A Novel Approach Using Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Ali Chami Khazraji

    2013-01-01

    Full Text Available The hydrophilic/hydrophobic nature of cellulose is based on its structural anisotropy. Cellulose chains are arranged in a parallel manner and are organized in sheets stabilized by interchain OH–O hydrogen bonds, whereas the stacking of sheets is stabilized by both van der Waals (vdW dispersion forces and weak CH–O hydrogen bonds. Cellulose has a strong affinity to itself and materials containing hydroxyls, especially water. Based on the preponderance of hydroxyl functional groups, cellulose polymer is very reactive with water. Water molecular smallness promotes the reaction with the cellulose chains and immediately formed hydrogen bonds. Besides that, vdW dispersion forces play an important role between these two reactive entities. They stabilize the cellulose structure according to the considerable cohesive energy in the cellulose network. Hydrogen bonding, electrostatic interactions, and vdW dispersion forces play an important role in determining the cellulose crystal structure during the cellulose-water interactions. As a result of these interactions, the volume of cellulose undergoes a meaningful change expressed not only by an exponential growth in amorphous regions, but also by an expansion in nanocrystalline regions. In addition, the volume change is associated with the swelling material expressed as a weight gain of the cellulose polymer. Molecular modeling using Accelrys Materials Studio allowed us to open a new horizon and is helpful for understanding cellulose-water interactions.

  13. HII region G46.5-0.2: the interplay between ionizing radiation, molecular gas and star formation

    CERN Document Server

    Paron, S; Dubner, G; Yuan, Jing-Hua; Petriella, A; Giacani, E; Li, Jin Zeng; Wu, Yuefang; Liu, Hongli; Huang, Ya Fang; Zhang, Si-Ju

    2015-01-01

    HII regions are particularly interesting because they can generate dense layers of gas and dust, elongated columns or pillars of gas pointing towards the ionizing sources, and cometary globules of dense gas, where triggered star formation can occur. Understanding the interplay between the ionizing radiation and the dense surrounding gas is very important to explain the origin of these peculiar structures, and hence to characterize triggered star formation. G46.5-0.2 (G46), a poorly studied galactic HII region located at about 4 kpc, is an excellent target to perform this kind of studies. Using public molecular data extracted from the Galactic Ring Survey (13CO J=1-0) and from the James Clerk Maxwell Telescope data archive (12CO, 13CO, C18O J=3-2, HCO+ and HCN J=4-3), and infrared data from the GLIMPSE and MIPSGAL surveys, we perform a complete study of G46, its molecular environment and the young stellar objects placed around it. We found that G46, probably excited by an O7V star, is located close to the edge...

  14. Density Profiles in Molecular Cloud Cores Associated with High-Mass Star-Forming Regions

    CERN Document Server

    Pirogov, Lev E

    2009-01-01

    Radial density profiles for the sample of dense cores associated with high-mass star-forming regions from southern hemisphere have been derived using the data of observations in continuum at 250 GHz. Radial density profiles for the inner regions of 16 cores (at distances $\\la 0.2-0.8$ pc from the center) are close on average to the $\\rho\\propto r^{-\\alpha}$ dependence, where $\\alpha=1.6\\pm 0.3$. In the outer regions density drops steeper. An analysis with various hydrostatic models showed that the modified Bonnor-Ebert model, which describes turbulent sphere confined by external pressure, is preferable compared with the logotrope and polytrope models practically in all cases. With a help of the Bonnor-Ebert model, estimates of central density in a core, non-thermal velocity dispersion and core size are obtained. The comparison of central densities with the densities derived earlier from the CS modeling reveals differences in several cases. The reasons of such differences are probably connected with the presen...

  15. High field FT-ICR mass spectrometry for molecular characterization of snow board from Moscow regions.

    Science.gov (United States)

    Mazur, Dmitry M; Harir, Mourad; Schmitt-Kopplin, Philippe; Polyakova, Olga V; Lebedev, Albert T

    2016-07-01

    High field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry analysis of eight snow samples from Moscow city allowed us to identify more than 2000 various elemental compositions corresponding to regional air pollutants. The hierarchical cluster analysis (HCA) of the data showed good concordance of three main groups of samples with the main wind directions. The North-West group (A1) is represented by several homologous CHOS series of aliphatic organic aerosols. They may form as a result of enhanced photochemical reactions including oxidation of hydrocarbons with sulfonations due to higher amount of SO2 emissions in the atmosphere in this region. Group A2, corresponding to the South-East part of Moscow, contains large amount of oxidized hydrocarbons of different sources that may form during oxidation in atmosphere. These hydrocarbons appear correlated to emissions from traffic, neighboring oil refinery, and power plants. Another family of compounds specific for this region involves CHNO substances formed during oxidation processes including NOx and NO3 radical since emissions of NOx are higher in this part of the city. Group A3 is rich in CHO type of compounds with high H/C and low O/C ratios, which is characteristic of oxidized hydrocarbon-like organic aerosol. CHNO types of compounds in A3 group are probably nitro derivatives of condensed hydrocarbons such as PAH. This non-targeted profiling revealed site specific distribution of pollutants and gives a chance to develop new strategies in air quality control and further studies of Moscow environment.

  16. Molecular analysis of the F plasmid traVR region: traV encodes a lipoprotein.

    OpenAIRE

    Doran, T J; Loh, S M; Firth, N; Skurray, R A

    1994-01-01

    The nucleotide sequences of the conjugative F plasmid transfer region genes, traV and traR, have been determined. The deduced amino acid sequence of TraV indicated that it may be a lipoprotein; this was confirmed by examining the effect of globomycin on traV-encoded polypeptides synthesized in minicells. An open reading frame that may represent a previously undetected transfer gene, now designated trbG, was identified immediately upstream of traV. The deduced product of traR was found to shar...

  17. Investigating Molecular Inheritance of Carbon in Star-forming Regions along a Galactic Gradient

    KAUST Repository

    Smith, Rachel L.

    2015-04-01

    Observations of CO isotopologues taken at high spectral resolution toward young stellar objects (YSOs) are valuable tools for investigating protoplanetary chemical reservoirs, and enable robust comparisons between YSOs and solar system material (meteorites and the Sun). Investigating a range of YSO environments also helps parameterize variations in the distribution and evolution of carbon-based molecules, furthering an understanding of prebiotic chemistry. We have begun a wide survey of massive YSOs using Keck-NIRSPEC at high spectral resolution (R=25,000). Fundamental and first-overtone near-IR CO rovibrational absorption spectra have thus far been obtained toward 14 massive, luminous YSOs at Galactocentric radii (RGC) ranging from ~4.5 to 9.7 kpc. From these data we can obtain precise [12CO]/[13CO] gas-phase abundance ratios along a Galactic gradient, and [12CO]/[13CO]Gas can be further evaluated against published [12CO2]/[13CO2]Ice and [12CO]/[13CO]Ice because all observations are in absorption, a robust study of molecular inheritance is possible by virtue of comparing 12C/13C along the same lines-of-sight. Initial results for cold CO gas at RGC ~ 6.1 kpc and 9.4 kpc reveal [12C16O]/[13C16O] of 59+/‑8 and 74+/‑3, respectively, roughly following an expected 12C/13C Galactic gradient. Thus far, we find [12CO]/[13CO] in the cold CO gas to be lower than [12CO2]/[13CO2]Ice, suggesting that CO2 may not originate from CO reservoirs as often assumed. While very high-resolution observations of CO gas toward low-mass YSOs observed with VLT-CRIRES show significant heterogeneity in [12CO]/[13CO] at RGC ~ 8 kpc, this dispersion is not found for the massive YSOs. Both the low-mass and massive YSOs have higher [12CO]/[13CO] in warm vs. cold gas, and both show signatures suggesting possible interplay between CO ice and gas reservoirs. Overall, our results indicate that carbon isotopic evolution in massive YSO environments may follow different paths compared to low-mass YSOs

  18. Molecular cloning and biologically active production of IpaD N-terminal region.

    Science.gov (United States)

    Hesaraki, Mahdi; Saadati, Mojtaba; Honari, Hossein; Olad, Gholamreza; Heiat, Mohammad; Malaei, Fatemeh; Ranjbar, Reza

    2013-07-01

    Shigella is known as pathogenic intestinal bacteria in high dispersion and pathogenic bacteria due to invasive plasmid antigen (Ipa). So far, a number of Ipa proteins have been studied to introduce a new candidate vaccine. Here, for the first time, we examined whether the N-terminal region of IpaD(72-162) could be a proper candidate for Shigella vaccine. Initially, the DNA sequence coding N-terminal region was isolated by PCR from Shigella dysenteriae type I and cloned into pET-28a expression vector. Then, the heterologous protein was expressed, optimized and purified by affinity Ni-NTA column. Western blot analysis using, His-tag and IpaD(72-162) polyclonal antibodies, confirmed the purity and specificity of the recombinant protein, respectively. Subsequently, the high immunogenicity of the antigen was shown by ELISA. The results of the sereny test in Guinea pigs showed that IpaD(72-162) provides a protective system against Shigella flexneri 5a and S. dysenteriae type I. Copyright © 2013. Published by Elsevier Ltd.

  19. Molecular Phylogenetic Screening of Withania somnifera Relative From Indonesia Based on Internal Transcribed Spacer Region

    Directory of Open Access Journals (Sweden)

    Topik Hidayat

    2016-04-01

    Full Text Available Withania somnifera (family Solanaceae, known commonly as Ashwaganda, is one of the important medicinal plants, and recent studies reported that Withanone, one of the chemical components in this plant, has ability to kill cancer cell. Because of endemic state of this plant to South Asia, exploring plant species under the same family which grow well in Indonesia has been of interest. The purpose of this study was to screen the Indonesian plant which has strong phylogenetic relationship with Ashwaganda. Thus, phylogenetic analysis using DNA sequences of internal transcribed spacer (ITS region was conducted. Thus, 19 species of Solanaceae and two species of Convolvulaceae as outgroup were examined. Five ITS regions of Ashwaganda retrieved from GenBank were included in the phylogenetic analysis. Parsimony analysis showed that Indonesia Solanaceae comprises seven groups which is consistent with the global Solanaceae relationship as previously reported. Furthermore, our study revealed that two species, Physalis angulata and Physalis peruviana, are relative to W. somnifera. Morphologically, they share characters of flower and fruit. This result indicated that these two species are potential to have similar chemical properties as Ashwaganda, thus we can have new variants of Withanone originated from Indonesia with similar effect.

  20. Biomechanical and molecular characteristics of hereditary equine regional dermal asthenia in Quarter Horses.

    Science.gov (United States)

    Grady, Jesse G; Elder, Steven H; Ryan, Peter L; Swiderski, Cyprianna E; Rashmir-Raven, Ann M

    2009-10-01

    Hereditary equine regional dermal asthenia (HERDA) is an autosomal recessive skin disorder that has yet to be fully characterized. HERDA is predominately expressed in Quarter Horses, with the majority of these disseminating from elite cutting horse bloodlines, leading to the increased incidence of HERDA in recent years. Affected horses have loose, hyper-extensible, fragile skin and are frequently euthanized due to poor wound healing and disfiguring scars. This study sought to better characterize HERDA by analysis of the biomechanical parameters of tensile strength, modulus of elasticity, energy to failure and thickness of skin from 10 affected and 6 unaffected horses using an Instron Universal Testing Instrument. In addition, total soluble collagen and glycosaminoglycan concentrations of skin were analysed from 13 affected and 12 unaffected horses using Sircol Soluble Collagen and Blyscan Sulfated Glycosaminoglycan assays respectively. Affected horses exhibited a two to threefold reduction in tensile strength versus unaffected horses with statistically significant differences at six of seven sample locations (P horses exhibited significantly higher amounts of total soluble collagen than unaffected horses (P horses demonstrated uniformly weaker skin across sample locations, indicating the biomechanical properties of HERDA are not regionally confined to specific areas of the horses' skin.

  1. Molecular characterization of genes encoding the quinolone resistance determining regions of Malaysian Streptococcus pneumoniae strains

    Directory of Open Access Journals (Sweden)

    Kumari N

    2008-01-01

    Full Text Available Genes encoding the quinolones resistance determining regions (QRDRs in Streptococcus pneumoniae were detected by PCR and the sequence analysis was carried out to identify point mutations within these regions. The study was carried out to observe mutation patterns among S. pneumoniae strains in Malaysia. Antimicrobial susceptibility testing of 100 isolates was determined against various antibiotics, out of which 56 strains were categorised to have reduced susceptibility to ciprofloxacin (≥2 μg/mL. These strains were subjected to PCR amplification for presence of the gyrA, parC , gyrB and parE genes. Eight representative strains with various susceptibilities to fluoroquinolones were sequenced. Two out of the eight isolates that were sequenced were shown to have a point mutation in the gyrA gene at position Ser81. The detection of mutation at codon Ser81 of the gyrA gene suggested the potential of developing fluoroquinolone resistance among S. pneumoniae isolates in Malaysia. However, further experimental work is required to confirm the involvement of this mutation in the development of fluoroquinolone resistance in Malaysia.

  2. Molecular detection of bovine immunodeficiency virus in water buffaloes (Bubalus bubalis) from the Amazon region, Brazil.

    Science.gov (United States)

    Albernaz, Tatiane Teles; Leite, Rômulo Cerqueira; Reis, Jenner Karlison Pimenta; de Sousa Rodrigues, Ana Paula; da Cunha Kassar, Telissa; Resende, Claudia Fideles; de Oliveira, Cairo Henrique Sousa; Silva, Rafaela das Mercês; Salvarani, Felipe Masiero; Barbosa, José Diomedes

    2015-12-01

    Bovine immunodeficiency is a chronic progressive disease caused by a lentivirus that affects cattle and buffaloes. Although the infection has been described in cattle in some countries, including in Brazil, there are only two reports of infection in buffaloes: one in Pakistan and one in Cambodia. The aim of the present study was to survey the occurrence of bovine immunodeficiency virus (BIV) in water buffaloes from the Amazon region, Pará state, Brazil. BIV proviral DNA was surveyed in 607 whole blood samples of water buffaloes from 10 farms located in the state of Pará using semi-nested polymerase chain reaction (PCR) (PCR-SN) to amplify the pol region of the viral genome. Of the 607 samples tested, 27 (4.4 %) were positive for BIV proviral DNA. The amplified fragments were confirmed by sequence analysis after cloning and nucleotide sequencing. The sequence obtained had 99 % similarity to the reference strain (R-29). The present study provides important epidemiological data because BIV was detected for the first time in water buffaloes in Brazil. Further, the results suggest the possibility of the virus being a risk factor for herd health because it may be a potential causal agent of chronic disease and, also may be associated to other infectious diseases.

  3. Molecular structure and translocation of a multiple antibiotic resistance region of a Psychrobacter psychrophilus permafrost strain.

    Science.gov (United States)

    Petrova, Mayya; Gorlenko, Zhosephine; Mindlin, Sofia

    2009-06-01

    A Psychrobacter psychrophilus strain resistant to tetracycline and streptomycin was isolated from a 15,000-35,000-year-old permafrost subsoil sediment sampled from the coast of the Eastern-Siberian Sea. The genes conferring antibiotic resistance were localized on an c. 30-kb pKLH80 plasmid. It was shown that the antibiotic resistance region of this plasmid has a mosaic structure and contains closely linked streptomycin resistance (strA-strB) and tetracycline resistance [tetR-tet(H)] genes, followed by a novel IS element (ISPpy1) belonging to the IS3 family. Both the strA-strB and tetR-tet(H) genes of pKLH80 were highly similar to those found in modern clinical bacterial isolates. It was shown that the ISPpy1 element of pKLH80 can direct translocation of the adjacent antibiotic resistance genes to different target plasmids, either by one-ended transposition or by formation of a composite transposon resulting from the insertion of the ISPpy1 second copy at the other side of the antibiotic resistance region. Thus, our data demonstrate that clinically important antibiotic resistance genes originated long before the introduction of antibiotics into clinical practice and confirm an important role of horizontal gene transfer in the distribution of these genes in natural bacterial populations.

  4. The molecular composition of the planet-forming regions of protoplanetary disks across the luminosity regime

    CERN Document Server

    Walsh, Catherine; van Dishoeck, Ewine F

    2015-01-01

    (Abridged) Near- to mid-IR observations of protoplanetary disks show that the inner regions (<10AU) are rich in small organic volatiles (e.g., C2H2 and HCN). Trends in the data suggest that disks around cooler stars (~3000K) are potentially more carbon- and molecule-rich than their hotter counterparts. Our aims are to explore the composition of the planet-forming region of disks around stars from M dwarf to Herbig Ae and compare with the observed trends. Models of the disk physical structure are coupled with a gas-grain chemical network to map the abundances in the planet-forming zone. N2 self shielding, X-ray-induced chemistry, and initial abundances, are investigated. The composition in the 'observable' atmosphere is compared with that in the midplane where the planet-building reservoir resides. M dwarf disk atmospheres are relatively more molecule rich than those for T Tauri or Herbig Ae disks. The weak far-UV flux helps retain this complexity which is enhanced by X-ray-induced ion-molecule chemistry. N...

  5. A GMRT survey of regions towards the Taurus Molecular Cloud at 323 and 608 MHz

    CERN Document Server

    Ainsworth, Rachael E; Green, David A; Scaife, Anna M M; Ray, Tom P

    2016-01-01

    We present observations of three active sites of star formation in the Taurus Molecular Cloud complex taken at 323 and 608 MHz (90 and 50 cm, respectively) with the Giant Metrewave Radio Telescope (GMRT). Three pointings were observed as part of a pathfinder project, targeted at the young stellar objects (YSOs) L1551 IRS 5, T Tau and DG Tau (the results for these target sources were presented in a previous paper). In this paper, we search for other YSOs and present a survey comprising of all three fields; a by-product of the large instantaneous field of view of the GMRT. The resolution of the survey is of order 10 arcsec and the best rms noise at the centre of each pointing is of order $100\\,\\mu$Jy beam$^{-1}$ at 323 MHz and $50\\,\\mu$Jy beam$^{-1}$ at 608 MHz. We present a catalogue of 1815 and 687 field sources detected above $5\\,\\sigma_{\\rm rms}$ at 323 and 608 MHz, respectively. A total of 440 sources were detected at both frequencies, corresponding to a total unique source count of 2062 sources. We compar...

  6. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region

    Directory of Open Access Journals (Sweden)

    van Pittius Nicolaas

    2009-09-01

    -encoding region of the M. tuberculosis genome is hypervariable. The observation that numerous different mutations have become fixed within specific lineages demonstrates that this genomic region is undergoing rapid molecular evolution and that further lineage-specific evolutionary expansion and diversification has occurred subsequent to the lineage-defining mutational events. We predict that functional loss of these genes could aid immune evasion. Finally, we also show that the PPE38 region of the published M. tuberculosis H37Rv whole genome sequence is not representative of the ATCC H37Rv reference strain.

  7. Molecular analysis of the F plasmid traVR region: traV encodes a lipoprotein.

    Science.gov (United States)

    Doran, T J; Loh, S M; Firth, N; Skurray, R A

    1994-07-01

    The nucleotide sequences of the conjugative F plasmid transfer region genes, traV and traR, have been determined. The deduced amino acid sequence of TraV indicated that it may be a lipoprotein; this was confirmed by examining the effect of globomycin on traV-encoded polypeptides synthesized in minicells. An open reading frame that may represent a previously undetected transfer gene, now designated trbG, was identified immediately upstream of traV. The deduced product of traR was found to share amino acid similarity with proteins from the bacteriophages 186 and P2 and with the dosage-dependent dnaK suppressor DksA.

  8. Molecular markers detect stable genomic regions underlying tomato fruit shelf life and weight

    Directory of Open Access Journals (Sweden)

    Guillermo Raúl Pratta

    2011-01-01

    Full Text Available Incorporating wild germplasm such as S. pimpinellifolium is an alternative strategy to prolong tomato fruit shelf life(SL without reducing fruit quality. A set of recombinant inbred lines with discrepant values of SL and weight (FW were derived byantagonistic-divergent selection from an interspecific cross. The general objective of this research was to evaluate Genotype x Year(GY and Marker x Year (MY interaction in these new genetic materials for both traits. Genotype and year principal effects and GYinteraction were statistically significant for SL. Genotype and year principal effects were significant for FW but GY interaction wasnot. The marker principal effect was significant for SL and FW but both year principal effect and MY interaction were not significant.Though SL was highly influenced by year conditions, some genome regions appeared to maintain a stable effect across years ofevaluation. Fruit weight, instead, was more independent of year effect.

  9. Molecular and serological prevalence of Babesia bovis and Babesia bigemina in water buffaloes in the northeast region of Thailand.

    Science.gov (United States)

    Terkawi, Mohamad Alaa; Huyen, Nguyen Xuan; Shinuo, Cao; Inpankaew, Tawin; Maklon, Khuanwalai; Aboulaila, Mahmoud; Ueno, Akio; Goo, Youn-Kyoung; Yokoyama, Naoaki; Jittapalapong, Sathaporn; Xuan, Xuenan; Igarashi, Ikuo

    2011-06-10

    Bovine babesiosis is a tick-transmitted hemoprotozoan disease that is mainly caused by Babesia bovis and Babesia bigemina and is characterized by significant morbidity and mortality worldwide. The disease is widespread in the northeastern region of Thailand, where an increasingly large part of the livestock is composed of water buffaloes. The present study was therefore conducted to investigate the epidemiological distribution of B. bovis and B. bigemina in water buffaloes in the northeastern region of Thailand. A total of 305 buffalo blood samples were randomly collected from five provinces and simultaneously analyzed by the nested PCR (nPCR) assay, ELISA, and IFAT techniques. The overall prevalence of B. bovis and B. bigemina was 11.2% and 3.6% by nPCR, 14.7% and 5.9% by ELISA, and 16.8% and 5.6% by IFAT, respectively. The high concordance between the molecular and the serological detection tests revealed the specificity and sensitivity of the diagnostic assays used for the detection of infection as well as the endemic stability status of the parasites in the surveyed areas. Statistically significant differences in the prevalence of the two infections were observed on the basis of age and location but not gender. Our data provide valuable information regarding the epidemiology of B. bovis and B. bigemina infection in water buffaloes in the northeastern region of Thailand which will likely be very beneficial for management and control programs of this disease.

  10. Molecular Epidemiology and Sequencing of the G-L Intergenic Region of Rabies Viruses Isolated in China

    Institute of Scientific and Technical Information of China (English)

    Sheng-Li MENG; QI-You XIAO; Guan-Mu DONG; Ge-Lin XU; Jia-Xin YAN; Ping-Gang MING; Jie WU; Xiao-Ming YANG; He-Tian MING; Feng-Cai ZHU; Dun-Jin ZHOU

    2007-01-01

    A group of 25 rabies viruses (RABVs),recovered from 24 dogs and one human case,were collected from various areas in China between 2004 and 2006.Genetic and phylogenetic analyses of the G-L intergenic region were carried out in 25 street RABV isolates and CTN vaccine strains of 7 generations.The study was based on the comparison of a 519 bp nucleotide sequence,encompassing the G-L intergenic region.The nucleotide sequence homologies of Chinese street strains were from 95.5% to 100%.The phylogenetic analysis showed that all Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and they were distributed according to their geographical origins.All of the Chinese strains were closely related but they could still be divided into two groups:group of street strains and group of CTN strains.This study presents details about the molecular epidemiology of rabies viruses based on the sequences of the G-L Intergenic region.

  11. A study of dynamical processes in the Orion KL region using ALMA-- Probing molecular outflow and inflow

    CERN Document Server

    Wu, Yuefang; Qin, Sheng-Li

    2014-01-01

    This work reports a high spatial resolution observations toward Orion KL region with high critical density lines of CH$_{3}$CN (12$_{4}$-11$_{4}$) and CH$_{3}$OH (8$_{-1, 8}$-7$_{0, 7}$) as well as continuum at $\\sim$1.3 mm band. The observations were made using the Atacama Large Millimeter/Submillimeter Array with a spatial resolution of $\\sim$1.5$^{\\prime\\prime}$ and sensitives about 0.07 K and $\\sim$0.18 K for continuum and line, respectively. The observational results showed that the gas in the Orion KL region consists of jet-propelled cores at the ridge and dense cores at east and south of the region, shaped like a wedge ring. The outflow has multiple lobes, which may originate from an explosive ejection and is not driven by young stellar objects. Four infrared bubbles were found in the Spitzer/IRAC emissions. These bubbles, the distributions of the previously found H$_2$ jets, the young stellar objects and molecular gas suggested that BN is the explosive center. The burst time was estimated to be $\\leq$...

  12. Molecular and morphological systematics of Elysia Risso, 1818 (Heterobranchia: Sacoglossa) from the Caribbean region.

    Science.gov (United States)

    Krug, Patrick J; Vendetti, Jann E; Valdés, Ángel

    2016-08-09

    The Caribbean is a biodiversity hotspot for photosynthetic sea slugs, with about 27 described species in the genus Elysia Risso, 1818. However, many species are poorly known or have complex taxonomic histories, complicating assessments of regional biodiversity and impeding studies of plastid symbiosis, speciation, and larval biology. Using an integrative approach, we address the taxonomy and systematics of Caribbean elysiids by performing robust tests of existing species hypotheses, and describe six new species. Species delimitation included DNA barcoding of up to 189 nominal conspecific specimens; nuclear gene sequences were then used to confirm that divergent lineages were genetically distinct candidate species. New synonymies and species descriptions are based on external anatomy, penial and radular morphology, developmental characters, and host ecology of all species described from the region, plus a critical review of the literature. We synonymized three species (Elysia annedupontae Ortea, Espinosa & Caballer in Ortea, Caballer, Moro & Espinosa, 2005, Elysia clarki Pierce et al. 2006, and Elysia leeanneae Caballer, Ortea & Espinosa in Ortea, Espinosa, Buske & Caballer, 2013), transfered one species from Bosellia (Elysia marcusi), and described six new species (Elysia pawliki n. sp., Elysia zemi n. sp., Elysia christinae n. sp., Elysia hamanni n. sp., Elysia taino n. sp., and Elysia buonoi n. sp.). We resurrected the name Elysia velutinus Pruvot-Fol, 1947, a senior synonym of Elysia tuca Ev. Marcus & Er. Marcus, 1967. Based on a four-gene phylogeny of 76 Elysia spp., we identified shifts in host use and penial armature that may explain patterns of endemic diversification in Elysia, invoking both ecological and non-ecological mechanisms. Non-monophyly of stylet-bearing species rejects previous attempts to classify species based on presence of a stylet (i.e., the genus Checholysia Ortea, Caballer, Moro & Espinosa, 2005). Our findings show how integrative

  13. MOLECULAR CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS STRAINS CIRCULATING IN THE URAL REGION, RUSSIA

    Directory of Open Access Journals (Sweden)

    T. V. Umpeleva

    2013-01-01

    Full Text Available Abstract. Overall 178 Mycobacterium tuberculosis isolates recovered in 2009–2011 from newly diagnosed epidemiologically unlinked to TB patients in the Ural region of Russia have been studied. The absolute concentration method was used for drug susceptibility testing. Mutations katG, inhA and rpoB associated with resistance to isoniazid and rifampicin were detected by microchip technology («TB-Biochip». The isolates were genotyped by real-time PCR for the detection of Beijing/non-Beijing genotypes and 15-locus MIRU-VNTR typing according to «MIRU-VNTRplus» (http://www.miru-vntrplus.org. More than half (55.1% of 178 isolates belonged to the Beijing family, 58.7% of them were multiple drug resistant (MDR mostly due to rpoBSer531→Leu and katGSer315→Thr1 substitutions. Fifty VNTR profiles were found in 98 Beijing isolates; 57 of them grouped into 9 clusters. The largest VNTR cluster included 23 (23.5% Beijing isolates and 21 of them were MDR. The 80 non-Beijing isolates showed 64 distinct VNTR patterns which belonged to 6 genetic families: LAM, Ural, Haarlem, etc. Among LAM and Ural isolates 30.4% and 28.6% were MDR, respectively. The 5 of 7 MDR LAM isolates had specific mutation profile:  rpoBAsp516→Val substitution and mutations katGSer315→Thr1 and inhA_T15. The MDR Ural isolates showed the heterogeneity of mutations in rpoB gene compared to other genotypes. Taken together, these findings suggest the emergence and spread of MDR-TB in the Ural region which is characterized by circulation of MDR strains of different genotypes with the Beijing family genotype to be predominant.

  14. Molecular analysis of the Adh region of the genome of Drosophila melanogaster.

    Science.gov (United States)

    Chia, W; Karp, R; McGill, S; Ashburner, M

    1985-12-20

    A small region of the genome of Drosophila melanogaster has been cloned in a series of overlapping phage. A length of 165 X 10(3) base-pairs of contiguous DNA that spans polytene chromosome region 35A4 to 35B1 and includes the structural gene for alcohol dehydrogenase (Adh) as well as at least two other genes, outspread (osp) and no-ocelli (noc), has been characterized by mapping chromosome aberrations to the DNA. The relationship between osp and Adh is surprising: of nine osp alleles associated with chromosome breakpoints, five map distal (i.e. 5') to Adh and four map proximal (i.e. 3') to this gene. None affects the expression of Adh. As defined by these and other breakpoints, the osp gene spans at least 52 X 10(3) base-pairs and overlaps the Adh gene. The noc gene, as defined by the mapping of nearly 30 breakpoints, is at least 50 X 10(3) base-pairs in size. Alleles of noc and noc- deletions show either of two kinds of interaction with the recessive lethality of l(2)br29ScoR+1, a lethal that maps immediately distal to noc. One class of noc allele is viable when heterozygous with ScoR+1, while the other class is lethal or semi-lethal. Both classes, however, are homozygous or hemizygous viable. The locations of these two classes of noc allele on the DNA fall into two clusters, with those that are viable with ScoR+1 located proximal to those that are not. The physical boundary between these classes lies at a site just distal to that of the breakpoint of the inversion associated with ScoR+1 itself.

  15. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    Science.gov (United States)

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  16. A regional study of the seasonal variation in the molecular composition of rainwater

    Science.gov (United States)

    Cottrell, Barbara A.; Gonsior, Michael; Isabelle, Lorne M.; Luo, W.; Perraud, Véronique; McIntire, Theresa M.; Pankow, James F.; Schmitt-Kopplin, Philippe; Cooper, William J.; Simpson, André J.

    2013-10-01

    Rainwater is not only a critical source of drinking and agricultural water but it plays a key role in the fate and transport of contaminants through their removal by wet deposition. Rainwater is a complex mixture of organic compounds yet despite its importance its spatial and temporal variability are not well understood and less than 50% of the organic matter has been characterized. In-depth analytical approaches were used in this study to characterize the seasonal variation in rainwater composition. Rainwater samples were collected over a one-year period in Scarborough, Ontario, Canada. The seasonal variation of atmospheric organic carbon (AOC) in rainwater was analyzed by excitation-emission matrix spectroscopy (EEMs), 1D and 2D NMR with compound identification by spectral database matching, GC-MS, FT-ICR-MS, and GC × GC-TOFMS. This combination of techniques provided four complementary datasets, with less than 10% overlap, of anthropogenic and biogenic AOC. NMR with database matching identified over 100 compounds, primarily carboxylic acids, carbohydrates, and nitrogen-containing compounds. GC × GC-TOFMS analysis identified 344 compounds in two rain events with 33% of the compounds common to both events. FT-ICR-MS generated a seasonally dependent profile of 1226-1575 molecular ions of CHO, CHOS, and CHON elemental composition. FT-ICR-MS and GC × GC-TOFMS datasets were compared using van Krevelen diagrams (H/C vs. O/C), the H/C ratio vs. mass/charge (m/z), and the carbon oxidation state/carbon number matrix. Fluorescence patterns were correlated with NMR results resulting in the identification one seasonally-dependent component of chromophoric dissolved organic matter (CDOM). This study demonstrated the importance of using of an integrated analytical approach to monitor the compositional variation of AOC.

  17. Molecular cloning of αRYR hotspot region 1 from broiler chicken

    Directory of Open Access Journals (Sweden)

    Iris Lamberti Ziober

    2009-11-01

    Full Text Available Samples of Pectoralis major m. were collected, and an RT-PCR analysis of the a-Ryanodine receptor (a RYR from chicken mRNA hotspot region spanning aminoacid residues 386 to 540, numbered according to the turkey sequence, revealed two classes of transcripts. The sequences of the first class were similar to turkey and human with 97% and 74% of identity, respectively, and included all transcripts with substitutions in the nucleotide sequence. The second class was characterized by the deletion of nucleotides, leading to a premature stop codon and coding for a truncated and nonfunctional protein. These results are to date the first report related to the sequencing of the chicken αRYR hotspot region 1, which will possibility serve as a guide for further studies regarding a solution in the poultry production chain related to the problem of pale, soft and exudative (PSE meat.Amostras do músculo Pectoralis major foram coletadas e uma RT-PCR foi conduzida para avaliar a sequência do mRNA do αRYR, região compreendida entre os resíduos de aminoácido 386-540, numerado de acordo com a sequência de perus. Os resultados revelaram duas classes de transcritos. O primeiro teve 97% e 74% de identidade com as sequências de αRyR e RyR1 de perus e humanos, respectivamente, e incluiu todos os transcritos com substituições de nucleotídeos. A segunda classe de transcritos foi caracterizada pela deleção de bases que levaram a um stop códon prematuro e a uma proteína truncada não-funcional. Esses resultados são até o momento, o primeiro relato de sequenciamento do αRYR, região hotspot1 de frangos e podem servir como guia para estudos futuros na tentativa de se encontrar uma solução para os problemas na cadeia de produção de frangos relacionados com as carnes PSE (pálida, flácida e exsudativa.

  18. Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA

    Directory of Open Access Journals (Sweden)

    Majid Talebi

    2016-06-01

    Full Text Available The present study describes plastid DNA polymorphism and reports a comparative analysis of two non-coding cpDNA regions (trnC–trnD and atpB–rbcL in pistachio. Seventeen different genotypes of domestic and wild pistachio from Iran, Syria, Turkey and America were sampled. Total genomic DNA was extracted and amplified with trnC–trnD and atpB–rbcL specific primers and then were sequenced. Phylogenetic relationships and depiction of phylogenetic trees were conducted. Cultivated genotypes of Pistacia vera were classified in a group regardless of their geographic location. P. vera was isolated from Sarakhs but they placed in the two close groups. Among cultivated genotypes, Jalab was separated from other cultivated genotypes. Pistacia Khinjuk was classified with Pistacia atlantica subsp. mutica. The findings confirm the common splitting hypothesis for commercial pistachio genotypes of the P. vera wild-type and also indicated the direct impact of Iranian genotypes in the evolutionary process of cultivated pistachios in other parts of the world. In conclusion it can be inferred that cultivated varieties of pistachio and P. vera var. sarakhs have the same origin, moreover genomic chloroplast could appropriately identify the interspecies relationships of pistachios.

  19. Biological and Molecular Variability of Alfalfa mosaic virus Affecting Alfalfa Crop in Riyadh Region

    Directory of Open Access Journals (Sweden)

    Mohammed A. AL-Saleh

    2013-12-01

    Full Text Available In 2011–2012, sixty nine samples were collected from alfalfa plants showing viral infection symptoms in Riyadh region. Mechanical inoculation with sap prepared from two collected samples out of twenty five possitive for Alfalfa mosaic virus (AMV by ELISA were produced systemic mosaic on Vigna unguiculata and Nicotiana tabacum, local lesion on Chenopodium amaranticolor and C. quinoa. Vicia faba indicator plants that induce mosaic and mottle with AMV-Sagir isolate and no infection with AMV-Wadi aldawasser isolate. Approximately 700-bp was formed by RT-PCR using AMV coat protein specific primer. Samples from infected alfalfa gave positive results, while healthy plant gave negative result using dot blot hybridization assay. The nucleotide sequences of the Saudi isolates were compared with corresponding viral nucleotide sequences reported in GenBank. The obtained results showed that the AMV from Australia, Brazil, Puglia and China had the highest similarity with AMV-Sajer isolate. While, the AMV from Spain and New Zealaland had the lowest similarity with AMV-Sajer and Wadi aldawasser isolates. The data obtained in this study has been deposited in the GenBank under the accession numbers KC434083 and KC434084 for AMV-Sajer and AMV- Wadialdawasser respectively. This is the first report regarding the gnetic make up of AMV in Saudi Arabia.

  20. Assessing the regional impact of Indonesian biomass burning emissions based on organic molecular tracers and chemical mass balance modeling

    Directory of Open Access Journals (Sweden)

    G. Engling

    2014-01-01

    Full Text Available Biomass burning activities commonly occur in Southeast Asia (SEA, and are particularly intense in Indonesia during dry seasons. The effect of biomass smoke emissions on air quality in the city state of Singapore was investigated during a haze episode in October 2006. Substantially increased levels of airborne particulate matter (PM and associated chemical species were observed during the haze period. Specifically, the enhancement in the concentration of molecular tracers for biomass combustion such as levoglucosan by as much as two orders of magnitude and diagnostic ratios of individual organic compounds indicated that biomass burning emissions caused a regional smoke haze episode due to their long-range transport by prevailing winds. With the aid of air mass back trajectories and chemical mass balance modeling, large-scale forest and peat fires in Sumatra and Kalimantan were identified as the sources of the smoke aerosol, exerting a significant impact on air quality in downwind areas, such as Singapore.

  1. Assessing the regional impact of indonesian biomass burning emissions based on organic molecular tracers and chemical mass balance modeling

    Science.gov (United States)

    Engling, G.; He, J.; Betha, R.; Balasubramanian, R.

    2014-08-01

    Biomass burning activities commonly occur in Southeast Asia (SEA), and are particularly intense in Indonesia during the dry seasons. The effect of biomass smoke emissions on air quality in the city state of Singapore was investigated during a haze episode in October 2006. Substantially increased levels of airborne particulate matter (PM) and associated chemical species were observed during the haze period. Specifically, the enhancement in the concentration of molecular tracers for biomass combustion such as levoglucosan by as much as two orders of magnitude and the diagnostic ratios of individual organic compounds indicated that biomass burning emissions caused a regional smoke haze episode due to their long-range transport by prevailing winds. With the aid of air mass backward trajectories and chemical mass balance modeling, large-scale forest and peat fires in Sumatra and Kalimantan were identified as the sources of the smoke aerosol, exerting a significant impact on air quality in downwind areas, such as Singapore.

  2. Molecular characterisation of Cryptosporidium spp. in lambs in the South Central region of the State of São Paulo

    Directory of Open Access Journals (Sweden)

    A.S. Zucatto

    2015-04-01

    Full Text Available Considering the proximity of sheep farmers to animals that are possibly diseased or releasing fecal oocysts into the environment and the marked pathogenicity in lambs, the aim of this study was to determine the occurrence and to molecularly characterize the infection by Cryptosporidium spp. in lambs in the South Central region of the state of São Paulo, Brazil. A total of 193 fecal samples were collected from sheep of several breeds, males and females, aged up to one year. Polymerase chain reaction (nested-PCR was used to amplify DNA fragments from the subunit 18S rRNA gene and indicated 15% positivity; sequencing of amplified fragments was possible for 19 samples. Analysis of the obtained sequences showed that the identified species were Cryptosporidium xiaoi for 15 samples, constituting thus the first molecular characterization study of this Cryptosporidium species in Brazil. Cryptosporidium ubiquitum was identified for three samples and Cryptosporidium meleagridis for one sample; the latter two are considered zoonotic species.

  3. Molecular identification of Theileria and Babesia in sheep and goats in the Black Sea Region in Turkey.

    Science.gov (United States)

    Aydin, Mehmet Fatih; Aktas, Munir; Dumanli, Nazir

    2013-08-01

    This study was carried out to investigate presence and distribution of Theileria and Babesia species via microscopic examination and reverse line blotting (RLB) techniques in sheep and goats in the Black Sea region of Turkey. For this purpose, 1,128 blood samples (869 sheep and 259 goats) were collected by active surveillance from sheep and goats in different provinces of various cities in the region in the years 2010 and 2011. Smears were prepared from the blood samples, stained with Giemsa, and examined under the light microscope for Theileria and Babesia piroplasms. The genomic DNAs were extracted from blood samples. The length of 360-430-bp fragment in the variable V4 region of 18S SSU rRNA gene of Theileria and Babesia species was amplified using the gDNAs. The polymerase chain reaction products were hybridized to the membrane-connected species-specific probes. A total of 38 animals (3.37%) including 34 sheep (3.91%) and 4 goats (1.54%) were found to be positive for Theileria spp. piroplasms in microscopic examination of smears while Babesia spp. piroplasm could not detected. Infection rates were 34.64% in sheep, 10.04% in goats, and totally 28.99% for Theileria ovis while 0.58% in sheep and totally 0.44% for Babesia ovis. However, Theileria sp. OT3 was detected in 2.65% of sheep and 2.04% of all animals; besides Theileria sp., MK had 0.58% prevalence in sheep and 0.77% in goats, with a total 0.62% with RLB. Although T. ovis and Theileria sp. MK were determined in both sheep and goats, B. ovis and Theileria sp. OT3 were observed only in the sheep. These results provide the first detailed molecular data for sheep and goat theileriosis and babesiosis in the region.

  4. Molecular characterisation of Newcastle disease virus isolates from different geographical regions in Mozambique in 2005

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    Raul Fringe

    2012-02-01

    Full Text Available Newcastle disease (ND is regarded as a highly contagious and economically important disease in poultry and has a worldwide distribution. Viral determinants for Newcastle disease virus (NDV virulence are not completely understood and viruses of different pathotypes can be found at live-bird markets in different geographical areas. The prevalence of Newcastle disease in village poultry in Mozambique is not well documented and strains of NDV involved in yearly outbreaks are unknown. The fusion (F protein is an important determinant of pathogenicity of the virus and is used commonly for phylogenetic analysis. Newcastle disease viruses from various geographical regions of Mozambique were sequenced and compared genetically to published sequences obtained from GenBank. Samples were collected in three different areas of Mozambique and NDV was isolated by infection of embryonated chicken eggs. Sequence analysis of the F-protein encoding gene was used to classify 28 isolates from Mozambique into genotypes and compare these genotypes phylogenetically with existing genotypes found in GenBank. The isolates obtained from Mozambique grouped mainly into two clades. In the first clade, 12 isolates grouped together with sequences of isolates representing genotypes from Mozambique that were previously described. In the second clade, 16 isolates group together with sequences obtained from GenBank originating from Australia, China, South Africa and the USA. Eleven of these isolates showed a high similarity with sequences from South Africa. The number of samples sequenced (n = 28, as well as the relatively small geographical collection area used in this study, are too small to be a representation of the circulating viruses in Mozambique in 2005. Viruses characterised in this study belonged to lineage 5b, a similar finding of a previous study 10 years ago. From this data, it merely can be concluded that no new introduction of the virus occurred from 1995 to 2005 in

  5. Molecular characterisation of Newcastle disease virus isolates from different geographical regions in Mozambique in 2005.

    Science.gov (United States)

    Fringe, Raul; Bosman, Anna-Mari; Ebersohn, Karen; Bisschop, Shahn; Abolnik, Celia; Venter, Estelle

    2012-08-31

    Newcastle disease (ND) is regarded as a highly contagious and economically important disease in poultry and has a worldwide distribution. Viral determinants for Newcastle disease virus (NDV) virulence are not completely understood and viruses of different pathotypes can be found at live-bird markets in different geographical areas. The prevalence of Newcastle disease in village poultry in Mozambique is not well documented and strains of NDV involved in yearly outbreaks are unknown. The fusion (F) protein is an important determinant of pathogenicity of the virus and is used commonly for phylogenetic analysis. Newcastle disease viruses from various geographical regions of Mozambique were sequenced and compared genetically to published sequences obtained from GenBank. Samples were collected in three different areas of Mozambique and NDV was isolated by infection of embryonated chicken eggs. Sequence analysis of the F-protein encoding gene was used to classify 28 isolates from Mozambique into genotypes and compare these genotypes phylogenetically with existing genotypes found in GenBank. The isolates obtained from Mozambique grouped mainly into two clades. In the first clade, 12 isolates grouped together with sequences of isolates representing genotypes from Mozambique that were previously described. In the second clade, 16 isolates group together with sequences obtained from GenBank originating from Australia, China, South Africa and the USA. Eleven of these isolates showed a high similarity with sequences from South Africa. The number of samples sequenced (n = 28), as well as the relatively small geographical collection area used in this study, are too small to be a representation of the circulating viruses in Mozambique in 2005. Viruses characterised in this study belonged to lineage 5b, a similar finding of a previous study 10 years ago. From this data, it merely can be concluded that no new introduction of the virus occurred from 1995 to 2005 in Mozambique.

  6. Identification and molecular analysis of infectious bursal disease in broiler farms in the Kurdistan Regional Government of Iraq.

    Science.gov (United States)

    Amin, Oumed Gerjis M; Jackwood, Daral J

    2014-10-01

    The present study was undertaken to characterize field isolates of infectious bursal disease virus (IBDV). The identification was done using reverse transcription-polymerase chain reaction (RT-PCR) and partial sequencing of the VP2 gene. Pooled bursal samples were collected from commercial broiler farms located in the Kurdistan Regional Government (KRG) of Iraq. The genetic material of the IBDV was detected in 10 out of 29 field samples. Sequences of the hypervariable VP2 region were determined for 10 of these viruses. Molecular analysis of the VP2 gene of five IBDVs showed amino acid sequences consistent with the very virulent (vv) IBDV. Two samples were identified as classic vaccine viruses, and three samples were classic vaccine viruses that appear to have mutated during replication in the field. Phylogenetic analysis showed that all five field IBDV strains of the present study were closely related to each other. On the basis of nucleotide sequencing and phylogenetic analysis, it is very likely that IBD-causing viruses in this part of Iraq are of the very virulent type. These IBDVs appear to be evolving relative to their type strains.

  7. Molecular composition and indigenity of organic matter in Late Neoproterozoic sedimentary rocks from the Yangtze region, South China

    Institute of Scientific and Technical Information of China (English)

    LI Meijun; WANG Tieguan; WANG Chunjiang; ZHANG Weibiao

    2006-01-01

    Diamictites from Late Neoproterozoic Nantuo tillites (~600 Ma), and dolomites from the overlying Dousantuo and Dengying formations in the Yangtze region, southern China, were analyzed for solvent extractable hydrocarbons. Even though all these samples have low contents of TOC and have undergone overmature thermal evolution, there has been still preserved quite a large amount of hydrocarbons. Analysis of the extracts by gas chromatography-mass spectrometry (GC-MS) revealed the presence of n-alkanes, regular acyclic isoprenoids, tricyclic terpanes, hopanes, gammacerane, steranes, and polyaromatic hydrocarbons. Strict experimental measurements were performed in the analytical procedure to prevent any potential contaminants from being introduced. All these bitumens have molecular markers of Precambrian characteristics and no external organics derived from current contamination events or migrated hydrocarbons from younger strata. The maturity parameters for bitumens indicate that the hydrocarbons are of over-maturity, which is consistent with the thermal maturity of the host rocks. Consequently, it is concluded that the Late Neoproterozoic bitumens in the Yangtze region, South China, are indigenous to their host rocks, which provides the basis for our organic geochemical research on "Snowball Earth" and "Cambrian Explosion."

  8. Cryptosporidium hominis Is a Newly Recognized Pathogen in the Arctic Region of Nunavik, Canada: Molecular Characterization of an Outbreak.

    Directory of Open Access Journals (Sweden)

    Karine Thivierge

    2016-04-01

    Full Text Available Cryptosporidium is a leading cause of childhood diarrhea in low-resource settings, and has been repeatedly associated with impaired physical and cognitive development. In May 2013, an outbreak of diarrhea caused by Cryptosporidium hominis was identified in the Arctic region of Nunavik, Quebec. Human cryptosporidiosis transmission was previously unknown in this region, and very few previous studies have reported it elsewhere in the Arctic. We report clinical, molecular, and epidemiologic details of a multi-village Cryptosporidium outbreak in the Canadian Arctic.We investigated the occurrence of cryptosporidiosis using a descriptive study of cases with onset between April 2013 and April 2014. Cases were defined as Nunavik inhabitants of any age presenting with diarrhea of any duration, in whom Cryptosporidium oocysts were detected by stool microscopy in a specialised reference laboratory. Cryptosporidium was identified in stool from 51 of 283 individuals. The overall annual incidence rate (IR was 420 / 100,000 inhabitants. The IR was highest among children aged less than 5 years (1290 /100,000 persons. Genetic subtyping for stool specimens from 14/51 cases was determined by DNA sequence analysis of the 60 kDa glycoprotein (gp60 gene. Sequences aligned with C. hominis subtype Id in all cases. No common food or water source of infection was identified.In this first observed outbreak of human cryptosporidiosis in this Arctic region, the high IR seen is cause for concern about the possible long-term effects on growth and development of children in Inuit communities, who face myriad other challenges such as overcrowding and food-insecurity. The temporal and geographic distribution of cases, as well as the identification of C. hominis subtype Id, suggest anthroponotic rather than zoonotic transmission. Barriers to timely diagnosis delayed the recognition of human cryptosporidiosis in this remote setting.

  9. Molecular identification of Theileria and Babesia in ticks collected from sheep and goats in the Black Sea region of Turkey.

    Science.gov (United States)

    Aydin, Mehmet Fatih; Aktas, Munir; Dumanli, Nazir

    2015-01-01

    A molecular survey was undertaken in the Black Sea region of Turkey to determine the presence of Theileria and Babesia species of medical and veterinary importance. The ticks were removed from sheep and goats, pooled according to species and locations, and analyzed by PCR-based reverse line blot (RLB) and sequencing. A total of 2241 ixodid ticks belonging to 5 genus and 12 species were collected and divided into 310 pools. Infection rates were calculated as the maximum likelihood estimation (MLE) with 95% confidence intervals (CI). Of the 310 pools tested, 46 (14.83%) were found to be infected with Theileria or Babesia species, and the overall MLE of the infection rate was calculated as 2.27% (CI 1.67-2.99). The MLE of the infection rates were calculated as 0.691% (CI 0.171-1.78) in Haemaphysalis parva, 1.47% (CI 0.081-6.37) in Rhipicephalus sanguineus, 1.84% (CI 0.101-7.87) in Ixodes ricinus, 2.86% (CI 1.68-4.48) in Rhipicephalus turanicus, 5.57% (CI 0.941-16.3) in Hyalomma marginatum, and 6.2% (CI 4.02-9.02) in Rhipicephalus bursa. Pathogens identified in ticks included Theileria ovis, Babesia ovis, Babesia bigemina, and Babesia microti. Most tick pools were infected with a single pathogen. However, five pools displayed mixed infections with T. ovis and B. ovis. This study provides the first molecular evidence for the presence of B. microti in ticks in Turkey.

  10. Minimum Cost Estimation of a Baseline Survey for a Molecular Epidemiology Cohort Study: Collecting Participants in a Model Region in Japan

    Science.gov (United States)

    Sawada, Norie; Iwasaki, Motoki; Ohashi, Kayo; Tsugane, Shoichiro

    2016-01-01

    Background Some recent molecular epidemiology studies of the effects of genetic and environmental factors on human health have required the enrollment of more than 100 000 participants and the involvement of regional study offices across the country. Although regional study office investigators play a critical role in these studies, including the acquisition of funds, this role is rarely discussed. Methods We first differentiated the functions of the regional and central study offices. We then investigated the minimum number of items required and approximate cost of a molecular epidemiology study enrolling 7400 participants from a model region with a population of 100 000 for a 4-year baseline survey using a standard protocol developed based on the protocol of Japan Public Health Center-based Prospective Study for the Next Generation. Results The functions of the regional study office were identified, and individual expenses were itemized. The total cost of the 4-year baseline survey was 153 million yen, excluding consumption tax. Accounting difficulties in conducting the survey were clarified. Conclusions We investigated a standardized example of the tasks and total actual costs of a regional study office. Our approach is easy to utilize and will help improve the management of regional study offices in future molecular epidemiology studies. PMID:27001116

  11. CH(+) Destruction by Reaction with H: Computing Quantum Rates To Model Different Molecular Regions in the Interstellar Medium.

    Science.gov (United States)

    Bovino, S; Grassi, T; Gianturco, F A

    2015-12-17

    A detailed analysis of an ionic reaction that plays a crucial role in the carbon chemistry of the interstellar medium (ISM) is carried out by computing ab initio reactive cross sections with a quantum method and by further obtaining the corresponding CH(+) destruction rates over a range of temperatures that shows good overall agreement with existing experiments. The differences found between all existing calculations and the very-low-T experiments are discussed and explored via a simple numerical model that links these cross section reductions to collinear approaches where nonadiabatic crossing is expected to dominate. The new rates are further linked to a complex chemical network that models the evolution of the CH(+) abundance in the photodissociation region (PDR) and molecular cloud (MC) environments of the ISM. The abundances of CH(+) are given by numerical solutions of a large set of coupled, first-order kinetics equations that employs our new chemical package krome. The analysis that we carry out reveals that the important region for CH(+) destruction is that above 100 K, hence showing that, at least for this reaction, the differences with the existing laboratory low-T experiments are of essentially no importance within the astrochemical environments discussed here because, at those temperatures, other chemical processes involving the title molecule are taking over. A detailed analysis of the chemical network involving CH(+) also shows that a slight decrease in the initial oxygen abundance might lead to higher CH(+) abundances because the main chemical carbon ion destruction channel is reduced in efficiency. This might provide an alternative chemical route to understand the reason why general astrochemical models fail when the observed CH(+) abundances are matched with the outcomes of their calculations.

  12. Molecular identification of blood source animals from black flies (Diptera: Simuliidae) collected in the alpine regions of Japan.

    Science.gov (United States)

    Imura, Takayuki; Sato, Yukita; Ejiri, Hiroko; Tamada, Asumi; Isawa, Haruhiko; Sawabe, Kyoko; Omori, Sumie; Murata, Koichi; Yukawa, Masayoshi

    2010-01-01

    One of vector-borne avian protozoa, Leucocytozoon lovati, has been found in the Japanese rock ptarmigans (Lagopus mutus japonicus), the endangered bird species distributed in the alpine regions in Japan. Vector arthropod species of L. lovati has also been estimated as Simuliidae black flies distributed in the same habitat of the host bird, however, possible blood meals of the black flies were not identified yet. To reveal host animals of black flies, we estimated the blood resources by using molecular techniques. Black flies were collected at Mt. Chogatake, one of the alpine regions of Japan in which Japanese rock ptarmigans live in June 2005. The analyzed 144 specimens were morphologically identified into five species including Simulium japonicum (n = 87), Prosimulium hirtipes (n = 48), Prosimulium yezoense (n = 3), Twinnia japonensis (n = 3), and Cnephia mutata (n = 3). Individually extracted DNA from the black flies was subjected to polymerase chain reaction (PCR) amplification targeting the partial mitochondrial cytochrome b gene of birds or mammals to identify the blood meals. Of 144 black flies examined, 34 specimens were PCR positive for avian hosts (23.6%). No mammalian-derived bloods were detected from the samples studied through. Sequences amplified from 11 black flies consist of S. japonicum, P. hirtipes, and C. mutata showed high similarity to that of the Japanese rock ptarmigan. Therefore, present results conclusively suggest that these three species of black flies might suck the bloods of Japanese rock ptarmigans and could be the vector for L. lovati infection among this endangered bird species of Japan.

  13. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  14. Tracing the general structure of Galactic molecular clouds using Planck data: I. The Perseus region as a test case

    CERN Document Server

    Stanchev, Orlin; Kauffmann, Jens; Donkov, Sava; Shetty, Rahul; Körtgen, Bastian; Klessen, Ralf S

    2015-01-01

    We present an analysis of probability distribution functions (pdfs) of column density in different zones of the star-forming region Perseus and its diffuse environment based on the map of dust opacity at 353 GHz available from the Planck archive. The pdf shape can be fitted by a combination of a lognormal function and an extended power-law tail at high densities, in zones centred at the molecular cloud Perseus. A linear combination of several lognormals fits very well the pdf in rings surrounding the cloud or in zones of its diffuse neighbourhood. The slope of the mean density scaling law $\\langle\\rho\\rangle_L \\propto L^\\alpha$ is steep ($\\alpha=-1.93$) in the former case and rather shallow ($\\alpha=-0.77\\pm0.11$) in the rings delineated around the cloud. We interpret these findings as signatures of two distinct physical regimes: i) a gravoturbulent one which is characterized by nearly linear scaling of mass and practical lack of velocity scaling; and ii) a predominantly turbulent one which is best described ...

  15. High molecular weight (C35+)n-alkanes of Neogene heavily biodegraded oil in the Qianmiqiao region, North China

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    With wax content of 1.62%, heavy oil has been produced from the sandstone reservoirs of Neogene Guantao Formation (Ng1Ⅲ). In the GC and GC-MS RIC profiles of its aliphatic fraction, n-alkanes are totally lost, which shows the result of heavy biodegradedation. However, the remaining trace C13-C36 n-alkanes can be still seen from its m/z 85 mass chromatogram. In addition, a complete series of C35-C73 high molecular weight (HMW) n-alkanes was detected by high-temperature gas chromatography (HTGC). The HMW n-alkane series shows a normal distribution pattern, a major peak at nC43, obvious odd-carbon-number predominance, CPI37-55 and OEP45-49 values up to 1.17 and 1.16-1.20 respectively. The present study not only has conformed the strong resistibility of HMW n-alkanes to biodegradation in crude oils as concluded by previous researchers, but also has provided some significant information on source input and maturity for the heavily biodegraded oil in the Qianmiqiao region.

  16. Thermodynamic study of simple molecular glasses: universal features in their heat capacity and the size of the cooperatively rearranging regions.

    Science.gov (United States)

    Tatsumi, Soichi; Aso, Shintaro; Yamamuro, Osamu

    2012-07-27

    We have obtained some universal thermodynamic properties on glass transitions of molecular liquids. The heat capacity C(p) of glassy propene, which was vitrified by using a vapor-deposition technique, was measured with a newly developed adiabatic calorimeter. Propene has the lowest glass transition temperature (T(g)=56 K), the largest C(p) jump at T(g) (C(p)(lq)/C(p)(gl)~2.5), and the lowest residual entropy (S(res)~Rln2) compared with glass-forming molecules measured before. We have analyzed the present data with other hydrocarbon molecules vitrified by liquid quenching and obtained the following results: (1) The excess heat capacities are scaled well by using a Kauzmann temperature T(K), (2) The size of the cooperative rearrangement region (CRR) frozen at T(g) increases with decreasing the temperature difference between T(g) and T(K) (Kauzmann temperature), and (3) The simpler the molecule is, the larger the frozen CRR becomes. These are all supporting the validity of the Adam-Gibbs theory.

  17. Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    Full Text Available OVO-like proteins (OVOL are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3 in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY. This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms.

  18. Water in star-forming regions with Herschel: highly excited molecular emission from the NGC 1333 IRAS 4B outflow

    CERN Document Server

    Herczeg, Gregory J; Bruderer, Simon; Kristensen, Lars E; van Dishoeck, Ewine F; Jørgensen, Jes K; Visser, Ruud; Wampfler, Susanne F; Bergin, Edwin A; Yildiz, Umut A; Pontoppidan, Klaus M; Gracia-Carpio, Javier

    2011-01-01

    During the embedded phase of pre-main sequence stellar evolution, a disk forms from the dense envelope while an accretion-driven outflow carves out a cavity within the envelope. Highly excited H2O emission in spatially unresolved Spitzer/IRS spectra of a low-mass Class 0 object, NGC 1333 IRAS 4B, has previously been attributed to the envelope-disk accretion shock but could instead be produced in an outflow. As part of the survey of low-mass sources in the Water in Star Forming Regions with Herschel (WISH-LM) program, we used Herschel/PACS to obtain a far-IR spectrum and several Nyquist-sampled spectral images with to determine the origin of excited H2O emission from NGC 1333 IRAS 4B. The spectrum has high signal-to-noise in a rich forest of H2O, CO, and OH lines, providing a near-complete census of far-IR molecular emission from a Class 0 protostar. The excitation diagrams for the three molecules all require fits with two excitation temperatures, indicating the presence of two physical components. The highly ...

  19. Spectral imaging of the Sagittarius B2 region in multiple 3-mm molecular lines with the Mopra telescope

    CERN Document Server

    Jones, P A; Cunningham, M R; Menten, K M; Schilke, P; Belloche, A; Leurini, S; Ott, J; Walsh, A J

    2007-01-01

    Using the Mopra telescope, we have undertaken a 3-mm spectral-line imaging survey of a 5 x 5 arcmin^2 area around Sgr B2. We covered almost the complete spectral the range from 81.7 to 113.5 GHz, with 2.2 MHz wide spectral channels or ~ 6 km/s, and have observed 24 lines, with 0.033 MHz wide, or ~ 0.1 km/s channels. We discuss the distribution of around 50 lines, and present velocity-integrated emission images for 38 of the lines. In addition, we have detected around 120 more lines, mostly concentrated at the particularly spectral line-rich Sgr B2(N) source. There are significant differences in molecular emission, pointing to both abundance and excitation differences throughout the region. Seven distinct spatial locations are identified for the emitting species, including peaks near the prominent star forming cores of Sgr B2(N), (M) and (S) that are seen in IR-to-radio continuum images. The other features are a 'North Ridge' and a 'North Cloud' to the north of the Sgr B2 N-M-S cores, a 'South-East Peak' and a...

  20. Characterization of the 5' flanking region of lipase gene from Penicillium expansum and its application in molecular breeding.

    Science.gov (United States)

    Zhang, Tian; Peng, Ying; Yu, Qingsheng; Wang, Jieliang; Tang, Kexuan

    2014-01-01

    A major challenge for further promotion of lipase productivity in Penicillium expansum PE-12 is to find a suitable promoter that can function efficiently in this industrial strain. In this study, the 5' flanking region of P. expansum lipase (Ppel) containing a putative novel promoter sequence was characterized by fusing to β-glucuronidase (GUS) and subsequently introducing into P. expansum. As a result, all the transformants showed blue color quickly after incubation in GUS detection buffer, suggesting a strong promoter activity of this fragment. Glucose repression was identified for the promoter, whereas olive oil acted as a positive regulator. Facilitated by this novel promoter, P. expansum PE-12 was genetically modified, with an improved lipase yield, via a recombinant plasmid with P. expansum lipase gene (PEL) under the control of Ppel promoter and TtrpC terminator. The highest lipase yield among the modified strains could attain 2,100 U/mL, which is more than twofold of the previous industrial strain (900 U/mL). The engineered strain through molecular breeding method as well as this new promoter has great value in lipase industry.

  1. Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

    Science.gov (United States)

    Machado Fritsch, Hegger; de Medeiros, Rúbia Marília; Maletich Junqueira, Dennis; Esteves de Matos Almeida, Sabrina; Pinto, Aguinaldo Roberto

    2016-01-01

    ABSTRACT The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1 env and pol genes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region. IMPORTANCE The AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our

  2. Molecular epidemiological study of Arctic rabies virus isolates from Greenland and comparison with isolates from throughout the Arctic and Baltic regions

    DEFF Research Database (Denmark)

    Mansfield, K.L.; Racloz, V.; McElhinney, L.M.

    2006-01-01

    We report a Molecular epidemiological study of rabies in Arctic Countries by comparing a panel of novel Greenland isolates to a larger cohort of viral sequences from both Arctic and Baltic regions. Rabies Virus isolates originating from wildlife (Arctic/red foxes, raccoon-dogs and reindeer), from...

  3. [Investigation of the presence of Francisella tularensis by culture, serology and molecular methods in mice of Thrace Region, Turkey].

    Science.gov (United States)

    Unal Yilmaz, Gülizar; Gurcan, Saban; Ozkan, Beytullah; Karadenizli, Aynur

    2014-04-01

    Tularemia is a disease that has been reported in Turkey since 1936. Although mice are considered to have a role in the transmission of Francisella tularensis to man, this has not been exactly confirmed yet. The aim of this study was to investigate the presence of F. tularensis in mice by using culture, serology and molecular methods. For this purpose, four villages (Edirne-Demirkoy, Kirklareli-Kaynarca, Tekirdag-Muzruplu, Tekirdag-Sinanli) were selected in Thrace Region of Turkey where tularemia cases had been reported previously. A total of 126 live-catch mouse traps were established in warehouses, barns, areas near wells, water tanks and creeks in the villages in December 2012. Traps were kept overnight and the next day the animals collected were identified at species-level. The live-captured mice were anesthetized and their heart blood samples were obtained. Subsequently, liver and spleen tissues were removed from every mouse under aseptic conditions in the class-2 safety cabinet. These tissues were cultivated in Francis medium containing 5% sheep blood, 0.1% cystein, 1% glucose and incubated for seven days in both normal atmosphere and 5% carbondioxide incubator at 37°C. Tularemia microagglutination test was performed by using the sera which were obtained from live-captured mice. Finally, DNAs were isolated from both liver and spleen tissues of mice, and real-time polymerase chain reaction (Tularemia RT-PCR; Public Health Agency of Turkey, Ankara) were performed. In our study, a total of 19 mice were captured and of these 11 were alive. Ten mice were identified as Apodemus flavicollis, seven were Mus macedonicus and two were Mus musculus. There were no Francisella tularensis isolation in the cultures of mice liver and spleen tissues. Serological tests yielded negative results for 10 mice whose serum samples could be obtained. In RT-PCR, positivity were detected in spleen tissues of two mice which were captured from Kaynarca where first tularemia cases in

  4. Effects of regional cerebral blood flow perfusion on learning and memory function and its molecular mechanism in rats

    Institute of Scientific and Technical Information of China (English)

    Cunli Xu; Wenhua Wu; Lingbin Kong

    2016-01-01

    Objective:To study the effects of regional cerebral blood flow (rCBF) perfusion on learning and memory function in special brain areas and its molecular mechanism in rat. Methods: Sixty-four adult male healthy Sprague-Dawley (SD) rats were randomly divided into two groups: Afalse operation group and an operation group. The false operation group was randomly divided into four subgroups (A0, B0, C0, and D0) and the operation group was randomly divided into four subgroups (A, B, C, and D), with eight rats in each subgroup. The operation group underwent bilateral common carotid artery permanent ligation, while the other group only underwent a skin incision without the bilateral common carotid artery permanent ligation. Learning memory function of rats in each subgroup was measured using a Y-maze at 4 h, 8 h, 24 h, and 3 days after surgery. The rCBF in the right frontal lobe and hippocampus was detected using the Periflux PF model laser Doppler flowmetry and c-fos, c-jun, Bcl-2, and Bax protein expression in the right frontal lobe and hippocampus was measured using immunohistochemistry. Results: The rCBF in the right frontal lobule division and right hippocampus division was significantly lower in the operation group than in the false operation group (P Conclusions:rCBF decrease can impair learning and memory function in rats, which may be related to the increased expression of c-fos, c-jun, Bcl-2, and Bax proteins in the frontal cortex and hippocampus.

  5. Taxonomic Notes on Nasutitermes and Bulbitermes (Termitidae, Nasutitermitinae from the Sunda region of Southeast Asia based on morphological and molecular characters

    Directory of Open Access Journals (Sweden)

    Syaukani Syaukani

    2011-11-01

    Full Text Available The Sunda region of Southeastern Asia is rich in termite fauna, but termites from this region have been poorly described. In this study, we described eight species from two diverse genera from this region, and from the family Termitidae. We describe Bulbitermes 4 spp. and Nasutitermes 4 spp. from new field collections. Where possible we examine original holotype specimens, and describe the essential morphological characters for soldier and worker castes. We devise two new bifurcating keys to guide the field identification of each species. In addition, we develop a nucleotide sequence profile for the COI gene. From this molecular character matrix, we use Neighbour-Joining analysis to test the monophyly of each morphospecies and genus. We find that the morphological and molecular characters are highly concordant, whereby all taxa appear to represent distinct molecular clades. For termites, there is therefore agreement between the morphological taxonomic characters used to sort species from a bifurcating key and the molecular taxonomic characters used to sort species on a bifurcating tree. This joint analysis suggests that DNA barcoding holds considerable promise for termite taxonomy, especially for diverse clades like Bulbitermes and Nasutitermes for which a global morphological key would be intractable.

  6. New structural insight of C-terminal region of Syntenin-1, enhancing the molecular dimerization and inhibitory function related on Syndecan-4 signaling

    DEFF Research Database (Denmark)

    Choi, Youngsil; Yun, Ji-Hye; Yoo, Jiho

    2016-01-01

    The PDZ domain-containing scaffold protein, syntenin-1, binds to the transmembrane proteoglycan, syndecan-4, but the molecular mechanism/function of this interaction are unknown. Crystal structure analysis of syntenin-1/syndecan-4 cytoplasmic domains revealed that syntenin-1 forms a symmetrical......-4 cytoplasmic domain, inhibiting the functions of syndecan-4 such as focal adhesion formation. Moreover, C-terminal region of syntenin-1 reveals an essential role for enhancing the molecular homodimerization. Mutation of key syntenin-1 residues involved in the syndecan-4 interaction or homodimer...

  7. Molecular epidemiology and BH4-responsiveness in patients with phenylalanine hydroxylase deficiency from Galicia region of Spain.

    Science.gov (United States)

    Couce, M L; Bóveda, M D; Fernández-Marmiesse, A; Mirás, A; Pérez, B; Desviat, L R; Fraga, J M

    2013-05-25

    Knowledge of hyperphenylalaninemia (HPA) mutational spectrum in a population allows in many cases an accurate prediction of the phenotype and tetrahydrobiopterin (BH4) responsiveness, thus selecting an adequate treatment. In this work, we have performed the molecular characterization of 105 HPA patients from Galicia, in the northwest region of Spain, evaluating their phenotype and BH4 response. The mutational spectrum analysis showed 47 distinct mutations in 89 families, 37 of them (78.7%) corresponding to missense mutations. Six mutations account for 47.2% of all the investigated alleles, each one with a frequency ≥ 5% (IVS10-11G>A, p.R261Q, p.V388M, p.R176L, p.E280K, p.A300S). The most prevalent HPA mutations in Galicia are the common Mediterranean mutation IVS10-11G>A and p.R261Q, with frequencies of 13.8% and 10.5%, respectively. One novel mutation (p.K361Q; c.1081A>C) was also reported. Although a good genotype-phenotype correlation is observed, there is no exact correlation for some genotypes involving mutations p.R261Q, p.I65T or IVS10-11G>A. Forty seven patients were monitored for post-challenge BH4, establishing genotype-based predictions of BH4-responsiveness in all of them. All phenylketonuric patients with 2 nonresponsive mutations were unresponsive to BH4 and patients with mutations previously associated with BH4 responsiveness in the two alleles had a clear positive response to the test, with the exception of 5 patients with mutations p.R261Q, p.I65T and p.R68S. Our study supports a similar degree of heterogeneity of the HPA mutation spectrum in Galicia compared to reported data from Southern Europe. Patients carrying null mutations in both alleles showed the highest degree of concordance with the most severe phenotypes. Genotype is a good predictor of BH4 response.

  8. Abundant molecular gas and inefficient star formation in intracluster regions: Ram pressure stripped tail of the Norma galaxy ESO137-001

    CERN Document Server

    Jachym, Pavel; Cortese, Luca; Sun, Ming; Kenney, Jeffrey D P

    2014-01-01

    For the first time, we reveal large amounts of cold molecular gas in a ram pressure stripped tail, out to a large, intracluster distance from the galaxy. With the ESO APEX telescope we have detected 12CO(2-1) emission corresponding to more than 10^9 Msun of molecular gas (assuming a Galactic value of the CO-to-H_2 conversion factor) in three Ha bright regions along the tail of the Norma cluster ram pressure stripped galaxy ESO137-001, out to a projected distance of 40 kpc from the disk. The amount of 1.5x10^8 Msun of H_2 found in the most distant region is similar to molecular masses of tidal dwarf galaxies. We speculate that a ram pressure dwarf galaxy (RPDG) could be forming in this location. Along the tail, the amount of molecular gas was found to drop, while masses of the X-ray emitting and diffuse ionized components stay roughly constant. Moreover, the amounts of hot and cold gas are large and similar, and together nearly account for the missing gas from the disk. We find a very low star formation effici...

  9. Molecular epidemiology of Theileria annulata and identification of 18S rRNA gene and ITS regions sequences variants in apparently healthy buffaloes and cattle in Pakistan.

    Science.gov (United States)

    Khan, Muhammad Kasib; He, Lan; Hussain, Altaf; Azam, Sabita; Zhang, Wen-Jie; Wang, Li-Xia; Zhang, Qing-Li; Hu, Min; Zhou, Yan-Qin; Zhao, Junlong

    2013-01-01

    A molecular epidemiological survey was conducted to determine the prevalence of piroplasms in buffaloes and cattle from Sheikhupura and Okara districts of Punjab, Pakistan using reverse line blot (RLB) hybridization assay. The genetic diversity within 18S rRNA gene and ITS regions sequences of various obtained Theileria species (spp.) was also investigated. Briefly, 102 blood samples from buffaloes and cattle in the study districts were collected on blood collection cards and brought to the laboratory. DNA was extracted; the V4 hypervariable region of 18S rRNA was amplified and analyzed using RLB. Out of total samples analyzed, 61 (59.8%) were hybridized with Babesia/Theileria (B/T) genus-specific probe. Only one species of piroplasm was detected in buffaloes and cattle in study districts, i.e. Theileria (T.) annulata. Six samples only hybridized with B/T genus-specific and Theileria genus-specific probes but not with any species-specific probe indicating the presence of novel species or variants. The sequences of 18S rRNA gene and ITS regions of these six samples revealed the presence of T. annulata variants as confirmed through sequence identity estimation and phylogenetic analyses. Meanwhile, an unexpected sequence variation was observed within the 18S rRNA gene and ITS regions sequences of T. annulata identified in the present study. This is the first report on the simultaneous detection of species of piroplasms infecting buffaloes and cattle in Pakistan and molecular characterization of T. annulata 18S rRNA gene and ITS regions. The present study may address the new insights into the epidemiology of theileriosis which will help researches in designing control strategies and developing various molecular diagnostic tools at national level.

  10. Regional molecular and cellular differences in the female rabbit Achilles tendon complex: potential implications for understanding responses to loading.

    Science.gov (United States)

    Huisman, Elise S; Andersson, Gustav; Scott, Alexander; Reno, Carol R; Hart, David A; Thornton, Gail M

    2014-05-01

    The aim of this study was: (i) to analyze the morphology and expression of extracellular matrix genes in six different regions of the Achilles tendon complex of intact normal rabbits; and (ii) to assess the effect of ovariohysterectomy (OVH) on the regional expression of these genes. Female New Zealand White rabbits were separated into two groups: (i) intact normal rabbits (n = 4); and (ii) OVH rabbits (n = 8). For each rabbit, the Achilles tendon complex was dissected into six regions: distal gastrocnemius (DG); distal flexor digitorum superficialis; proximal lateral gastrocnemius (PLG); proximal medial gastrocnemius; proximal flexor digitorum superficialis; and paratenon. For each of the regions, hematoxylin and eosin staining was performed for histological evaluation of intact normal rabbit tissues and mRNA levels for proteoglycans, collagens and genes associated with collagen regulation were assessed by real-time reverse transcription-quantitative polymerase chain reaction for both the intact normal and OVH rabbit tissues. The distal regions displayed a more fibrocartilaginous phenotype. For intact normal rabbits, aggrecan mRNA expression was higher in the distal regions of the Achilles tendon complex compared with the proximal regions. Collagen Type I and matrix metalloproteinase-2 expression levels were increased in the PLG compared to the DG in the intact normal rabbit tissues. The tendons from OVH rabbits had lower gene expressions for the proteoglycans aggrecan, biglycan, decorin and versican compared with the intact normal rabbits, although the regional differences of increased aggrecan expression in distal regions compared with proximal regions persisted. The tensile and compressive forces experienced in the examined regions may be related to the regional differences found in gene expression. The lower mRNA expression of the genes examined in the OVH group confirms a potential effect of systemic estrogen on tendon.

  11. The Far‐Infrared Spectrum of the Sagittarius B2 Region: Extended Molecular Absorption, Photodissociation, and Photoionization

    OpenAIRE

    Goicoechea, Javier R.; Nemesio J. Rodríguez-Fernández; Cernicharo, José

    2003-01-01

    We present large scale 9'x 27'(25 pc x 70 pc) far-IR observations around Sgr B2 using the Long-wavelength spectrometer (LWS) on board the Infrared Space Observatory (ISO). The spectra are dominated by the strong continuum emission of dust, the widespread molecular absorption of light hydrides (OH, CH and H2O) and the fine structure lines of [NII], [NIII], [OIII], [CII] and [OI]. The molecular richness in the outer layers of Sgr B2 is probed by the ISO-LWS Fabry-Perot (35 km s^-1) detections t...

  12. A molecular outflow evidencing star formation activity in the vicinity of the HII region G034.8-0.7 and the SNR W44

    CERN Document Server

    Paron, S; Rubio, M; Dubner, G

    2009-01-01

    This work aims at investigating the molecular gas component in the vicinity of two young stellar object (YSO) candidates identified at the border of the HII region G034.8-0.7 that is evolving within a molecular cloud shocked by the SNR W44. The purpose is to explore signatures of star forming activity in this complex region. We performed a near and mid infrared study towards the border of the HII region G034.8-0.7 and observed a 90" X 90" region near 18h 56m 48s, +01d 18' 45" (J2000) using the Atacama Submillimeter Telescope Experiment (ASTE) in the 12CO J=3--2, 13CO J=3--2, HCO+ J=4--3 and CS J=7--6 lines with an angular resolution of 22". Based on the infrared study we propose that the source 2MASS 18564827+0118471 (IR1 in this work) is a YSO candidate. We discovered a bipolar 12CO outflow in the direction of the line of sight and a HCO+ clump towards IR1, confirming that it is a YSO. From the detection of the CS J=7--6 line we infer the presence of high density (>10^7 cm^-3) and warm (>60 K) gas towards IR...

  13. Abundant molecular gas and inefficient star formation in intracluster regions: ram pressure stripped tail of the Norma galaxy ESO137-001

    Energy Technology Data Exchange (ETDEWEB)

    Jáchym, Pavel [Astronomical Institute, Academy of Sciences of the Czech Republic, Boční II 1401, 14100 Prague (Czech Republic); Combes, Françoise [Observatoire de Paris, LERMA, 61 Av. de l' Observatoire, F-75014 Paris (France); Cortese, Luca [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Mail H30, P.O. Box 218, Hawthorn, VIC 3122 (Australia); Sun, Ming [Department of Physics, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899 (United States); Kenney, Jeffrey D. P., E-mail: jachym@ig.cas.cz [Department of Astronomy, Yale University, 260 Whitney Avenue, New Haven, CT 06511 (United States)

    2014-09-01

    For the first time, we reveal large amounts of cold molecular gas in a ram-pressure-stripped tail, out to a large 'intracluster' distance from the galaxy. With the Actama Pathfinder EXperiment (APEX) telescope, we have detected {sup 12}CO(2-1) emission corresponding to more than 10{sup 9} M {sub ☉} of H{sub 2} in three Hα bright regions along the tail of the Norma cluster galaxy ESO 137-001, out to a projected distance of 40 kpc from the disk. ESO 137-001 has an 80 kpc long and bright X-ray tail associated with a shorter (40 kpc) and broader tail of numerous star forming H II regions. The amount of ∼1.5 × 10{sup 8} M {sub ☉} of H{sub 2} found in the most distant region is similar to molecular masses of tidal dwarf galaxies, though the standard Galactic CO-to-H{sub 2} factor could overestimate the H{sub 2} content. Along the tail, we find the amount of molecular gas to drop, while masses of the X-ray-emitting and diffuse ionized components stay roughly constant. Moreover, the amounts of hot and cold gas are large and similar, and together nearly account for the missing gas from the disk. We find a very low SFE (τ{sub dep} > 10{sup 10} yr) in the stripped gas in ESO 137-001 and suggest that this is due to a low average gas density in the tail, or turbulent heating of the interstellar medium that is induced by a ram pressure shock. The unprecedented bulk of observed H{sub 2} in the ESO 137-001 tail suggests that some stripped gas may survive ram pressure stripping in the molecular phase.

  14. Molecular cytogenetic analysis of Inv Dup(15) chromosomes, using probes specific for the Pradar-Willi/Angelman syndrome region: Clinical implications

    Energy Technology Data Exchange (ETDEWEB)

    Leana-Cox, J. (Univ. of Maryland School of Medicine, Baltimore, MD (United States)); Jenkins, L. (Kaiser Permanente Medical Group, San Jose, CA (United States)); Palmer, C.G.; Plattner, R. (Indiana School of Medicine, Indianapolis, IN (United States)); Sheppard, L. (Palo Verde Laboratory, Inc., Chandler, AZ (United States)); Flejter, W.L. (Univ. of Michigan, Ann Arbor, MI (United States)); Zackowski, J. (Univ. of Florida Health Science Center, Gainsville, FL (United States)); Tsien, F. (Tulane Univ. School of Medicine, New Orleans, LA (United States)); Schwartz, S. (Case Western Reserve Univ., Cleveland, OH (United States))

    1994-05-01

    Twenty-seven cases of inverted duplications of chromosome 15 (inv dup[15]) were investigated by FISH with two DNA probes specific for the Prader-Willi syndrome/Angelman syndrome (PWS/AS) region on proximal 15q. Sixteen of the marker chromosomes displayed two copies of each probe, while in the remaining 11 markers no hybridization was observed. A significant association was found between the presence of this region and an abnormal phenotype (P<.01). This is the largest study to date of inv dup(15) chromosomes, that uses molecular cytogenetic methods and is the first to report a significant association between the presence of a specific chromosomal region in such markers and an abnormal phenotype. 30 refs., 1 fig., 4 tabs.

  15. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF mediated gene expression pattern in Elaeis guineensis compared to other species.

    Directory of Open Access Journals (Sweden)

    Xintao Lei

    Full Text Available Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors of COG (Cluster of Orthologous Group annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR. CBFs reached maximum transcript level both at medium (4 h and long period time points (7 days, contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  16. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

    Science.gov (United States)

    Lei, Xintao; Xiao, Yong; Xia, Wei; Mason, Annaliese S; Yang, Yaodong; Ma, Zilong; Peng, Ming

    2014-01-01

    Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  17. Hybridization Dynamics of Invasive Cattail (Typhaceae) Stands in the Western Great Lakes Region of North America: A Molecular Analysis

    National Research Council Canada - National Science Library

    Steven E. Travis; Joy E. Marburger; Steve Windels; Barbora Kubátová

    2010-01-01

    ... angustifolia occur together in the Western Great Lakes Region of North America. 4. Based on microsatellite markers, we documented F1 hybrids as the most common class at five intensively sampled sites, constituting up to 90...

  18. The Study of Cellular and Molecular Physiological Characteristics of Sperm in Men Living in the Aral Sea Region

    Directory of Open Access Journals (Sweden)

    Berikbay Z. Kultanov

    2015-12-01

    CONCLUSIONS: Men living in environmentally disadvantaged areas of Kyzylorda region under the influence of dust and salt aerosols and other toxicants leads to disruption of the reproductive function in men.

  19. Dynamical Expansion of H II Regions from Ultracompact to Compact Sizes in Turbulent, Self-Gravitating Molecular Clouds

    CERN Document Server

    MacLow, M M; Oishi, J S; Abel, T; Low, Mordecai-Mark Mac; Toraskar, Jayashree; Oishi, Jeffrey S.; Abel, Tom

    2006-01-01

    The nature of ultracompact H II regions (UCHRs) remains poorly determined. In particular, they are about an order of magnitude more common than would be expected if they formed around young massive stars and lasted for one dynamical time, around 10^4 yr. We here perform three-dimensional numerical simulations of the expansion of an H II region into self-gravitating, radiatively cooled gas, both with and without supersonic turbulent flows. In the laminar case, we find that H II region expansion in a collapsing core produces nearly spherical shells, even if the ionizing source is off-center in the core. This agrees with analytic models of blast waves in power-law media. In the turbulent case, we find that the H II region does not disrupt the central collapsing region, but rather sweeps up a shell of gas in which further collapse occurs. Although this does not constitute triggering, as the swept-up gas would eventually have collapsed anyway, it does expose the collapsing regions to ionizing radiation. We suggest...

  20. A MOLECULARLY CHARACTERIZED INTERSTITIAL DELETION ENCOMPASSING THE 11q14.1-q23.3 REGION IN A CASE WITH MULTIPLE CONGENITAL ABNORMALITIES.

    Science.gov (United States)

    Cetin, Z; Altiok-Clark, O; Yakut, S; Guzel-Nur, B; Mihci, E; Berker-Karauzum, S

    2016-01-01

    Interstitial deletion of chromosome 11 long arm is a rare event. In most of the interstitial deletions on the long arm of chromosome 11 both the position and the size of these deletions are heterogeneous making a precise karyotype-phenotype correlation. In only a few of the reported cases has the deletion been molecularly characterized. Our patient was a 13-year-old male presented; mental motor retardation, strabismus, myopia, retinopathy, sensorineural hearing loss, a long and triangular face, a broad forehead, hypotelorism, nasal septal deviation, a beaked nose, hypoplastic ala nasie, bilateral low-set ears, a high arched palate, crowded teeth, retrognathia, thin lips, a long neck, and sloping shoulders, hyperactive behavior, pulmonary stenosis and lumbar scoliosis. Conventional cytogenetic analysis revealed 46,XY,del(11)(q14.1-q23.3) karyotype in the patient. Array-CGH analysis of the patient's DNA revealed an interstitial deletion encompassing 33.2 Mb in the 11q14.1-q23.3 genomic region (chr11: 83,161,443-116,401,751 ; Hg19). In this report, we present a patient with an interstitial deletion on the long arm of chromosome 11 that encompassed the 11q14.1-q23.3 region; and, using array-CGH analysis, we molecularly characterized the deleted region.

  1. Molecular and morphological data support recognition of a new genus of New World direct-developing frog (Anura: Terrarana) from an under-sampled region of South America.

    Science.gov (United States)

    Heinicke, Matthew P; Barrio-Amorós, César L; Hedges, S Blair

    2015-07-16

    We describe a new genus of New World direct-developing frog (Terrarana) from the northern Andes of Venezuela and adjacent Colombia. Tachiramantis gen. nov. includes three species formerly placed in the large genus Pristimantis. Molecular phylogenetic analysis of data from five nuclear and mitochondrial genes shows that Tachiramantis is not part of Pristimantis or any other named genus in its family (Craugastoridae or Strabomantidae). Morphological evidence further supports the distinctiveness of Tachiramantis, which has several aspects of skull morphology that are rare or absent in Pristimantis and synapomorphic for Tachiramantis, including frontoparietal-prootic fusion and degree of vomer development. The terminal phalanges, which narrow greatly before expanding at the tips, may represent an additional morphological synapomorphy. One species, T. prolixodiscus, also displays a fenestra between the posterior portions of the frontoparietals, a character state otherwise present in only 1 of 98 other sampled terraranan species. We use mapped ranges of most New World direct-developing frogs to show that Tachiramantis occurs in a geographic region that had been under-sampled in previous molecular studies of New World direct-developing frogs. Other under-sampled regions are identified in western Peru, Colombia, and northern Central America; these regions should provide fruitful target taxa for future phylogenetic studies.

  2. Sequence analysis of the 3’-untranslated region of HSP70 (type I genes in the genus Leishmania: its usefulness as a molecular marker for species identification

    Directory of Open Access Journals (Sweden)

    Requena Jose M

    2012-04-01

    Full Text Available Abstract Background The Leishmaniases are a group of clinically diverse diseases caused by parasites of the genus Leishmania. To distinguish between species is crucial for correct diagnosis and prognosis as well as for treatment decisions. Recently, sequencing of the HSP70 coding region has been applied in phylogenetic studies and for identifying of Leishmania species with excellent results. Methods In the present study, we analyzed the 3’-untranslated region (UTR of Leishmania HSP70-type I gene from 24 strains representing eleven Leishmania species in the belief that this non-coding region would have a better discriminatory capacity for species typing than coding regions. Results It was observed that there was a remarkable degree of sequence conservation in this region, even between species of the subgenus Leishmania and Viannia. In addition, the presence of many microsatellites was a common feature of the 3´-UTR of HSP70-I genes in the Leishmania genus. Finally, we constructed dendrograms based on global sequence alignments of the analyzed Leishmania species and strains, the results indicated that this particular region of HSP70 genes might be useful for species (or species complex typing, improving for particular species the discrimination capacity of phylogenetic trees based on HSP70 coding sequences. Given the large size variation of the analyzed region between the Leishmania and Viannia subgenera, direct visualization of the PCR amplification product would allow discrimination between subgenera, and a HaeIII-PCR-RFLP analysis might be used for differentiating some species within each subgenera. Conclusions Sequence and phylogenetic analyses indicated that this region, which is readily amplified using a single pair of primers from both Old and New World Leishmania species, might be useful as a molecular marker for species discrimination.

  3. Sequence analysis of the 3'-untranslated region of HSP70 (type I) genes in the genus Leishmania: its usefulness as a molecular marker for species identification.

    Science.gov (United States)

    Requena, Jose M; Chicharro, Carmen; García, Lineth; Parrado, Rudy; Puerta, Concepción J; Cañavate, Carmen

    2012-04-28

    The Leishmaniases are a group of clinically diverse diseases caused by parasites of the genus Leishmania. To distinguish between species is crucial for correct diagnosis and prognosis as well as for treatment decisions. Recently, sequencing of the HSP70 coding region has been applied in phylogenetic studies and for identifying of Leishmania species with excellent results. In the present study, we analyzed the 3'-untranslated region (UTR) of Leishmania HSP70-type I gene from 24 strains representing eleven Leishmania species in the belief that this non-coding region would have a better discriminatory capacity for species typing than coding regions. It was observed that there was a remarkable degree of sequence conservation in this region, even between species of the subgenus Leishmania and Viannia. In addition, the presence of many microsatellites was a common feature of the 3'-UTR of HSP70-I genes in the Leishmania genus. Finally, we constructed dendrograms based on global sequence alignments of the analyzed Leishmania species and strains, the results indicated that this particular region of HSP70 genes might be useful for species (or species complex) typing, improving for particular species the discrimination capacity of phylogenetic trees based on HSP70 coding sequences. Given the large size variation of the analyzed region between the Leishmania and Viannia subgenera, direct visualization of the PCR amplification product would allow discrimination between subgenera, and a HaeIII-PCR-RFLP analysis might be used for differentiating some species within each subgenera. Sequence and phylogenetic analyses indicated that this region, which is readily amplified using a single pair of primers from both Old and New World Leishmania species, might be useful as a molecular marker for species discrimination.

  4. [Molecular analysis of a copy of the novel mobile element Burdock and the region of its insertion into the cut locus of Drosophila melanogaster].

    Science.gov (United States)

    Ponomarenko, N A; Aĭrikh, L G; Bannikov, V M; Anashchenko, V A; Churikov, N A

    1997-01-01

    Molecular analysis of a copy of the novel mobile element burdock and its insertion region into the cut locus of Drosophila was performed. The burdock was shown to be a retrotransposon containing a single open reading frame (ORF). It does not contain domens coding for protease, RNAse H, reverse transcriptase, and integrase, which are required for transposition. However, multiple insertions of this copy of the mobile element into a definite region of the cut locus (hot site) were observed earlier. The polypeptide encoded by the burdock ORF contains two successive regions homologous to the proteins encoded by the ORF1 and ORF2 of the gypsy retrotransposon in N and C regions, respectively. The burdock insertion into this region of the cut locus interrupts its ORF, since the mobile element is transcribed in the opposite direction compared with the transcription in the locus. This is presumed to account for the arising of a lethal mutation. The hot site of this element integration into the locus corresponds to the recognition site of Drosophila topoisomerase II.

  5. Prenatal diagnosis of chromosome 15 abnormalities in the Prader-Willi/Angelman syndrome region by traditional and molecular cytogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Toth-Fejel, S.; Magenis, R.E.; Leff, S. [Oregon Health Sciences Univ., Portland, OR (United States)] [and others

    1995-02-13

    With improvements in culturing and banding techniques, amniotic fluid studies now achieve a level of resolution at which the Prader-Willi syndrome (PWS) and Angelman syndrome (AS) region may be questioned. Chromosome 15 heteromorphisms, detected with Q- and R-banding and used in conjunction with PWS/AS region-specific probes, can confirm a chromosome deletion and establish origin to predict the clinical outcome. We report four de novo cases of an abnormal-appearing chromosome 15 in amniotic fluid samples referred for advanced maternal age or a history of a previous chromosomally abnormal child. The chromosomes were characterized using G-, Q-, and R-banding, as well as isotopic and fluorescent in situ hybridization of DNA probes specific for the proximal chromosome 15 long arm. In two cases, one chromosome 15 homolog showed a consistent deletion of the ONCOR PWS/AS region A and B. In the other two cases, one of which involved an inversion with one breakpoint in the PWS/AS region, all of the proximal chromosome 15 long arm DNA probes used in the in situ hybridization were present on both homologs. Clinical follow-up was not available on these samples, as in all cases the parents chose to terminate the pregnancies. These cases demonstrate the ability to prenatally diagnose chromosome 15 abnormalities associated with PWS/AS. In addition, they highlight the need for a better understanding of this region for accurate prenatal diagnosis. 41 refs., 5 figs.

  6. Molecular fingerprint-region spectroscopy from 5 to 12  μm using an orientation-patterned gallium phosphide optical parametric oscillator.

    Science.gov (United States)

    Maidment, Luke; Schunemann, Peter G; Reid, Derryck T

    2016-09-15

    We report a femtosecond optical parametric oscillator (OPO) based on the new semiconductor gain material orientation-patterned gallium phosphide (OP-GaP), which enables the production of high-repetition-rate femtosecond pulses spanning 5-12 μm with average powers in the few to tens of milliwatts range. This is the first example of a broadband OPO operating across the molecular fingerprint region, and we demonstrate its potential by conducting broadband Fourier-transform spectroscopy using water vapor and a polystyrene reference standard.

  7. Molecular fingerprint-region spectroscopy from 5 to 12 μm using an orientation-patterned gallium phosphide optical parametric oscillator

    Science.gov (United States)

    Maidment, Luke; Schunemann, Peter G.; Reid, Derryck T.

    2016-09-01

    We report a femtosecond optical parametric oscillator (OPO) based on the new semiconductor gain material orientation patterned gallium phosphide (OP-GaP), which enables the production of high-repetition-rate femtosecond pulses spanning 5-12 \\mu m with average powers in the few to tens of milliwatts range. This is the first example of a broadband OPO operating across the molecular fingerprint region, and we demonstrate its potential by conducting broadband Fourier-transform spectroscopy using water vapor and a polystyrene reference standard.

  8. Molecular fingerprint-region spectroscopy from 5-12 \\mu m using an orientation-patterned gallium phosphide optical parametric oscillator

    CERN Document Server

    Maidment, Luke; Reid, Derryck T

    2016-01-01

    We report a femtosecond optical parametric oscillator (OPO) based on the new semiconductor gain material orientation patterned gallium phosphide (OP-GaP), which enables the production of high-repetition-rate femtosecond pulses spanning 5-12 \\mu m with average powers in the few to tens of milliwatts range. This is the first example of a broadband OPO operating across the molecular fingerprint region, and we demonstrate its potential by conducting broadband Fourier-transform spectroscopy using water vapor and a polystyrene reference standard.

  9. Información molecular obtenida a partir de pieles de la colección del Museo Regional Fagnano, Río Grande, Tierra del Fuego

    OpenAIRE

    2014-01-01

    En el presente trabajo se aplicaron técnicas moleculares sobre muestras poco conservadas de pieles depositadas en la colección del Museo Regional Monseñor Fagnano, Tierra del Fuego, Argentina, con el objetivo de identificar la especie con la que fueron confeccionadas. Se extrajeron pelos de mantas realizadas con pieles de guanaco (Lama guanicoe) por Selk’nam y de una piel de puma (Puma concolor) procedente de la provincia de Santa Cruz. Ambas muestras se encontraban almacenadas en el Museo Re...

  10. Prevalence, risk factors and molecular epidemiology of highly resistant gram negative rods in hospitalized patients in the Dutch region Kennemerland

    NARCIS (Netherlands)

    Souverein, Dennis; Euser, Sjoerd M; Herpers, Bjorn L; Diederen, Bram; Houtman, Patricia; van Seventer, Marina; van Ess, Ingeborg; Kluytmans, Jan; Rossen, John W A; Den Boer, Jeroen W

    2016-01-01

    BACKGROUND: This paper describes (1) the Highly Resistant Gram Negative Rod (HR-GNR) prevalence rate, (2) their genotypes, acquired resistance genes and (3) associated risk factors of HR-GNR colonization among the hospitalized population in the Dutch region Kennemerland. METHODS: Between 1 October 2

  11. Prevalence, risk factors and molecular epidemiology of highly resistant gram negative rods in hospitalized patients in the Dutch region Kennemerland

    NARCIS (Netherlands)

    Souverein, Dennis; Euser, Sjoerd M.; Herpers, Bjorn L.; Diederen, Bram; Houtman, Patricia; van Seventer, Marina; van Ess, Ingeborg; Kluytmans, Jan; Rossen, John W. A.; Den Boer, Jeroen W.

    2016-01-01

    Background: This paper describes (1) the Highly Resistant Gram Negative Rod (HR-GNR) prevalence rate, (2) their genotypes, acquired resistance genes and (3) associated risk factors of HR-GNR colonization among the hospitalized population in the Dutch region Kennemerland. Methods: Between 1 October 2

  12. Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal.

    Science.gov (United States)

    Santos, A; Isidro, J; Silva, C; Boaventura, L; Diogo, J; Faustino, A; Toscano, C; Oleastro, M

    2016-08-01

    Clostridium difficile infection (CDI) represents a great healthcare burden in developed countries. The emergence of the epidemic PCR ribotype (RT) 027 and its acquired fluoroquinolones resistance have accentuated the need for an active surveillance of CDI. Here we report the first countrywide study of CDI in Portugal with the characterization of 498 C. difficile clinical isolates from 20 hospitals in four regions in Portugal regarding RT, virulence factors and antimicrobial susceptibility. We identified 96 RTs with marked variations between and within regions, as only six RTs appeared in all four regions. RT027 was the most frequent RT overall (18.5%) and among healthcare facility-associated isolates (19.6%), while RT014 was the most common among community-associated isolates (12%). The north showed a high RT diversity among isolates and a low moxifloxacin (MXF) resistance rate (11.9%), being the only region in which RT027 was not predominant. In contrast, the isolates from the centre presented the highest RT027 frequency, and 53.4% were resistant to MXF. Overall, MXF resistance (33.2%) was associated (p Portugal, with a high frequency of hypervirulent RTs and the emergence of virulence factors in non-027 RTs, emphasizing the need for a surveillance system for CDI in Portugal.

  13. Morphological and molecular observations on the cereal cyst nematode Heterodera filipjevi from the Volga and South Ural regions of Russia

    Science.gov (United States)

    During 2010-2012, a survey was conducted to determine the distribution and species diversity of the cereal cyst nematode Heterodera filipjevi within the Volga and South Ural regions of the Russian Federation. A total of 270 soil samples were collected. Seven populations of CCN were found in the rhiz...

  14. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines

    NARCIS (Netherlands)

    Loywyck, V.; Bed'hom, B.; Pinard-van der Laan, M.H.; Pitel, F.; Verrier, E.; Bijma, P.

    2008-01-01

    We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantit

  15. Structural and Dynamic Characterization of the Molecular Hub Early Region 1A (E1A) from Human Adenovirus.

    Science.gov (United States)

    Hošek, Tomáš; Calçada, Eduardo O; Nogueira, Marcela Oliveira; Salvi, Michele; Pagani, Talita Duarte; Felli, Isabella C; Pierattelli, Roberta

    2016-09-05

    The small-DNA human adenovirus encodes one of the most versatile molecular hubs, the E1A protein. This protein is essential for productive viral infection in human cells and a vast amount of biologically relevant data are available on its interactions with host proteins. Up to now, however, no high-resolution structural and dynamic information on E1A is available despite its important biological role. Among the different spliced variants of E1A, two are expressed at high level in the early stage of infection. These are 243 and 289 residues isoforms. Herein, we present their NMR characterization, showing that they are both highly disordered, but also demonstrate a certain heterogeneous behavior in terms of structural and dynamic properties. Furthermore, we present the characterization of the isolated domain of the longer variant, known as CR3. This study opens the way to understanding at the molecular level how E1A functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Characterizing and sourcing ambient PM2.5 over key emission regions in China II: Organic molecular markers and CMB modeling

    Science.gov (United States)

    Zhou, Jiabin; Xiong, Ying; Xing, Zhenyu; Deng, Junjun; Du, Ke

    2017-08-01

    From November 2012 to July 2013, a sampling campaign was completed for comprehensive characterization of PM2.5 over four key emission regions in China: Beijing-Tianjin-Hebei (BTH), Yangzi River Delta (YRD), Pearl River Delta (PRD), and Sichuan Basin (SB). A multi-method approach, adopting different analytical and receptor modeling methods, was employed to determine the relative abundances of region-specific air pollution constituents and contributions of emission sources. This paper is focused on organic molecular marker based source apportionment using chemical mass balance (CMB) receptor modeling. Analyses of the organic molecular markers revealed that vehicle emission, coal combustion, biomass burning, meat cooking and natural gas combustion were the major contributors to organic carbon (OC) in PM2.5. The vehicle emission dominated the sources contributing to OC in spring at four sampling sites. During wintertime, the coal combustion had highest contribution to OC at BTH site, while the major source contributing to OC at YRD and PRD sites was vehicle emission. In addition, the relative contributions of different emission sources to PM2.5 mass at a specific location site and in a specific season revealed seasonal and spatial variations across all four sampling locations. The largest contributor to PM2.5 mass was secondary sulfate (14-17%) in winter at the four sites. The vehicle emission was found to be the major source (14-21%) for PM2.5 mass at PRD site. The secondary ammonium has minor variation (4-5%) across the sites, confirming the influences of regional emission sources on these sites. The distinct patterns of seasonal and spatial variations of source apportionment observed in this study were consistent with the findings in our previous paper based upon water-soluble ions and carbonaceous fractions. This makes it essential for the local government to make season- and region-specific mitigation strategies for abating PM2.5 pollution in China.

  17. Molecular epidemiology of trichophyton tonsurans isolated in Japan using RFLP analysis of non-transcribed spacer regions of ribosomal RNA genes.

    Science.gov (United States)

    Mochizuki, Takashi; Kawasaki, Masako; Tanabe, Hiroshi; Anzawa, Kazushi; Ishizaki, Hiroshi; Choi, Jong Soo

    2007-07-01

    Trichophyton tonsurans has been reported to be the causative agent of an epidemic of tinea corporis and tinea capitis among Japanese judoists and wrestlers. A molecular method using restriction enzyme analysis of PCR-amplified fragments targeting the non-transcribed spacer (NTS) region of ribosomal RNA genes in fungal nuclei was applied to a total of 232 strains of T. tonsurans isolated in Japan. Six molecular types, i.e., NTS types I, II, III, IV, V, and VI, were clearly detected in restriction analysis of fragments digested with MvaI and AvaI together. Of the 232 strains, 199 were classified as NTS I, 21 as NTS II, 7 as NTS III, 3 as NTS IV, 1 as type V, and 1 as type VI. Whereas the NTS I strains were found nationwide, most of the NTS II and NTS III strains were limited to central Japan. Of 164 strains isolated from judoists, 160 were classified as NTS I, which suggests that the majority of the cases were caused by a clonal lineage. On the other hand, the 48 strains isolated from wrestlers showed more variety, with 27 strains classified as NTS I, 17 as NTS II, and 4 as NTS III. We concluded that the epidemic was caused by at least three lineages of T. tonsurans. NTS VI strains, the major molecular type among sporadically isolated strains, were not observed among the epidemic strains, and strains of this type did not contribute to the present epidemic.

  18. Chloroplast DNA analysis of Tunisian cork oak populations (Quercus suber L.): sequence variations and molecular evolution of the trnL (UAA)-trnF (GAA) region.

    Science.gov (United States)

    Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi

    2016-10-24

    Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.

  19. Molecular dissection of the intrinsic factor-vitamin B12 receptor, cubilin, discloses regions important for membrane association and ligand binding.

    Science.gov (United States)

    Kristiansen, M; Kozyraki, R; Jacobsen, C; Nexø, E; Verroust, P J; Moestrup, S K

    1999-07-16

    Cubilin, the receptor for intrinsic factor-vitamin B12, is a novel type of high molecular weight receptor consisting of a 27 CUB (complement components C1r/C1s, Uegf, and bone morphogenic protein-1) domain cluster preceded by 8 epidermal growth factor repeats and a short N-terminal sequence. In addition to binding the vitamin B12-carrier complex, cubilin also binds receptor-associated protein. To delineate the structures for membrane association and ligand binding we established a panel of stable transfected Chinese hamster ovary cells expressing overlapping segments of rat cubilin. Analysis of conditioned media and cell extracts of transfected cells revealed that the N-terminal cubilin region conveys membrane association. Helical plotting of this region demonstrated a conserved amphipathic helix pattern (Lys74-Glu109) as a candidate site for hydrophobic interactions. Ligand affinity chromatography and surface plasmon resonance analysis of the secreted cubilin fragments showed ligand binding in the CUB domain region. Further dissection of binding-active fragments localized the binding site for intrinsic factor-vitamin B12 to CUB domains 5-8 and a receptor-associated protein-binding site to CUB domains 13-14. In conclusion, the N-terminal cubilin region seems crucial for membrane association, whereas the CUB domain cluster harbors distinct sites for ligand binding.

  20. Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish.

    Science.gov (United States)

    Martin, A P; Bermingham, E

    2000-06-07

    The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.

  1. Información molecular obtenida a partir de pieles de la colección del Museo Regional Fagnano, Río Grande, Tierra del Fuego

    Directory of Open Access Journals (Sweden)

    Petrigh, Romi

    2014-10-01

    Full Text Available En el presente trabajo se aplicaron técnicas moleculares sobre muestras poco conservadas de pieles depositadas en la colección del Museo Regional Monseñor Fagnano, Tierra del Fuego, Argentina, con el objetivo de identificar la especie con la que fueron confeccionadas. Se extrajeron pelos de mantas realizadas con pieles de guanaco (Lama guanicoe por Selk’nam y de una piel de puma (Puma concolor procedente de la provincia de Santa Cruz. Ambas muestras se encontraban almacenadas en el Museo Regional Monseñor Fagnano y en la Misión Salesiana Candelaria en Rio Grande, Tierra del Fuego, Argentina. La extracción de ADN de los fragmentos de pelos de 5mm de longitud se realizó en un buffer de lisis PCR-compatible. Se amplificaron por PCR fragmentos específicos de ADN mitocondrial y se secuenciaron. Las secuencias fueron comparadas con las depositadas en la base de secuencias de nucleótidos del National Center for Biotechnology Information (NCBI de Estados Unidos. La aplicación de técnicas moleculares permitió recuperar secuencias de ADN de muestras de pieles con un estado de conservación poco óptimo para análisis genéticos, pudiendo extenderse a otras fuentes de pelos como las fibras textiles de origen arqueológico de la región.

  2. In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

    Science.gov (United States)

    Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

    2013-01-01

    We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.

  3. X-ray emission from the giant molecular clouds in the Galactic Center region and the discovery of new X-ray sources

    CERN Document Server

    Sidoli, L; Treves, A; Parmar, A N; Turolla, R; Favata, F

    2001-01-01

    We report the results of X-ray (2-10 keV) observations of the giant molecular clouds SgrB, SgrC and SgrD in the Galactic Center region, together with the discovery of the point-like source SAXJ1748.2-2808. The data have been obtained with the MECS instrument on the BeppoSAX satellite. The core of SgrB2 has an X-ray luminosity of 6x10^34 erg/s and its spectrum is characterized by a strong Fe emission line at 6.5 keV with an equivalent width of 2 keV. Faint diffuse X-ray emission is detected from SgrC and from the SNR G1.05-0.15 (SgrD). A new, unresolved source with a strong Fe line has been discovered in the SgrD region. This source, SAXJ1748.2-2808, is probably associated with a SiO and OH maser source at the Galactic Center distance. If so, its luminosity is 10^34 erg/s. We propose that the X-ray emission from SAX J1748.2-2808 is produced either by protostars or by a giant molecular cloud core. Emission from sources similar to SAX J1748.2-2808 could have an impact on the expected contribution on the observed...

  4. Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish.

    OpenAIRE

    Martin, A. P.; Bermingham, E.

    2000-01-01

    The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining t...

  5. Species of the Paramecium aurelia complex in Russia (western region of European Russia) with molecular characteristics of Paramecium novaurelia.

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Potekhin, Alexey

    2006-01-01

    The presence of P. primaurelia, P. biaurelia, P. triaurelia, and P. novaurelia of the P. aurelia complex was revealed in the studied region of Russia. RAPD-PCR fingerprints (band patterns) of newly identified P. novaurelia strains from Russia were compared to those characteristic for the other chosen European strains of the species. The strains revealed intraspecific polymorphism as several groups of genotypes confirming the existence of polymorphism within P. novaurelia.

  6. First evidence for molecular interfaces between outflows and ambient cloud in high-mass star forming regions?

    CERN Document Server

    Codella, C; Viti, S; Williams, D A

    2006-01-01

    We present new observations of the CepA-East region of massive star formation and describe an extended and dynamically distinct feature not previously recognised. This feature is present in emission from H2CS, OCS, CH3OH, and HDO at -5.5 km/s, but is not traced by conventional tracers of star forming regions H2S, SO2, SO, CS. The feature is extended up to at least 0.1 pc. We show that the feature is neither a hot core nor a shocked outflow. However, the chemistry of the feature is consistent with predictions of a model of an eroding interface between a fast wind and a dense core; mixing between the two media occurs in the interface on a timescale of 10-50 years. If these observations are confirmed by detailed maps and by detections in species also predicted to be abundant (e.g. HCO+, H2CO, and NH3) this feature would be the first detection of such an interface in regions of massive star formation. An important implication of the model is that a significant reservoir of sulfur in grain mantles is required to b...

  7. The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein.

    Directory of Open Access Journals (Sweden)

    Kenrick A Vassall

    Full Text Available The classic isoforms of myelin basic protein (MBP are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99- containing a putative SH3-ligand, adjacent to a region that forms an amphipathic α-helix (P82-I90 upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP kinases. Here, we have investigated the structure of the α-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the α-helical region, by utilizing four 36-residue peptides (S72-S107 with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the α-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012. Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic α-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the α-helix upon temperature perturbation and affect the

  8. The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein.

    Science.gov (United States)

    Vassall, Kenrick A; Bessonov, Kyrylo; De Avila, Miguel; Polverini, Eugenia; Harauz, George

    2013-01-01

    The classic isoforms of myelin basic protein (MBP) are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99-) containing a putative SH3-ligand, adjacent to a region that forms an amphipathic α-helix (P82-I90) upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP) kinases. Here, we have investigated the structure of the α-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the α-helical region, by utilizing four 36-residue peptides (S72-S107) with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the α-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012). Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic α-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the α-helix upon temperature perturbation and affect the global structure

  9. Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region

    Energy Technology Data Exchange (ETDEWEB)

    Perry, D.S. [Univ. of Akron, OH (United States)

    1993-12-01

    Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

  10. Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region.

    Directory of Open Access Journals (Sweden)

    Abdulahi Alfonso-Morales

    Full Text Available Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV; it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV strains.Sequences of the hyper-variable region of the VP2 (HVR-VP2 gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST, Bayesian Tip-association Significance testing (BaTS and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium in 1987, Africa (Egypt around 1990, East Asia (China and Japan in 1993, the Caribbean Region (Cuba by 1995 and South America (Brazil around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection.To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

  11. Population Genetics of Jaguars (Panthera onca) in the Brazilian Pantanal: Molecular Evidence for Demographic Connectivity on a Regional Scale.

    Science.gov (United States)

    Valdez, Fernanda Pedone; Haag, Taiana; Azevedo, Fernando C C; Silveira, Leandro; Cavalcanti, Sandra M C; Salzano, Francisco M; Eizirik, Eduardo

    2015-01-01

    Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Molecular cloning, SNP detection and association analysis of 5' flanking region of the goat IGF1 gene with prolificacy.

    Science.gov (United States)

    Thomas, Naicy; Venkatachalapathy, Thirupathy; Aravindakshan, Thazhathuveettil; Raghavan, K C

    2016-04-01

    The insulin-like growth factor 1 has an important role in reproduction, foetal development and growth. It regulates the secretion of gonadotrophin releasing hormone, stimulates ovarian function and steroidogenesis. The present study was conducted to characterise the 5' flanking region of goat IGF 1 gene, ascertain ovarian expression of the IGF1 gene, detect SNPs and assess the association with prolificacy in the two indigenous goat breeds of South India viz., low prolific Attappady Black and high prolific Malabari. The 5' flanking region of IGF1 gene was PCR amplified, cloned and sequenced from both breeds. Genotyping was performed in 277 goats from the two genetic groups using the PCR-Single Strand Conformational Polymorphism (SSCP) and the expression of the IGF1 gene in the ovary was analysed by quantitative real time PCR. The 5' flanking region of the IGF1 gene was 601 bp long and located at 450 bp upstream of the start codon. Sequence exhibited 97-99% similarity with that of the sheep, cattle and sika deer IGF1 genes. Three genotypes, PP, PQ and QR were observed at this locus with the frequency of 0.62, 0.30 and 0.08, respectively. Sequencing of the representative PCR products from each genotype revealed two SNPs, g.224A>G and g.227C>T. The population was found to be in Hardy-Weinberg disequilibrium at both loci. Statistical results indicated that these loci were associated with litter size (P ≤ 0.05). However, no significant difference was found in the expression of the IGF1 gene in the ovaries of the two goat breeds. These results suggest the significant influence of the IGF1 gene on prolificacy in goats and identified SNPs would benefit the selection of prolific animals in future breeding programs.

  13. Molecular and biological characterization of Potato mop-top virus (PMTV, Pomovirus) isolates from potato-growing regions in Colombia

    DEFF Research Database (Denmark)

    Gil, José; Adams, Ian; Boonham, Neil

    2016-01-01

    samples were taken from the main potato-producing regions in Colombia and virus was recovered by planting Nicotiana benthamiana as bait plants. The complete genomes of five isolates were sequenced and three of the isolates were inoculated to four different indicator plants. Based on sequence comparisons......Potato mop-top virus (PMTV) causes necrotic flecks inside and on tubers in temperate countries. In South America, these symptoms have not been observed, although the presence of the virus has been confirmed in the Andes and in Central America. To characterize PMTV isolates from the Andes, soil...

  14. Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)

    Institute of Scientific and Technical Information of China (English)

    Jiapu Zhang; Yuanli Zhang

    2013-01-01

    Prion diseases,traditionally referred to as transmissible spongiform encephalopathies,are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species,manifesting as scrapie in sheep,bovine spongiform encephalopathy (or 'madcow' disease) in cattle,and Creutzfeldt-Jakob disease,Gerstmann-Strussler-Scheinker syndrome,fatal familial insomnia (FFI),and Kulu in humans,etc.These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrPC) into insoluble abnormally folded infectious prions (prpSc).The hydrophobic region PrP(109-136) controls the formation of diseased prions:the normal PrP(113-120) AGAAAAGA palindrome is an inhibitor/blocker of prion diseases and the highly conserved glycine-xxx-glycine motif PrP(119-131) can inhibit the formation of infectious prion proteins in cells.This article gives detailed reviews on the PrP(109-136) region and presents the studies of its three-dimensional structures and structural dynamics.

  15. Molecular and pathogenic characterization of new Xanthomonas oryzae pv. oryzae strains from the coastline region of Fangchenggang city in China.

    Science.gov (United States)

    Yang, Shu-Qing; Liu, Shu-Yan; Zhao, Shuai; Yu, Yan-Hua; Li, Rong-Bai; Duan, Cheng-Jie; Tang, Ji-Liang; Feng, Jia-Xun

    2013-04-01

    Virulence assays and DNA polymorphism analyses were used to characterize 33 Xanthomonas oryzae pv. oryzae (Xoo) strains collected from the coastline region of Fangchenggang city in China. Two new pathogenic races (FXP1 and FXP2), were determined by leaf-clipping inoculation of 12 near-isogenic International Rice-Bacterial Blight (IRBB) rice lines, each containing a single resistance gene. Race FXP1 consisted of twenty-eight strains that were incompatible on IRBB5 and IRBB7, while race FXP2 included five strains that were incompatible on IRBB5 and IRBB7 and moderately virulent on IRBB8 containing the xa8 gene. Restriction fragment length polymorphism (RFLP) analysis revealed that each probe of avrXa10 and IS1112 resolved two haplotypes. In a dendrogram generated from the combined RFLP data, the 33 Xoo strains were resolved into two clusters. There was a weak correlation (r = 0.53) between race and haplotype. All of the rice cultivars planted in the coastline region of Fangchenggang city were susceptible to the representative Xoo strains tested above. However, we found that four rice cultivars used as breeding materials in the laboratory could fully resist infection by the Xoo strains, suggesting that the isolated Xoo strains could be used to detect resistant rice cultivars suitable for planting in the local rice field.

  16. Molecular authentication of Gynostemma pentaphyllum through development and application of random amplification polymorphic DNA sequence-characterized amplified region marker.

    Science.gov (United States)

    Zhou, J; Wu, Y S; Zhao, R Q; Jiang, J F; Luo, Y; Ma, C T; Qian, J Y

    2015-12-08

    Due to the morphological similarities of aerial parts, it is difficult to distinguish Gynostemma pentaphyllum from Cayratia japonica, which is usually an adulterant of the former. To develop a reliable method for the identification and authentication of G. pentaphyllum, a combination of random amplification polymorphic DNA (RAPD) technique with sequence-characterized amplified region (SCAR) markers was studied. Twenty-five samples of G. pentaphyllum and two samples of C. japonica were collected from different regions in Guangxi or bought from different provinces in China. Through the RAPD analysis, significant genetic polymorphism was observed among the intraspecies samples of G. pentaphyllum. Furthermore, a specific marker, J-750, was obtained for authentication. Therefore, the SCAR marker for G. pentaphyllum (359 bp) was developed from the RAPD amplicon. With PCR amplification using the SCAR primers, a specific band of 359 bp was distinctly visible for all tested samples of G. pentaphyllum, but was absent in the samples of C. japonica. Furthermore, the results revealed that the SCAR marker was useful for the identification and authentication of G. pentaphyllum irrespective of whether samples were fresh, dry, or of commercial origin. The SCAR marker obtained in this study successfully authenticated G. pentaphyllum through an integrated PCR system containing SCAR and control primer combinations of two pairs. In addition, it was also used for simultaneous discrimination of G. pentaphyllum from C. japonica.

  17. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

    Science.gov (United States)

    Manara, Richard M. A.; Tomasio, Susana; Khalid, Syma

    2015-01-01

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  18. Morphology and Kinematics of Warm Molecular Gas in the Nuclear Region of Arp 220 as Revealed by ALMA

    CERN Document Server

    Rangwala, Naseem; Wilson, Christine; Glenn, Jason; Kamenetzky, Julia; Spinoglio, Luigi

    2015-01-01

    We present Atacama Large Millimeter Array (ALMA) Cycle-0 observations of the CO J = 6-5 line in the advanced galaxy merger Arp 220. This line traces warm molecular gas, which dominates the total CO luminosity. The CO emission from the two nuclei is well resolved by the 0.39" x 0.22" beam and the exceptional sensitivity and spatial/spectral resolution reveal new complex features in the morphology and kinematics of the warm gas. The line profiles are asymmetric between the red and blue sides of the nuclear disks and the peak of the line emission is offset from the peak of the continuum emission in both nuclei by about 100 pc in the same direction. CO self-absorption is detected at the centers of both nuclei but it is much deeper in the eastern nucleus. We also clearly detect strong, highly redshifted CO absorption located near the southwest side of each nucleus. For the eastern nucleus, we reproduce the major line profile features with a simple kinematic model of a highly turbulent, rotating disk with a substan...

  19. Comparison of Prestellar Core Elongations and Large-scale Molecular Cloud Structures in the Lupus I Region

    Science.gov (United States)

    Poidevin, Frédérick; Ade, Peter A. R.; Angile, Francesco E.; Benton, Steven J.; Chapin, Edward L.; Devlin, Mark J.; Fissel, Laura M.; Fukui, Yasuo; Gandilo, Natalie N.; Gundersen, Joshua O.; Hargrave, Peter C.; Klein, Jeffrey; Korotkov, Andrei L.; Matthews, Tristan G.; Moncelsi, Lorenzo; Mroczkowski, Tony K.; Netterfield, Calvin B.; Novak, Giles; Nutter, David; Olmi, Luca; Pascale, Enzo; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Diego Soler, Juan; Tachihara, Kengo; Thomas, Nicholas E.; Truch, Matthew D. P.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

    2014-08-01

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.

  20. Comparison of Prestellar Core Elongations and Large-Scale Molecular Cloud Structures in the Lupus I Region

    CERN Document Server

    Poidevin, F; Angile, F E; Benton, S J; Chapin, E L; Devlin, M J; Fissel, L M; Fukui, Y; Gandilo, N N; Gundersen, J O; Hargrave, P C; Klein, J; Korotkov, A L; Matthews, T G; Moncelsi, L; Mroczkowski, T K; Netterfield, C B; Novak, G; Nutter, D; Olmi, L; Pascale, E; Savini, G; Scott, D; Shariff, J A; Soler, J D; Tachihara, K; Thomas, N E; Truch, M D P; Tucker, C E; Tucker, G S; Ward-Thompson, D

    2014-01-01

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on subparsec to 100 parsec scales, leading to the formation of starless cores, is not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 $\\mu$m maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to a large-scale filament shape model for Lupus I, or relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 $\\mu$m with the Balloon-borne Large Aperture Telescope for Polarimetry (BLASTPol) during its 2010 campaign. Here again...

  1. Molecular characterization of rotavirus isolated from alpaca (Vicugna pacos) crias with diarrhea in the Andean Region of Cusco, Peru.

    Science.gov (United States)

    Garmendia, Antonio E; Lopez, Wellington; Ortega, Nastassja; Chamorro, Marycris J

    2015-10-22

    Alpacas (Vicugna pacos), a species of South American camelids (SAC), suffer high morbidity and mortality from infectious diseases. Diarrhea is one of the leading causes of alpaca cria mortality in Peru and elsewhere. In order to develop appropriate control and/or treatment, it is necessary to identify infectious pathogens that cause diarrhea in crias. Rotavirus was isolated in cell culture from feces collected from crias with acute diarrhea that tested positive to rotaviral antigen by rapid immunochromatographic methods in an earlier study. The isolates were identified as rotaviruses by RT-PCR run with specific primers for human rotavirus VP7 coding sequences using total RNA extracted from cells displaying cytopathic effects as template. These alpaca isolates were further identified as group A rotaviruses by means of a VP6-specific PCR and were designated as ALRVA-K'ayra/Perú/3368-10 and ALRVA-K'ayra/Perú/3386-10. Molecular G and P typing, placed the former as G3/P11 and the latter as G3/P?. Sequence analysis of two genome segments (coding for VP4 and VP7) from the alpaca isolates revealed partial homologies to swine and human rotaviruses, respectively. These results demonstrate that rotaviruses are associated with a proportion of cases of diarrhea in crias, although prevalence and impact remain to be determined. The isolation of rotaviruses from alpaca crias with diarrhea will contribute positively to further understand the pathogen and its role in the diarrhea complex.

  2. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.

    Science.gov (United States)

    Manara, Richard M A; Tomasio, Susana; Khalid, Syma

    2015-01-27

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is "exonuclease sequencing", in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  3. Molecular identification of poisonous mushrooms using nuclear ITS region and peptide toxins: a retrospective study on fatal cases in Thailand.

    Science.gov (United States)

    Parnmen, Sittiporn; Sikaphan, Sujitra; Leudang, Siriwan; Boonpratuang, Thitiya; Rangsiruji, Achariya; Naksuwankul, Khwanruan

    2016-02-01

    Cases of mushroom poisoning in Thailand have increased annually. During 2008 to 2014, the cases reported to the National Institute of Health included 57 deaths; at least 15 died after ingestion of amanitas, the most common lethal wild mushrooms inhabited. Hence, the aims of this study were to identify mushroom samples from nine clinically reported cases during the 7-year study period based on nuclear ITS sequence data and diagnose lethal peptide toxins using a reversed phase LC-MS method. Nucleotide similarity was identified using BLAST search of the NCBI database and the Barcode of Life Database (BOLD). Clade characterization was performed by maximum likelihood and Bayesian phylogenetic approaches. Based on BLAST and BOLD reference databases our results yielded high nucleotide similarities of poisonous mushroom samples to A. exitialis and A. fuliginea. Detailed phylogenetic analyses showed that all mushroom samples fall into their current classification. Detection of the peptide toxins revealed the presence of amatoxins and phallotoxins in A. exitialis and A. fuliginea. In addition, toxic α-amanitin was identified in a new provisional species, Amanita sp.1, with the highest toxin quantity. Molecular identification confirmed that the mushrooms ingested by the patients were members of the lethal amanitas in the sections Amanita and Phalloideae. In Thailand, the presence of A. exitialis was reported here for the first time and all three poisonous mushroom species provided new and informative data for clinical studies.

  4. Comparison of prestellar core elongations and large-scale molecular cloud structures in the Lupus I region

    Energy Technology Data Exchange (ETDEWEB)

    Poidevin, Frédérick [UCL, KLB, Department of Physics and Astronomy, Gower Place, London WC1E 6BT (United Kingdom); Ade, Peter A. R.; Hargrave, Peter C.; Nutter, David [School of Physics and Astronomy, Cardiff University, Queens Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); Angile, Francesco E.; Devlin, Mark J.; Klein, Jeffrey [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Benton, Steven J.; Netterfield, Calvin B. [Department of Physics, University of Toronto, 60 St. George Street, Toronto, ON M5S 1A7 (Canada); Chapin, Edward L. [XMM SOC, ESAC, Apartado 78, E-28691 Villanueva de la Canãda, Madrid (Spain); Fissel, Laura M.; Gandilo, Natalie N. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Fukui, Yasuo [Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Gundersen, Joshua O. [Department of Physics, University of Miami, 1320 Campo Sano Drive, Coral Gables, FL 33146 (United States); Korotkov, Andrei L. [Department of Physics, Brown University, 182 Hope Street, Providence, RI 02912 (United States); Matthews, Tristan G.; Novak, Giles [Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Moncelsi, Lorenzo; Mroczkowski, Tony K. [California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Olmi, Luca, E-mail: fpoidevin@iac.es [Physics Department, University of Puerto Rico, Rio Piedras Campus, Box 23343, UPR station, San Juan, PR 00931 (United States); and others

    2014-08-10

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.

  5. Molecular characterization of Leishmania infantum in domestic cats in a region of Brazil endemic for human and canine visceral leishmaniasis.

    Science.gov (United States)

    Metzdorf, Isabel Parizotto; da Costa Lima, Manoel Sebastião; de Fatima Cepa Matos, Maria; de Souza Filho, Antonio Francisco; de Souza Tsujisaki, Rosianne A; Franco, Karina Garcia; Shapiro, Julie Teresa; de Almeida Borges, Fernando

    2017-02-01

    Leishmaniasis is a "neglected tropical disease" and serious public health issue in Brazil. While dogs are recognized as particularly important reservoirs, recent reports of domestic cats infected with Leishmania sp. in urban areas suggest their participation in the epidemiological chain of the parasite in endemic areas. The aim of this study was to screen domestic cats for Leishmania sp. infection in an area where human and canine visceral leishmaniasis are endemic, followed by the identification of the species circulating in cats. We collected peripheral blood, lymph-node aspirates and bone marrow from 100 adult animals, both male and female, and analyzed the samples using cytological and molecular (PCR) detection techniques. We detected Leishmania in 6% of animals, which were then analyzed by RFLP-PCR to identify the species. Leishmania infantum (synonym: L. chagasi), a species responsible for visceral leishmaniasis in humans and other animals, was identified from all six samples. Amastigotes were observed in the peripheral blood, bone marrow and lymph-node aspirates in 4 of the 6 PCR-positive animals. The presence of infected cats in endemic areas should not be neglected, because it demonstrates the potential role of these animals in the biological cycle of the pathogen. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Molecular characterization of two proximal deletion breakpoint regions in both Prader-Willi and Angelman syndrome patients

    Energy Technology Data Exchange (ETDEWEB)

    Christian, S.L.; Huang, B.; Ledbetter, D.H. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1995-07-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct mental retardation syndromes caused by paternal and maternal deficiencies, respectively, in chromosome 15q11{minus}q13. Approximately 70% of these patients have a large deletion of {approximately}4 Mb extending from D15S9 (ML34) through D15S12 (IR10A). To further characterize the deletion breakpoints proximal to D15S9, three new polymorphic microsatellite markers were developed that showed observed heterozygosities of 60%-87%. D15S541 and D15S542 were isolated for YAC A124A3 containing the D15S18 (IR39) locus. D15S543 was isolated from a cosmid cloned from the proximal right end of YAC 254B5 containing the D15S9 (ML34) locus. Gene-centromere mapping of these markers, using a panel of ovarian teratomas of known meiotic origin, extended the genetic map of chromosome 15 by 2-3 cM toward the centromere. Analysis of the more proximal S541/S542 markers on 53 Prader-Willi and 33 Angelman deletion patients indicated two classes of patients: 44% (35/80) of the informative patients were deleted for these markers (class I), while 56% (45/80) were not deleted (class II), with no difference between PWS and AS. In contrast, D15S543 was deleted in all informative patients (13/48) or showed the presence of a single allele (in 35/48 patients), suggesting that this marker is deleted in the majority of PWS and AS cases. These results confirm the presence of two common proximal deletion breakpoint regions in both Prader-Willi and Angelman syndromes and are consistent with the same deletion mechanism being responsible for paternal and maternal deletions. One breakpoint region lies between D15S541/S542 and D15S543, with an additional breakpoint region being proximal to D15S541/S542. 46 refs., 2 figs., 3 tabs.

  7. Molecular clonality and antimicrobial resistance in Salmonella enterica serovars Enteritidis and Infantis from broilers in three Northern regions of Iran

    DEFF Research Database (Denmark)

    Rahmani, Maral; Peighambari, Seyed Mostafa; Svendsen, Christina Aaby

    2013-01-01

    in Salmonella isolates from broiler farms in different regions of Iran covering a time period of four years. RESULTS: From 2007 to 2011, 36 Salmonella strains were isolated from broiler farms located in three northern provinces of Iran. The isolates were serotyped, antimicrobial susceptibility tested......) were resistant to tetracycline, spectinomycin, streptomycin, and sulfamethoxazole and harbored the associated resistance genes; tetA, dfrA14, aadA1, and sulI together with class 1 integrons. The isolates revealed highly similar PFGE patterns indicating clonal relatedness across different geographical...... locations. CONCLUSION: The data provided fundamental information applicable when launching future control programs for broilers in Iran with the aim to conserve the effectiveness of important antimicrobials for treatment in humans....

  8. Prevalence, risk factors and molecular epidemiology of highly resistant gram negative rods in hospitalized patients in the Dutch region Kennemerland

    Directory of Open Access Journals (Sweden)

    Dennis Souverein

    2016-03-01

    Full Text Available Abstract Background This paper describes (1 the Highly Resistant Gram Negative Rod (HR-GNR prevalence rate, (2 their genotypes, acquired resistance genes and (3 associated risk factors of HR-GNR colonization among the hospitalized population in the Dutch region Kennemerland. Methods Between 1 October 2013 and 31 March 2014, cross-sectional prevalence measurements were performed in three regional hospitals as part of each hospitals infection control program. Rectal swabs were analyzed at the Regional Public Health Laboratory Kennemerland by direct culturing. Genotypes and acquired resistance genes of positive isolates were determined using Whole Genome Sequencing with the MiSeq instrument (Illumina. Association between several independent variables and HR-GNR positivity was examined using logistic regression models. Results Out of 427 patients, 24 HR-GNR positive isolates were recovered from 22 patients, resulting in a regional HR-GNR colonization prevalence (95 % CI of 5.2 % (3.6–7.9. Of these 22 positive patients, 15 were Extended Spectrum Beta-Lactamase (ESBL positive (3.5 % (2.1–5.7, 7 patients were positive for a Fluoroquinolones and Aminoglycosides (Q&A resistant Enterobacteriaceae (1.6 % (0.8–3.3 and from one patient (0.2 % (0–1.3 a Stenotrophomonas maltophilia resistant towards co-trimoxazole was isolated. No carbapenemase producing Enterobacteriaceae (CPE, multi-resistant Acinetobacter species or multi-resistant Pseudomonas aeruginosa were isolated. The ESBL genes found were bla CTX-M-1 (n = 4, 25.0 %, bla CTX-M-15 (n = 3, 18.8 %, bla CTX-M-27 (n = 2, 12.5 %, bla CTX-M-14b (n = 2, 12.5 %, bla CTX-M-9 (n = 2, 12.5 %, bla CTX-M-14 (n = 1, 6.3 %, bla CTX-M-3 (n = 1, 6.3 %, bla SHV-11 (n = 1, 6.3 % and bla SHV-12 (n = 1, 6.3 %. Being known HR-GNR positive in the past was the only significant associated risk factor for HR-GNR positivity, odds ratio (95 % CI: 7.32 (1.82–29.35, p

  9. Molecular archaeology of Flaviviridae untranslated regions: duplicated RNA structures in the replication enhancer of flaviviruses and pestiviruses emerged via convergent evolution.

    Science.gov (United States)

    Gritsun, Dmitri J; Jones, Ian M; Gould, Ernest A; Gritsun, Tamara S

    2014-01-01

    RNA secondary structures in the 3'untranslated regions (3'UTR) of the viruses of the family Flaviviridae, previously identified as essential (promoters) or beneficial (enhancers) for replication, have been analysed. Duplicated enhancer elements are revealed as a global feature in the evolution of the 3'UTR of distantly related viruses within the genera Flavivirus and Pestivirus. For the flaviviruses, duplicated structures occur in the 3'UTR of all four distantly related ecological virus subgroups (tick-borne, mosquito-borne, no known vector and insect-specific flaviviruses (ISFV). RNA structural differences distinguish tick-borne flaviviruses with discrete pathogenetic characteristics. For Aedes- and Culex-associated ISFV, secondary RNA structures with different conformations display numerous short ssRNA direct repeats, exposed as loops and bulges. Long quadruplicate regions comprise almost the entire 3'UTR of Culex-associated ISFV. Extended duplicated sequence and associated RNA structures were also discovered in the 3'UTR of pestiviruses. In both the Flavivirus and Pestivirus genera, duplicated RNA structures were localized to the enhancer regions of the 3'UTR suggesting an adaptive role predominantly in wild-type viruses. We propose sequence reiteration might act as a scaffold for dimerization of proteins involved in assembly of viral replicase complexes. Numerous nucleotide repeats exposed as loops/bulges might also interfere with host immune responses acting as a molecular sponge to sequester key host proteins or microRNAs.

  10. Molecular dissection of a contiguous gene syndrome: Frequent submicroscopic deletions, evolutionarily conserved sequences, and a hypomethylated island in the Miller-Dieker chromosome region

    Energy Technology Data Exchange (ETDEWEB)

    Ledbetter, D.H.; Ledbetter, S.A.; vanTuinen, P.; Summers, K.M.; Robinson, T.J.; Nakamura, Yusuke; Wolff, R.; White, R.; Barker, D.F.; Wallace, M.R.; Collins, F.S.; Dobyns, W.B. (Baylor College of Medicine, Houston, TX (USA))

    1989-07-01

    The Miller-Dieker syndrome (MDS), composed of characteristic facial abnormalities and a severe neuronal migration disorder affecting the cerebral cortex, is caused by visible or submicroscopic deletions of chromosome band 17p13. Twelve anonymous DNA markers were tested against a panel of somatic cell hybrids containing 17p deletions from seven MDS patients. All patients, including three with normal karyotypes, are deleted for a variable set of 5-12 markers. Two highly polymorphic VNTR (variable number of tandem repeats) probes, YNZ22 and YNH37, are codeleted in all patients tested and make molecular diagnosis for this disorder feasible. By pulsed-field gel electrophoresis, YNZ22 and YNH37 were shown to be within 30 kilobases (kb) of each other. Cosmid clones containing both VNTR sequences were identified, and restriction mapping showed them to be <15 kb apart. Three overlapping cosmids spanning >100 kb were completely deleted in all patients, providing a minimum estimate of the size of the MDS critical region. A hypomethylated island and evolutionarily conserved sequences were identified within this 100-kb region, indications of the presence of one or more expressed sequences potentially involved in the pathophysiology of this disorder. The conserved sequences were mapped to mouse chromosome 11 by using mouse-rat somatic cell hybrids, extending the remarkable homology between human chromosome 17 and mouse chromosome 11 by 30 centimorgans, into the 17p telomere region.

  11. The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients

    Directory of Open Access Journals (Sweden)

    Novo Carlos

    2008-09-01

    Full Text Available Abstract Background This study was designed to investigate, for the first time, the short-term molecular evolution of the HIV-2 C2, V3 and C3 envelope regions and its association with the immune response. Clonal sequences of the env C2V3C3 region were obtained from a cohort of eighteen HIV-2 chronically infected patients followed prospectively during 2–4 years. Genetic diversity, divergence, positive selection and glycosylation in the C2V3C3 region were analysed as a function of the number of CD4+ T cells and the anti-C2V3C3 IgG and IgA antibody reactivity Results The mean intra-host nucleotide diversity was 2.1% (SD, 1.1%, increasing along the course of infection in most patients. Diversity at the amino acid level was significantly lower for the V3 region and higher for the C2 region. The average divergence rate was 0.014 substitutions/site/year, which is similar to that reported in chronic HIV-1 infection. The number and position of positively selected sites was highly variable, except for codons 267 and 270 in C2 that were under strong and persistent positive selection in most patients. N-glycosylation sites located in C2 and V3 were conserved in all patients along the course of infection. Intra-host variation of C2V3C3-specific IgG response over time was inversely associated with the variation in nucleotide and amino acid diversity of the C2V3C3 region. Variation of the C2V3C3-specific IgA response was inversely associated with variation in the number of N-glycosylation sites. Conclusion The evolutionary dynamics of HIV-2 envelope during chronic aviremic infection is similar to HIV-1 implying that the virus should be actively replicating in cellular compartments. Convergent evolution of N-glycosylation in C2 and V3, and the limited diversification of V3, indicates that there are important functional constraints to the potential diversity of the HIV-2 envelope. C2V3C3-specific IgG antibodies are effective at reducing viral population size

  12. Incidencia de potyvirus y caracterización molecular de PVY en regiones productoras de papa (Solanum tuberosum L. de Colombia

    Directory of Open Access Journals (Sweden)

    José Miguel Cotes

    2011-08-01

    Full Text Available Incidence of potyvirus and molecular characterization of PVY in potato (Solanum tuberosum L. growing regions of ColombiaTítulo corto: Incidencia de potyvirus en cultivos de papa de Colombia ResumenLos problemas virales reducen los rendimientos y la calidad del tubérculo semilla en cultivos de papa de todo el mundo. Esta investigación se planteó con el fin de evaluar los niveles de incidencia de potyvirus en diez de las principales regiones cultivadoras de papa de los departamentos de Antioquia, Boyacá, Cundinamarca y Nariño (Colombia, y las características genotípicas del virus Y de la papa (Potato virus Y, PVY, seleccionado por ser el potyvirus más limitante de este cultivo. Para la evaluación de la incidencia se utilizaron pruebas de Elisa con anticuerpos que reconocen epítopes comunes a los potyvirus, mientras que las pruebas moleculares incluyeron el análisis filogenético de secuencias parciales del gen de la cápside viral de 33 aislamientos, así como la secuenciación de una porción de los extremos 5´ y 3´del genoma de dos cepas colombianas de este virus. Los resultados confirmaron la presencia de potyvirus en los cultivos de los cuatro departamentos evaluados, con una incidencia promedio del 72%, siendo este nivel superior al 56% en todas las zonas evaluadas. Los análisis moleculares del PVY, permitieron asociar las cepas colombianas estudiadas con las razas PVYN y la variante PVYNTN, esta última responsable de la enfermedad conocida en el mundo como PTNRD (Potato tuber necrotic ringspot disease. Palabras clave: cápside, Elisa, RT-PCR, secuenciación.  AbstractPotato viruses are responsible for significant reductions in seed quality and crop yields around the world. In this study, we evaluate the levels of incidence of potyvirus in ten potato growing regions of Colombia from the provinces of Antioquia, Boyacá, Cundinamarca and Nariño. As PVY is the most limiting potyvirus in potato farming, a molecular

  13. Molecular typing of Salmonella enterica subspecies enterica serovar Typhimurium isolated in Abruzzo region (Italy from 2008 to 2010

    Directory of Open Access Journals (Sweden)

    Alessandra Alessiani

    2014-03-01

    Full Text Available In this study, 47 antibiotic-resistant strains of Salmonella enterica subspecies enterica serovar Typhimurium (ST were characterised, including 15 monophasic variants 1, 4, [5], 12:i:-, (STm isolated from different matrices. They were all selected from 389 Salmonella enterica subspecies enterica strains isolated during 2008-2010 in Abruzzo region (Italy. Thirty-seven strains showed to be resistant to more than 1 antibiotic. Among 47 isolates, phage type U311 and DT104 were identified. The ASSuT resistance pattern was predominant in mST strains and ACSSuT in ST DT104 and U302. A multiplex Polimerase Chain Reaction (PCR method was used to investigate 4 genes: fluorfenicol (floSt, virulence (spvC, invasine (invA and integrase (int. All ST the strain were positive for invA gene and 28,32% of strains were positive for spvC gene. PFGE analysis revealed a large number of small clonal populations, however not ascrivable to outbreaks.

  14. Molecular typing of Salmonella enterica subspecies enterica serovar Typhimurium isolated in Abruzzo region (Italy) from 2008 to 2010.

    Science.gov (United States)

    Alessiani, Alessandra; Sacchini, Lorena; Pontieri, Eugenio; Gavini, Jacopo; Di Giannatale, Elisabetta

    2014-01-01

    In this study, 47 antibiotic-resistant strains of Salmonella enterica subspecies enterica serovar Typhimurium (ST) were characterised, including 15 monophasic variants 1, 4, [5], 12:i:-, (STm) isolated from different matrices. They were all selected from 389 Salmonella enterica subspecies enterica strains isolated during 2008-2010 in Abruzzo region (Italy). Thirty-seven strains showed to be resistant to more than 1 antibiotic. Among 47 isolates, phage type U311 and DT104 were identified. The ASSuT resistance pattern was predominant in mST strains and ACSSuT in ST DT104 and U302. A multiplex Polimerase Chain Reaction (PCR) method was used to investigate 4 genes: fluorfenicol (floSt), virulence (spvC), invasine (invA) and integrase (int). All ST the strain were positive for invA gene and 28,32% of strains were positive for spvC gene. PFGE analysis revealed a large number of small clonal populations, however not ascrivable to outbreaks.

  15. Molecular Identification of Isolated Fungi from Unopened Containers of Greek Yogurt by DNA Sequencing of Internal Transcribed Spacer Region

    Directory of Open Access Journals (Sweden)

    Irshad M. Sulaiman

    2014-06-01

    Full Text Available In our previous study, we described the development of an internal transcribed spacer (ITS1 sequencing method, and used this protocol in species-identification of isolated fungi collected from the manufacturing areas of a compounding company known to have caused the multistate fungal meningitis outbreak in the United States. In this follow-up study, we have analyzed the unopened vials of Greek yogurt from the recalled batch to determine the possible cause of microbial contamination in the product. A total of 15 unopened vials of Greek yogurt belonging to the recalled batch were examined for the detection of fungi in these samples known to cause foodborne illness following conventional microbiological protocols. Fungi were isolated from all of the 15 Greek yogurt samples analyzed. The isolated fungi were genetically typed by DNA sequencing of PCR-amplified ITS1 region of rRNA gene. Analysis of data confirmed all of the isolated fungal isolates from the Greek yogurt to be Rhizomucor variabilis. The generated ITS1 sequences matched 100% with the published sequences available in GenBank. In addition, these yogurt samples were also tested for the presence of five types of bacteria (Salmonella, Listeria, Staphylococcus, Bacillus and Escherichia coli causing foodborne disease in humans, and found negative for all of them.

  16. Far-infrared molecular lines from Low- to High-Mass Star Forming Regions observed with Herschel

    CERN Document Server

    Karska, A; Bruderer, S; Goicoechea, J R; Herczeg, G J; van Dishoeck, E F; José-García, I San; Contursi, A; Feuchtgruber, H; Fedele, D; Baudry, A; Braine, J; Chavarría, L; Cernicharo, J; van der Tak, F F S; Wyrowski, F

    2013-01-01

    (Abridged) We study the response of the gas to energetic processes associated with high-mass star formation and compare it with studies on low- and intermediate-mass young stellar objects (YSOs) using the same methods. The far-IR line emission and absorption of CO, H$_2$O, OH, and [OI] reveals the excitation and the relative contribution of different species to the gas cooling budget. Herschel-PACS spectra covering 55-190 um are analyzed for ten high-mass star forming regions of various luminosities and evolutionary stages at spatial scales of ~10^4 AU. Radiative transfer models are used to determine the contribution of the envelope to the far-IR CO emission. The close environments of high-mass YSOs show strong far-IR emission from molecules, atoms, and ions. Water is detected in all 10 objects even up to high excitation lines. CO lines from J=14-13 up to typically 29-28 show a single temperature component, Trot~300 K. Typical H$_2$O temperatures are Trot~250 K, while OH has Trot~80 K. Far-IR line cooling is ...

  17. Cholecystokinin in white sea bream: molecular cloning, regional expression, and immunohistochemical localization in the gut after feeding and fasting.

    Directory of Open Access Journals (Sweden)

    Valeria Micale

    Full Text Available BACKGROUND: The peptide hormone cholecystokinin (CCK, secreted by the midgut, plays a key role in digestive physiology of vertebrates including teleosts, by stimulating pancreatic secretion, gut motility, and gallbladder contraction, as well as by delaying gastric emptying. Moreover, CCK is involved in the regulation of food intake and satiation. Secretion of CCK by the hindgut is controversial, and its biological activity remains to be elucidated. The present paper addresses the regional distribution of intestinal CCK in the white sea bream, Diplodus sargus, as well as the possible involvement of hindgut CCK in digestive processes. METHODOLOGY/PRINCIPAL FINDINGS: Full-lengths mRNAs encoding two CCK isoforms (CCK-1 and CCK-2 were sequenced and phylogenetically analyzed. CCK gene and protein expression levels in the different gut segments were measured 3 h and 72 h after feeding, by quantitative real-time RT-PCR and Western blot, respectively. Moreover, endocrine CCK cells were immunoistochemically detected. Fasting induced a significant decrease in CCK-2 in all intestinal segments, including the hindgut. On the other hand, no significant difference was induced by fasting on hindgut CCK-1. CONCLUSIONS/SIGNIFICANCE: The results demonstrated two CCK isoforms in the hindgut of D.sargus, one of which (CCK-2 may be involved in the feedback control of uncompleted digestive processes. On the other hand, a functional role alternative to regulation of digestive processes may be inferred for D.sargus CCK-1, since its expression was unaffected by feeding or fasting.

  18. Preliminary study on the molecular structure of 3’ region of Duchenne muscular dystrophy (DMD) gene in Chinese

    Institute of Scientific and Technical Information of China (English)

    余龙; 赵寿元

    1996-01-01

    Number and order of HindⅢ exon-containing fragments (Hd) at 3’ region of DMD gene were studied systematically using 16 partly-overlapping cDNA subprobes which were produced from dystrophin cDNA 9- 14 with each of 9 restriction endonudeases. There are 25 Hd fragments corresponding to cDNA 9 -14 in DMD gene. Since then, the exact length and the new order of Hd fragments are established. A new 2.1 kb fragment (Hd 55) is revealed, a 5.2 kb fragment (formely designated as Hd 59) is excluded and the existence of a controversial 3.2 kb fragment (Hd 64) is confirmed. Besides, three new exons were revealed by comparing the PvuⅡ and the XbaⅠ hybridization patterns with the Hindlll hybridization patterns for these cDNA subprobes. It is concluded that there are at least 66 Hd fragments, or 79 exons in DMD gene basing on the discovery of three additional exons. The corresponding relationship between the 66 Hd fragments and the SfiⅠ large scale physical map has been studied, and at least 17 Hd fragments or 19 exo

  19. Identification of Perkinsus-like parasite in Manila clam, Ruditapes philippinarum using DNA molecular marker at ITS region

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Genomic DNA was extracted from hypnospores of Perkinsus-like parasite of Manila clam Ruditapes philippinarum collected at the fishing grounds in Huanghai Sea coast Shicheng Island and East China Sea coast Ningbo, China. The internal transcribed spacer(ITS)in rDNA was PCR-amplified, cloned, sequenced, and compared with that of five Perkinsus species in GenBank. The fragment amplified from DNA of parasite of either Shicheng Island or Ningbo contained 649 bp, including partial ssrRNA(51 bp) and ITS(+5.8 S)(598 bp) regions. The ITS(+5.8S) sequences of Perkinsus-like parasite of both Shicheng Island and Ningbo were all 99% identical to those ofPerkinsus atlanticus,and were not more than 95% identical to those of other four Perkinsus species including P. marinus, P.andrewsi, P. qugwadi and P. medierraneus.The ITS (+5.8S) sequence of Perkinsus-like parasite of Shicheng Island was 99% identical to that of Ningbo. These facts about nucleotide sequences suggested that the Perkinsus-like parasite in Manila clam, Ruditapes philippinarum collected from either the Huanghai Sea coast or the East China Sea coast was P. atlanticus, and might reflect P. atlanticus strains of distinct geographic distribution.

  20. Molecular characterization of peste des petits ruminants virus from the Karamoja region of Uganda (2007-2008).

    Science.gov (United States)

    Luka, Pam D; Erume, Joseph; Mwiine, Frank N; Ayebazibwe, Chrisostom

    2012-01-01

    Antibodies against peste des petits ruminants virus (PPRV) were first detected in goats in East Africa in 1995 without any clinical disease. It was not until during the years 2006 and 2007 that the disease outbreaks were first reported in Kenya and Uganda, respectively. This study was carried out to detect and characterize PPRV from a suspected outbreak in sheep and goats in the Karamoja region in 2007-2008. Oculo-nasal and blood samples were tested using F-gene-based primers, and their genetic relationships to other sequences in the GenBank database were investigated. A total of 383 samples suspected to contain PPRV were randomly collected and tested. Sixty-seven (17.5%) were positive when F protein gene primers were used. During the years 2007 and 2008, 38.1% (26/67) and 13.0% (41/316) of samples were positive by PCR, respectively. The 2007 sequences clustered with Asian sequences in lineage 4 and Cote d'Ivoire 86 (ICV 86) in lineage 2, while all of the 2008 samples clustered in lineage 1. Over the years, the implicated strains were genetically close (88%-91%) to the vaccine strain (Nig 75/1). Based on this study, the circulating PPR strains in Uganda are heterogeneous, and therefore, the disease may have been introduced from different sources.

  1. Molecular characterization of aflatoxigenic aspergilli-contaminated poultry and animal feedstuff samples from the western region of Saudi Arabia

    Directory of Open Access Journals (Sweden)

    YOUSSUF A. GHERBAWY

    2016-03-01

    Full Text Available The aflatoxigenic abilities of 64 and 17 isolates of Aspergillus flavus and A. parasiticus isolated from poultry and animal feedstuff samples collected from the western region of Saudi Arabia werestudied. Thirty-three (51.6% and 13 (76.5% isolates of A. flavus and A. parasiticus, respectively, were aflatoxigenic. The ranges of aflatoxins in A. flavus and A. parasiticus isolates were 4.4-110 and 143.6-271.3 ppm (μg/g, respectively. A. parasiticus isolates generally produced a greater amount of aflatoxins than A. flavus. A. flavus isolates from poultry, cattle, and camel and cattle feeds produced aflatoxin amounts in the range 5.7-110, 4.4-19.0, and 7.0-28.5 ppm, respectively.From poultry feedstuff samples, A. parasiticus produced aflatoxins in the range 212.5-232.4 ppm.Some aflatoxin biosynthesis genes (aflR, omt-1, ver-1, and nor-1 were detected with variable frequencies in all A. flavus and A. parasiticus isolates. The genetic diversity among 64 isolates of A.flavus using internal transcribed spacer sequence results and the amplification of some aflatoxin biosynthesis genes revealed that the investigated isolates showed high heterogeneity.

  2. Molecular characterisation of the clonal emergence of high-level ciprofloxacin-monoresistant Haemophilus influenzae in the Region of Southern Denmark

    DEFF Research Database (Denmark)

    Fuursted, Kurt; Hartmeyer, Gitte Nyvang; Stegger, Marc

    2016-01-01

    Haemophilus influenzae is an important human pathogen usually susceptible to quinolones. Here we report the emergence of high-level ciprofloxacin-monoresistant H. influenzae in the Region of Southern Denmark. Four isolates were collected for phenotypic and molecular characterisation using whole......-genome sequencing (WGS). During an 18-month period, the occurrence of high-level ciprofloxacin-monoresistant H. influenzae in patients aged 1-77 years from sputum, ear and eye samples was detected. An epidemiological link between the patients could not be identified. The isolates were non-encapsulated, biotype III...... and were demonstrated by WGS to be clonal belonging to a single clade with an unknown multilocus sequence type (double-locus variant of ST196). The antibiogram demonstrated that they were all monoresistant to ciprofloxacin with a minimum inhibitory concentration (MIC) >32mg/L. In silico resistome analysis...

  3. Molecular cloning, expression and identification of the promoter regulatory region for the neuropeptide trissin in the nervous system of the silkmoth Bombyx mori.

    Science.gov (United States)

    Roller, Ladislav; Čižmár, Daniel; Gáliková, Zuzana; Bednár, Branislav; Daubnerová, Ivana; Žitňan, Dušan

    2016-06-01

    Trissin has recently been identified as a conserved insect neuropeptide, but its cellular expression and function is unknown. We detected the presence of this neuropeptide in the silkworm Bombyx mori using in silico search and molecular cloning. In situ hybridisation was used to examine trissin expression in the entire central nervous system (CNS) and gut of larvae, pupae and adults. Surprisingly, its expression is restricted to only two pairs of small protocerebral interneurons and four to five large neurons in the frontal ganglion (FG). These neurons were further characterised by subsequent multiple staining with selected antibodies against insect neuropeptides. The brain interneurons innervate edges of the mushroom bodies and co-express trissin with myoinhibitory peptides (MIP) and CRF-like diuretic hormones (CRF-DH). In the FG, one pair of neurons co-express trissin with calcitonin-like diuretic hormone (CT-DH), short neuropeptide F (sNPF) and MIP. These neurons innervate the brain tritocerebrum and musculature of the anterior midgut. The other pair of trissin neurons in the FG co-express sNPF and project axons to the tritocerebrum and midgut. We also used the baculovirus expression system to identify the promoter regulatory region of the trissin gene for targeted expression of various molecular markers in these neurons. Dominant expression of trissin in the FG indicates its possible role in the regulation of foregut-midgut contractions and food intake.

  4. Molecular evidence of mother-to-child transmission of HTLV-IIc in the Kararao Village (Kayapo in the Amazon Region of Brazil

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    Ishak Ricardo

    2001-01-01

    Full Text Available Blood samples from native Indians in the Kararao village (Kayapo, were analysed using serological and molecular methods to characterize infection and analyse transmission of HTLV-II. Specific reactivity was observed in 3/26 individuals, of which two samples were from a mother and child. RFLP analysis of the pX and env regions confirmed HTLV-II infection. Nucleotide sequence of the 5' LTR segment and phylogenetic analysis showed a high similarity (98% between the three samples and prototype HTLV-IIa (Mot, and confirmed the occurrence of the HTLV-IIc subtype. There was a high genetic similarity (99.9% between the mother and child samples and the only difference was a deletion of two nucleotides (TC in the mother sequence. Previous epidemiological studies among native Indians from Brazil have provided evidence of intrafamilial and vertical transmission of HTLV-IIc. The present study now provides molecular evidence of mother-to-child transmission of HTLV-IIc, a mechanism that is in large part responsible for the endemicity of HTLV in these relatively closed populations. Although the actual route of transmission is unknown, breast feeding would appear to be most likely.

  5. Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability.

    Science.gov (United States)

    Joulié, Aurelien; Sidi-Boumedine, Karim; Bailly, Xavier; Gasqui, Patrick; Barry, Séverine; Jaffrelo, Lydia; Poncet, Charles; Abrial, David; Yang, Elise; Leblond, Agnès; Rousset, Elodie; Jourdain, Elsa

    2017-03-01

    Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need

  6. Molecular Basis of Interactions Between SH3 Domain-Containing Proteins and the Proline-Rich Region of the Ubiquitin Ligase Itch.

    Science.gov (United States)

    Desrochers, Guillaume; Cappadocia, Laurent; Lussier-Price, Mathieu; Ton, Anh-Tien; Ayoubi, Riham; Serohijos, Adrian; Omichinski, James G; Angers, Annie

    2017-02-24

    The ligase Itch plays major roles in signalling pathways by inducing ubiquitylation-dependent degradation of several substrates. Substrate recognition and binding is critical for the regulation of this reaction. Like closely related ligases, Itch can interact with proteins containing a PPxY motif via its WW domains. In addition to these WW domains, Itch possesses a proline-rich region (PRR) that has been shown to interact with several Src Homology 3 (SH3) domain-containing proteins. We have previously established that despite the apparent surface uniformity and conserved fold of SH3 domains, they display different binding mechanisms and affinities for their interaction with the PRR of Itch. Here, we attempt to determine the molecular bases underlying the wide range of binding properties of the Itch PRR. Using pull-down assays combined with mass spectrometry analysis, we show that the Itch PRR preferentially forms complexes with Endophilins, Amphyphisins and Pacsins, but can also target a variety of other SH3 domain-containing proteins. In addition, we map the binding sites of these proteins using a combination of PRR sub-sequences and mutants. We find that different SH3 domains target distinct proline-rich sequences overlapping significantly. We also structurally analyze these protein complexes using crystallography and molecular modelling. These structures depict the position of Itch PRR engaged in a 1:2 protein complex with β-PIX and a 1:1 complex with the other SH3 domain-containing proteins. Taken together, these results reveal the binding preferences of the Itch PRR towards its most common SH3 domain-containing partners, and demonstrate that the PRR region is sufficient for binding.

  7. First External Quality Assessment of Molecular and Serological Detection of Rift Valley Fever in the Western Mediterranean Region.

    Directory of Open Access Journals (Sweden)

    Federica Monaco

    Full Text Available Rift Valley fever (RVF is a mosquito-borne viral zoonosis which affects humans and a wide range of domestic and wild ruminants. The large spread of RVF in Africa and its potential to emerge beyond its geographic range requires the development of surveillance strategies to promptly detect the disease outbreaks in order to implement efficient control measures, which could prevent the widespread of the virus to humans. The Animal Health Mediterranean Network (REMESA linking some Northern African countries as Algeria, Egypt, Libya, Mauritania, Morocco, Tunisia with Southern European ones as France, Italy, Portugal and Spain aims at improving the animal health in the Western Mediterranean Region since 2009. In this context, a first assessment of the diagnostic capacities of the laboratories involved in the RVF surveillance was performed. The first proficiency testing (external quality assessment--EQA for the detection of the viral genome and antibodies of RVF virus (RVFV was carried out from October 2013 to February 2014. Ten laboratories participated from 6 different countries (4 from North Africa and 2 from Europe. Six laboratories participated in the ring trial for both viral RNA and antibodies detection methods, while four laboratories participated exclusively in the antibodies detection ring trial. For the EQA targeting the viral RNA detection methods 5 out of 6 laboratories reported 100% of correct results. One laboratory misidentified 2 positive samples as negative and 3 positive samples as doubtful indicating a need for corrective actions. For the EQA targeting IgG and IgM antibodies methods 9 out of the 10 laboratories reported 100% of correct results, whilst one laboratory reported all correct results except one false-positive. These two ring trials provide evidence that most of the participating laboratories are capable to detect RVF antibodies and viral RNA thus recognizing RVF infection in affected ruminants with the diagnostic methods

  8. A molecular analysis of quinolone-resistant Haemophilus influenzae: validation of the mutations in Quinolone Resistance-Determining Regions.

    Science.gov (United States)

    Shoji, Hisashi; Shirakura, Tetsuro; Fukuchi, Kunihiko; Takuma, Takahiro; Hanaki, Hideaki; Tanaka, Kazuo; Niki, Yoshihito

    2014-04-01

    The mechanism of quinolone-resistance is considered to be amino acid mutations in the type II topoisomerase. We validated the genetic mechanisms of quinolone resistance in Haemophilus influenzae. We obtained 29 H. influenzae strains from a nationwide surveillance program in Japan (including 11 quinolone-resistant strains [moxifloxacin: MFLX or levofloxacin MIC ≥2 μg/ml]). We analyzed the sequences of the Quinolone Resistance-Determining Regions (QRDRs) in GyrA, GyrB, ParC and ParE. Furthermore, we induced resistance in susceptible strains by exposing them to quinolone, and investigated the relationship between mutations in the QRDRs and the MICs. Five amino acid substitutions in GyrA (at Ser84 and Asp88) and ParC (at Gly82, Ser84 and Glu88) were found to be closely related to the MICs. The strains with a MFLX MIC of 0.125-1 and 2-4 μg/ml had one and two mutations, respectively. The strains with a MFLX MIC of ≥8 μg/ml had three or more mutations. The strains with induced resistance with MFLX MICs of 0.5-1 and ≥2 μg/ml also had one and two mutations, respectively. We confirmed that these five mutations strongly contribute to quinolone resistance and found that the degree of resistance is related to the number of the mutations. In addition, the three strains of 18 susceptible strains (16.7%) also had a single mutation. These strains may therefore be in the initial stage of quinolone resistance. Currently, the frequency of quinolone-resistant H. influenzae is still low. However, as has occurred with β-lactams, an increase in quinolone use may lead to more quinolone-resistant strains.

  9. The clinical and molecular spectrum of galactosemia in patients from the Cape Town region of South Africa

    Directory of Open Access Journals (Sweden)

    Brown Ruth

    2002-09-01

    Full Text Available Abstract Background The objective of this study was to document the clinical, laboratory and genetic features of galactosemia in patients from the Cape Town metropolitan region. Methods Diagnoses were based on thin layer chromatography for galactosuria/galactosemia and assays of erythrocyte galactose-1-phosphate uridyltransferase (GALT and galactokinase activities. Patients were screened for the common S135L and Q188R transferase gene mutations, using PCR-based assays. Screening for the S135L mutation in black newborns was used to estimate the carrier rate for galactosemia in black South Africans. Results A positive diagnosis of galactosemia was made in 17 patients between the years 1980 to 2001. All had very low or absent galactose-1-phosphate uridyltransferase (GALT activity, and normal galactokinase levels. The mean age at diagnosis was 5.1 months (range 4 days to 6.5 months. A review of 9 patients showed that hepatomegaly (9/9, and splenomegaly, failure to thrive, developmental delay, bilateral cataracts (6/9 were the most frequent features at diagnosis. Six had conjugated hyperbilirubinemia. Four experienced invasive E. coli infection before diagnosis. Ten patients were submitted to DNA analysis. All 4 black patients and 2 of mixed extraction were homozygous for the S135L allele, while all 3 white patients were homozygous for the Q188R allele. The remaining patient of mixed extraction was heterozygous for the Q188R allele. The estimated carrier frequency of the S135L mutation in 725 healthy black newborns was 1/60. Conclusions In the absence of newborn screening the delay in diagnosis is most often unacceptably long. Also, carrier frequency data predict a galactosemia incidence of approximately 1/14 400 for black newborns in the Cape Metropole, which is much higher than the current detection rate. It is thus likely that many patients go undetected.

  10. Prevalence of Giardiaduodenalis among children from a central region of Cuba: molecular characterization and associated risk factors.

    Science.gov (United States)

    Puebla, Luis Jerez; Núñez, Fidel A; García, Alexey Brito; Rivero, Lázara Rojas; Millán, Irais Atencio; Prado, Raúl Cordoví

    2017-06-01

    Giardia duodenalis is one of the most frequent intestinal parasitic infections in children worldwide. To date, eight main assemblages of G. duodenalis have been described, but only A and B genetic groups are known to infect humans. A cross-sectional study was conducted to determine the prevalence and risk factors of Giardia duodenalis infection in 417 preschool children from the Fomento municipality in the central region of Cuba between January and June 2013. The overall prevalence of Giardia infection was 10.79 %. Assemblage identification was carried out by the amplification of a fragment of the triose phosphate isomerase (tpi) gene. DNA from 36 of 45 (80 %) samples was successfully amplified by PCR-tpi. Assemblage B and mixed assemblages A + B represented 52.78 and 36.11 % respectively, of genotyped samples. Assemblage A accounts for only 11.11 %. Children who were cared for at home were associated with diarrhea caused by assemblage B. No associations were found between other clinical variables with infecting assemblage of Giardia. Univariate analysis identified the use of unsafe water resources (OR 2.9; CI 1.2-6.8) and-even more interestingly-keeping dogs indoor (OR 2.5; CI 1.2-5.4) were significant risk factors associated with Giardia infection among children. Multivariate analysis using introduction test logistic regression ratified the association of these two risk factors: kept dogs indoor (OR 2.8, CI 1.1-5.3), and untreated water (OR 1.4, CI 1.4-4.9) with Giardia infection. This information may be useful for an effective prevention and control programme of giardiasis in this population.

  11. Molecular Dynamic Simulations of Glass Transition Temperature and Mechanical Properties in the Amorphous Region of Oil-Immersed Transformer Insulation Paper

    Science.gov (United States)

    Wang, You-Yuan; Yang, Tao; Liao, Rui-Jin

    2012-07-01

    The glass transition temperature (Tg) in the amorphous region of an insulation paper is one of the most important characteristics for thermal stability. Molecular dynamic simulations have been performed on three micro-structural models, namely, amorphous pure cellulose, amorphous cellulose with water and amorphous cellulose with oil, to study the microscopic mechanism of the glass transition process for oil-immersed transformer insulation paper. Using the method of specific volume versus temperature curve, the Tg of amorphous pure cellulose, cellulose with water, and cellulose with oil was determined as 448, 418 and 440 K, respectively. The current study may provide some information for thermal aging. The simulation results show that during the glass transition process, both the chain motion and mechanical properties of cellulose changes significantly. Relative to the oil molecules, water molecules immersed in the amorphous region of insulation paper can disrupt hydrogen bonds between cellulose chains. This phenomenon results in a significant reduction in the glass transition temperature and affects the thermal stability of the insulation paper.

  12. Mid-infrared supercontinuum covering the 1.4-13.3 μm molecular fingerprint region using ultra-high NA chalcogenide step-index fibre

    Science.gov (United States)

    Petersen, Christian Rosenberg; Møller, Uffe; Kubat, Irnis; Zhou, Binbin; Dupont, Sune; Ramsay, Jacob; Benson, Trevor; Sujecki, Slawomir; Abdel-Moneim, Nabil; Tang, Zhuoqi; Furniss, David; Seddon, Angela; Bang, Ole

    2014-11-01

    The mid-infrared spectral region is of great technical and scientific interest because most molecules display fundamental vibrational absorptions in this region, leaving distinctive spectral fingerprints. To date, the limitations of mid-infrared light sources such as thermal emitters, low-power laser diodes, quantum cascade lasers and synchrotron radiation have precluded mid-infrared applications where the spatial coherence, broad bandwidth, high brightness and portability of a supercontinuum laser are all required. Here, we demonstrate experimentally that launching intense ultra-short pulses with a central wavelength of either 4.5 μm or 6.3 μm into short pieces of ultra-high numerical-aperture step-index chalcogenide glass optical fibre generates a mid-infrared supercontinuum spanning 1.5 μm to 11.7 μm and 1.4 μm to 13.3 μm, respectively. This is the first experimental demonstration to truly reveal the potential of fibres to emit across the mid-infrared molecular ‘fingerprint region’, which is of key importance for applications such as early cancer diagnostics, gas sensing and food quality control.

  13. Photon-Dominated Region Modeling of the [C I],[C II], and CO Line Emission from a Boundary in the Taurus Molecular Cloud

    CERN Document Server

    Orr, Matthew; Goldsmith, Paul

    2014-01-01

    We present [Ci] and [Cii] observations of a linear edge region in the Taurus molecular cloud, and model this region as a cylindrically symmetric PDR exposed to a low-intensity UV radiation field. The sharp, long profile of the linear edge makes it an ideal case to test PDR models and determine cloud parameters. We compare observations of the [C i], 3P1 -> 3P0 (492 GHz), [C i] 3P2 -> 3P1 (809 GHz), and [Cii] 2P3/2 -> 2P1/2 (1900 GHz) transitions, as well as the lowest rotational transitions of 12CO and 13CO, with line intensities produced by the RATRAN radiative transfer code from the results of the Meudon PDR code. We constrain the density structure of the cloud by fitting a cylindrical density function to visual extinction data. We study the effects of variation of the FUV field, 12C/13C isotopic abundance ratio, sulfur depletion, cosmic ray ionization rate, and inclination of the filament relative to the sky-plane on the chemical network of the PDR model and resulting line emission. We also consider the rol...

  14. Frequency Dependent Non- Thermal Effects of Oscillating Electric Fields in the Microwave Region on the Properties of a Solvated Lysozyme System: A Molecular Dynamics Study

    Science.gov (United States)

    Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas

    2017-01-01

    The use of microwaves in every day’s applications raises issues regarding the non thermal biological effects of microwaves. In this work we employ molecular dynamics simulations to advance further the dielectric studies of protein solutions in the case of lysozyme, taking into consideration possible frequency dependent changes in the structural and dynamic properties of the system upon application of electric field in the microwave region. The obtained dielectric spectra are identical with those derived in our previous work using the Fröhlich-Kirkwood approach in the framework of the linear response theory. Noticeable structural changes in the protein have been observed only at frequencies near its absorption maximum. Concerning Cα position fluctuations, different frequencies affected different regions of the protein sequence. Furthermore, the influence of the field on the kinetics of protein-water as well as on the water-water hydrogen bonds in the first hydration shell has been studied; an extension of the Luzar-Chandler kinetic model was deemed necessary for a better fit of the applied field results and for the estimation of more accurate hydrogen bond lifetime values. PMID:28129348

  15. Serological and molecular investigation of Ehrlichia spp. and Anaplasma spp. in ticks and blood of dogs, in the Thrace Region of Turkey.

    Science.gov (United States)

    Çetinkaya, Handan; Matur, Erdal; Akyazi, İbrahim; Ekiz, Elif Ergul; Aydin, Levent; Toparlak, Mufit

    2016-07-01

    In recent years, tick-borne diseases like ehrlichiosis and anaplasmosis became widespread worldwide threatening the health of both human and companion animals. Therefore, the aim of this study was to determine the presence of Anaplasma spp., and Ehrlichia spp. in dogs and ticks in the Thrace Region of Turkey. A total of 400 blood samples and 912 ticks were collected from dogs living in shelters that are located in four cities (Istanbul, Edirne, Tekirdag and Kirklareli) of the Thrace Region. Blood and buffy coat smears were prepared for microscopic examination. Hematologic and serologic analyses were performed using cell counter and commercial Snap3Dx test kit, respectively. Eight hundred fifty of collected ticks were classified as Rhipicephalus sanguineus, 33 as Rhipicephalus turanicus and 29 as Ixodes ricinus. After DNA extraction from blood samples and pooled ticks (127 tick pools, in total), nested PCR was performed to detect the DNA of Anaplasma spp., and Ehrlichia spp. The seroprevalence of Ehrlichia canis was 27.25% (109) by Snap3Dx test and the total molecular positivity was 11.75% (47) in dog blood samples and 21.25% (27) in tick pools by nested PCR. The frequencies of the infected blood samples with E. canis, Anaplasma phagocytophilum and Anaplasma platys were detected as 6%, 4% and 6%, respectively. E. canis and A. platys were detected in R. sanguineus pools with a ratio of 15.75% and 0.7%, respectively. In addition, A. platys was also detected in R. turanicus pools (0.7%). A. phagocytophilum was found only in I. ricinus pools (3.93%). Morulae of three species were detected in buffy coat and blood smears. While anemia was observed in dogs infected with E. canis and co-infected (with one or more species), thrombocytopenia was observed only in co-infected dogs. This is the first study providing evidence for the presence of Anaplasma spp. and Ehrlichia spp. in dogs and ticks in the Thrace Region of Turkey. Based on the results of the tests used in this study

  16. Abundance of questing ticks and molecular evidence for pathogens in ticks in three parks of Emilia-Romagna region of Northern Italy

    Directory of Open Access Journals (Sweden)

    Sara Aureli

    2015-09-01

    Full Text Available Introduction and objective. Infectious and parasitic diseases transmitted by ticks, such as Lyme diseases, granulocytic anaplasmosis and piroplasmosis, have been frequently reported in Europe, with increasing attention to them as an emerging zoonotic problem. The presented study was performed to assess the distribution and the density of questing ticks in three regional parks of Emilia-Romagna region of Northern Italy, and to seek molecular evidence of potential human pathogens in tick populations. Materials and Methods. In the period April-October 2010, 8,139 questing ticks were collected: 6,734 larvae, 1,344 nymphs and only a few adults – 28 females and 33 males. The abundance of[i] Ixodes ricinus[/i] questing ticks was compared among different sampling sites and related to microclimate parameters. 1,544 out of 8,139 ticks were examined for the presence of pathogens: PCR was used to detect piroplasms DNA and Real time Taqman PCR for [i]Anaplasma phagocytophilum[/i] and [i]Borrelia burgdorferi[/i] s.l. Results. The predominant species was [i]I. ricinus[/i] (overall abundance 1,075.9/100 m[sup]2[/sup] ; more rarely, [i]Dermacentor marginatus[/i] (n = 37 – 0.45%, [i]Scaphixodes frontalis[/i] (n = 13 – 0.16%, [i]Hyalomma[/i] spp. (n = 6 – 0.07% and [i]Ixodes acuminatus[/i] (n = 3 – 0.04% were also found. 28 out of 324 (8.6% samples of ticks were PCR-positive for piroplasm DNA. 11 amplicons of 18S rRNA gene were identical to each other and had 100% identity with[i] Babesia[/i] EU1 ([i]Babesia venatorum[/i] using BLAST analysis. Real time Taqman PCR gave positive results for [i]A. phagocytophilum[/i] in 23 out of 292 samples (7.9%, and for [i]B. burgdorferi[/i] s.l. in 78 out of 292 samples (26.7%. [i]I. ricinu[/i]s was the only species found positive for pathogens by molecular analysis; 16 tick samples were co-infected with at least 2 pathogens. Discussion. The peak of nymph presence was in May, and the higher prevalence of pathogens

  17. Photon-dominated region modeling of the [C I], [C II], and CO Line Emission From A Boundary In The Taurus molecular cloud

    Energy Technology Data Exchange (ETDEWEB)

    Orr, Matthew E. [Physics and Astronomy Department, University of Southern California, Los Angeles, CA 90089 (United States); Pineda, Jorge L.; Goldsmith, Paul F. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099 (United States)

    2014-11-01

    We present [C I] and [C II] observations of a linear edge region in the Taurus molecular cloud, and model this region as a cylindrically symmetric photon-dominated region (PDR) exposed to a low-intensity UV radiation field. The sharp, long profile of the linear edge makes it an ideal case to test PDR models and determine cloud parameters. We compare observations of the [C I], {sup 3} P {sub 1} → {sup 3} P {sub 0} (492 GHz), [C I] {sup 3} P {sub 2} → {sup 3} P {sub 1} (809 GHz), and [C II] {sup 2} P {sub 3/2} → {sup 2} P {sub 1/2} (1900 GHz) transitions, as well as the lowest rotational transitions of {sup 12}CO and {sup 13}CO, with line intensities produced by the RATRAN radiative transfer code from the results of the Meudon PDR code. We constrain the density structure of the cloud by fitting a cylindrical density function to visual extinction data. We study the effects of variation of the FUV field, {sup 12}C/{sup 13}C isotopic abundance ratio, sulfur depletion, cosmic ray ionization rate, and inclination of the filament relative to the sky-plane on the chemical network of the PDR model and resulting line emission. We also consider the role of suprathermal chemistry and density inhomogeneities. We find good agreement between the model and observations, and that the integrated line intensities can be explained by a PDR model with an external FUV field of 0.05 G {sub 0}, a low ratio of {sup 12}C to {sup 13}C ∼43, a highly depleted sulfur abundance (by a factor of at least 50), a cosmic ray ionization rate (3-6) × 10{sup –17} s{sup –1}, and without significant effects from inclination, clumping or suprathermal chemistry.

  18. Molecular investigation of Neorickettsia risticii in trematodes and snails in a region with serological evidence of this agent in horses, state of Rio de Janeiro

    Directory of Open Access Journals (Sweden)

    R.L. Costa

    Full Text Available ABSTRACT In Brazil, some studies have indicated that Neorickettsia risticii circulates in horses, but it is unclear which are the possible intermediate vectors of this bacterium in the country. The aim of this study was to use molecular techniques in order to analyze the presence of N. risticii in snails and larval stages of trematodes in farms in a region with a history of seroreactive horses towards this bacterium, in Rio de Janeiro, Brazil. Convenience sampling was used in the studied region. The collected snails were exposed to incandescent light (60W for 2-4 hours in order to investigate trematodes in larval forms. Deoxyribonucleic acid (DNA was extracted from snail tissue and trematode. Real-time PCR (qPCR technique was used to investigate the presence of a 16S rRNA gene fragment of N. risticii. Snail specimens (n=410 were collected from 11 horse-breeding farms, and the following species were identified: Melanoides tuberculata, Pomacea sp., Biomphalaria tenagophila, Physa acuta, Drepanotrema anatinum and Biomphalaria straminea. Only 3.17% (n=13/410 of the collected snails were infected by trematodes. The cercariae obtained from these snails were classified as Megalourous cercariae, Pleurolophocercus cercariae and Furcocercous cercariae. There was no amplification of the target DNA of N. risticii in the snail and trematode samples tested by qPCR. Based on these data, the transmission of N. risticii by trematodes using these snail species in this region does not appear to occur or occurs at very low rates. Thus, further studies are needed in order to clarify which species of invertebrate hosts are infected by this bacterium and potentially participate in the transmission chain of equine neorickettsiosis in the state of Rio de Janeiro, Brazil.

  19. Quantitative conformational analysis of the core region of N-glycans using residual dipolar couplings, aqueous molecular dynamics, and steric alignment

    Energy Technology Data Exchange (ETDEWEB)

    Almond, Andrew; Duus, Jens O. [Carlsberg Laboratory (Denmark)

    2001-08-15

    A method is described for quantitatively investigating the dynamic conformation of small oligosaccharides containing an {alpha}(1{sup {yields}}6) linkage. It was applied to the oligosaccharide Man-{alpha}(1{sup {yields}}3) {l_brace}Man-{alpha} (1{sup {yields}}6){r_brace}Man-{alpha}-O-Me, which is a core region frequently observed in N-linked glycans. The approach tests an aqueous molecular dynamics simulation, capable of predicting microscopic dynamics, against experimental residual dipolar couplings, by assuming that alignment is caused purely by steric hindrance. The experimental constraints were heteronuclear and homonuclear residual dipolar couplings, and in particular those within the {alpha}(1{sup {yields}}6) linkage itself. Powerful spin-state-selective pulse sequences and editing schemes were used to obtain the most relevant couplings for testing the model. Molecular dynamics simulations in water over a period of 50 ns were not able to predict the correct rotamer population at the {alpha}(1{sup {yields}}6) linkage to agree with the experimental data. However, this sampling problem could be corrected using a simple maximum likelihood optimisation, indicating that the simulation was modelling local dynamics correctly. The maximum likelihood prediction of the residual dipolar couplings was found to be an almost equal population of the gg and gt rotamer conformations at the {alpha}(1{sup {yields}}6) linkage, and the tg conformation was predicted to be unstable and unpopulated in aqueous solution. In this case all twelve measured residual dipolar couplings could be satisfied. This conformer population could also be used to make predictions of scalar couplings with the use of a previously derived empirical equation, and is qualitatively in agreement with previous predictions based on NMR, X-ray crystallography and optical data.

  20. Probing the conditions within Photo-dissociation Regions with high resolution near-infrared spectroscopy of UV-excited molecular hydrogen

    Science.gov (United States)

    Kaplan, Kyle; Dinerstein, Harriet L.; Jaffe, Daniel Thomas

    2017-01-01

    UV radiation regulates the energetics, ionization, and chemistry in much of the ISM. Regions between hot ionized and cool molecular gas where non-ionizing far-UV radiation dominates the state of the gas are called Photo-Dissociation or Photon-Dominated Regions (PDRs). PDRs are found in regions of high-mass star formation, planetary nebulae, and other environments that contain strong far-UV radiation fields. Hydrogen molecules (H2) are pumped by far-UV photons into excited rotational-vibrational levels of the ground electronic state, which give rise to a rich array of transitions in the near to mid-infrared. These transitions make an excellent probe of the physical conditions within a PDR. I will present near-IR spectra taken with the Immersion GRating Infrared Spectrometer (IGRINS; Park et al. 2014, Proc. SPIE, 9147), a novel, sensitive spectrometer with high spectral resolving power (R~45000) and instantaneous broad wavelength coverage (1.45-2.45 μm). Using IGRINS, I obtained deep spectra and measured up to 100 H2 rotational-vibrational transitions in the well-studied Orion Bar PDR, four other star formation complexes, and over a dozen planetary nebulae. Measurements of many lines from a wide range of vibrational states (v=1 to 13), rotational states (J=1 to 13), and excitation energies provides leverage for constraining the overall level populations and discerning the state of and physical processes within the gas. This combination of high spectral and spatial resolution enables us to distinguish previously unresolved spatio-kinematical components with distinct intrinsic spectra and excitation mechanisms (e.g. shocks vs. radiative excitation) within some individual planetary nebulae. I use the plasma simulation code Cloudy (Ferland et al. 2013, ApJ, 757, 79) as a tool for interpreting the observed H2 line ratios. Some sources are well fit by models with a single temperature and density, consistent with emission from a narrow region of the overall PDR structure

  1. Molecular Detection of Equine Herpesvirus Types 1 and 4 Infection in Healthy Horses in Isfahan Central and Shahrekord Southwest Regions, Iran

    Directory of Open Access Journals (Sweden)

    Taghi Taktaz Hafshejani

    2015-01-01

    Full Text Available This study was undertaken to investigate molecularly the occurrence of EHV-1 and EHV-4 infection among equine population in regions, Iran. Blood samples from 53 and 37 randomly selected horses settled in Isfahan and Shahrekord, Iran, respectively, were collected. Detection of EHV-1 and EHV-4 genes in the blood samples was done using polymerase chain reaction (PCR. Out of 53 and 37 samples from Isfahan and Shahrekord, 4 (18.18% and 3 (8.10% were positive for PCR of EHV-1, respectively. Nine (16.98% and 6 (16.21% were positive for PCR of EHV-4, while 6 (11.32% and 3 (8.10% were positive for PCR of both EHV-1 and EHV-4, in Isfahan and Shahrekord, respectively. Of the 7 blood samples positive for EHV-1, 4 (16.66% and 3 (8.10% were from horses >3 years old while 2 (18.18% and 1 (16.66% were from 2-3 years old horses, in Isfahan and Shahrekord, respectively. Out of the 7 and 3 samples positive for PCR of EHV-1 in Isfahan and Shahrekord, 4 (22.2% and 1 (7.69% were Standardbred, while 3 (14.28% and 2 (13.33% were Thoroughbreds, respectively. EHV-4 was detected in blood of 4 (22.22% and 2 (15.83% Standardbreds and from 4 (19.04% and 4 (26.66% Thoroughbred horses in Isfahan and Shahrekord, respectively. This study has shown that horses settled in Isfahan central and Shahrekord southwest regions, Iran, are infected by EHV-1 and EHV-4 and thus serve as potential reservoirs and disseminators of the viruses.

  2. Prevalence of infection and molecular confirmation by using ITS-2 region of Fasciola gigantica found in domestic cattle from Chiang Mai province, Thailand

    Institute of Scientific and Technical Information of China (English)

    Anawat Phalee; Chalobol Wongsawad

    2014-01-01

    Objective:To investigate the infection ofFasciola gigantica(F. gigantica) in domestic cattle from ChiangMai province and molecular confirmation usingITS-2 region.Methods:The liver and gall bladder ofBubalus bubalis(B. bubalis) andBos taurus(B. taurus) from slaughterhouses were examined adult worms and prevalence investigation.The species confirmation with phylogenetic analysis usingITS-2 sequences was performed by maximum likelihood andUPGMA methods. Results:The total prevalences of infection inB. bubalis andBubalus taurus(B. taurus) were 67.27% and52.94% respectively.The respective prevalence in bothB. bubalis andB. taurus were acquired fromDoi-Saket,Muang, andSanpatong districts, with81.25%,62.50% and60.00% for B. bubalis and62.50%,50.00% and47.06% forBos taurus respectively.The species confirmation ofF. gigantica and some related species by basing on maximum likelihood andUPGMA methods used,4 groups of trematodes weregenerated, firstF. gigantica group including specimen ofChiang Mai, second2 samples of F. hepatica, third group of3 rumen flukes;Orthocoelium streptocoelium, F. elongatus andParamphistomum epliclitum and fourth group of3 minute intestinal flukes;Haplorchis taichui, Stellantchasmu falcatus,Haplorchoides sp. and liver fluke;Opisthorchis viverrini respectively.Conclusions:These results can be confirmed theGiant liver fluke which mainly caused fascioliasis inChiangMai was identified asF. gigantica and specimens were the same as those ofF. gigantica recorded in other different countries.Nucleotide sequence of ITS-2 region has been proven as effective diagnostic tool for the identification ofF. gigantica.

  3. Nucleotide sequence and molecular genetic analysis of the vaccinia virus HindIII N/M region encoding the genes responsible for resistance to alpha-amanitin.

    Science.gov (United States)

    Tamin, A; Villarreal, E C; Weinrich, S L; Hruby, D E

    1988-07-01

    The genomic location of the gene(s) which provides vaccinia virus (VV) alpha-amanitin-resistant mutants with a drug-resistant phenotype have been mapped to the HindIII N/M region of the genome by the use of marker rescue techniques [E. C. Villarreal and D. E. Hruby (1986) J. Virol. 57, 65-70]. Nucleotide sequencing of a 2356-bp HindIII-Sau3A fragment of the vaccinia virus genome encompassing this region reveals the presence of two complete leftward-reading open reading frames (ORFs, N2 and M1) and two incomplete ORFs (N1 and M2). By computer analysis the N2 and M1 ORFs would be predicted to encode soluble VV polypeptides with molecular weights of approximately 20 and 48 kDa, respectively. The N2 and M1 ORFs have extremely A-T-rich 5'-proximal sequences, consistent with previous data regarding the location and A-T-richness of viral early promoters. Likewise, the consensus signal believed to be involved in terminating VV early gene transcription, TTTTTNT, was evident at the 3'-boundary of both the N2 and M1 ORFs suggesting that these genes may be VV early genes. The in vivo transcriptional activity, orientation, and limits of these putative transcriptional units were investigated by Northern blot, nuclease S1, and primer extension analysis. Both N2- and M1-specific transcripts were detected in the cytoplasm of VV-infected cells, suggesting that these loci are bonafide viral genes. Time-course nuclease S1 experiments revealed that the N2 gene was transcribed exclusively prior to VV DNA replication. In contrast, the M1 gene was transcribed throughout infection, although different start sites were used at early versus late times postinfection. These results are discussed in relation to the drug-resistant phenotype and future experiments to identify the viral gene product responsible.

  4. Characterization of low molecular weight allergens from English walnut (Juglans regia).

    Science.gov (United States)

    Downs, Melanie L; Semic-Jusufagic, Aida; Simpson, Angela; Bartra, Joan; Fernandez-Rivas, Montserrat; Rigby, Neil M; Taylor, Steve L; Baumert, Joseph L; Mills, E N Clare

    2014-12-03

    Although English walnut is a commonly allergenic tree nut, walnut allergens have been poorly characterized to date. The objective of this work was to characterize the natural, low molecular weight (LMW) allergens from walnut. A protocol was developed to purify LMW allergens (specifically 2S albumins) from English walnuts. In addition to 2S albumins, a series of peptides from the N-terminal region of the 7S seed storage globulin proprotein were also identified and characterized. These peptides comprised a four-cysteine motif (C-X-X-X-C-X10-12-C-X-X-X-C) repeated throughout the 7S N-terminal region. Upon IgE immunoblotting, 3/11 and 5/11 sera from walnut-allergic subjects showed IgE reactivity to the 7S N-terminal fragments and 2S albumin, respectively. The mature 7S protein and the newly described 7S N-terminal peptides represent two distinct types of allergens. Because the proteolytic processing of 7S globulins has not been elucidated in many edible plant species, similar protein fragments may be present in other nuts and seeds.

  5. Mid-infrared supercontinuum covering the 1.4–13.3 μm molecular fingerprint region using ultra-high NA chalcogenide step-index fibre

    DEFF Research Database (Denmark)

    Petersen, Christian Rosenberg; Møller, Uffe Visbech; Kubat, Irnis

    2014-01-01

    The mid-infrared spectral region is of great technical and scientific interest because most molecules display fundamental vibrational absorptions in this region, leaving distinctive spectral fingerprints. To date, the limitations of mid-infrared light sources such as thermal emitters, low...... the potential of fibres to emit across the mid-infrared molecular ‘fingerprint region’, which is of key importance for applications such as early cancer diagnostics3, gas sensing and food quality control....

  6. Molecular characteristics and evolution of the mitochondrial control region in three genera (Hipposideridae: Hipposideros Aselliscus and Coelops) of leaf-nosed bats.

    Science.gov (United States)

    Sun, Keping; Luo, Li; Zhang, Zhenzhen; Liu, Sen; Feng, Jiang

    2013-08-01

    The mitochondrial control region (CR) was sequenced for three genera of Hipposideridae to give a detailed overview of its features. The CR of leaf-nosed bats (1288-1560 bp) was divided into three domains like that of other mammals. In addition to the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2, and CSB3) found in all species, a CSB1-like element was also detected in the conserved sequence blocks (CSB). Repeated motifs were examined in the ETAS of Aselliscus stoliczkanus (26 bp) and Hipposideros bicolor (80 bp) and were present in the CSB of all individuals (6, 8, 16, and 20 bp). Phylogenetic reconstructions using the CR sequences indicated that the phylogenetic relationships among Hipposideros species were consistent with the results of other molecular and phenetic analyses. Aselliscus and Coelops had a closer relationship. But the central domain could not be used for phylogenetic analyses at family and genus levels due to its high conservation.

  7. Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C-H Region of DMSO as a Case Study

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; Mifflin, Amanda L.; Hess, Wayne P.; Wang, Hongfei; Cramer, Christopher J.; Govind, Niranjan

    2016-03-03

    Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical iden- tication of hydrocarbons and in vibrational sum-frequency generation (SFG) spec- *troscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a chal- lenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes chal- lenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show signicant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.

  8. Molecular characterisation of the clonal emergence of high-level ciprofloxacin-monoresistant Haemophilus influenzae in the Region of Southern Denmark.

    Science.gov (United States)

    Fuursted, Kurt; Hartmeyer, Gitte Nyvang; Stegger, Marc; Andersen, Paal Skytt; Justesen, Ulrik Stenz

    2016-06-01

    Haemophilus influenzae is an important human pathogen usually susceptible to quinolones. Here we report the emergence of high-level ciprofloxacin-monoresistant H. influenzae in the Region of Southern Denmark. Four isolates were collected for phenotypic and molecular characterisation using whole-genome sequencing (WGS). During an 18-month period, the occurrence of high-level ciprofloxacin-monoresistant H. influenzae in patients aged 1-77 years from sputum, ear and eye samples was detected. An epidemiological link between the patients could not be identified. The isolates were non-encapsulated, biotype III and were demonstrated by WGS to be clonal belonging to a single clade with an unknown multilocus sequence type (double-locus variant of ST196). The antibiogram demonstrated that they were all monoresistant to ciprofloxacin with a minimum inhibitory concentration (MIC) >32mg/L. In silico resistome analysis revealed identical, both previously characterised and novel, putative resistance-related mutations in gyrA (S84L and D88N), parC (K20R, S84I, D356A or T356A, and M481I) and parE (E151K, I159A, D420N and S599A) in all isolates. The isolates were otherwise negative for any resistance genes. This is the first description of the clonal emergence of high-level monoresistant H. influenzae due to amino acid substitutions in gyrA, parC and parE.

  9. Conformational choreography of a molecular switch region in myelin basic protein--molecular dynamics shows induced folding and secondary structure type conversion upon threonyl phosphorylation in both aqueous and membrane-associated environments.

    Science.gov (United States)

    Polverini, Eugenia; Coll, Eoin P; Tieleman, D Peter; Harauz, George

    2011-03-01

    The 18.5 kDa isoform of myelin basic protein is essential to maintaining the close apposition of myelin membranes in central nervous system myelin, but its intrinsic disorder (conformational dependence on environment), a variety of post-translational modifications, and a diversity of protein ligands (e.g., actin and tubulin) all indicate it to be multifunctional. We have performed molecular dynamics simulations of a conserved central segment of 18.5 kDa myelin basic protein (residues Glu80-Gly103, murine sequence numbering) in aqueous and membrane-associated environments to ascertain the stability of constituent secondary structure elements (α-helix from Glu80-Val91 and extended poly-proline type II from Thr92-Gly103) and the effects of phosphorylation of residues Thr92 and Thr95, individually and together. In aqueous solution, all four forms of the peptide bent in the middle to form a hydrophobic cluster. The phosphorylated variants were stabilized further by electrostatic interactions and formation of β-structures, in agreement with previous spectroscopic data. In simulations performed with the peptide in association with a dimyristoylphosphatidylcholine bilayer, the amphipathic α-helical segment remained stable and membrane-associated, although the degree of penetration was less in the phosphorylated variants, and the tilt of the α-helix with respect to the plane of the membrane also changed significantly with the modifications. The extended segment adjacent to this α-helix represents a putative SH3-ligand and remained exposed to the cytoplasm (and thus accessible to binding partners). The results of these simulations demonstrate how this segment of the protein can act as a molecular switch: an amphipathic α-helical segment of the protein is membrane-associated and presents a subsequent proline-rich segment to the cytoplasm for interaction with other proteins. Phosphorylation of threonyl residues alters the degree of membrane penetration of the

  10. The Molecular Structures of the Local Arm and Perseus Arm in the Galactic Region of l = [139.°75, 149.°75], b = [-5.°25, 5.°25

    Science.gov (United States)

    Du, Xinyu; Xu, Ye; Yang, Ji; Sun, Yan

    2017-04-01

    Using the Purple Mountain Observatory Delingha (PMODLH) 13.7 m telescope, we report a 96 deg2 12CO/13CO/C18O mapping observation toward the Galactic region of l = [139.°75,149.°75], b = [-5.°25, 5.°25]. The molecular structures of the Local Arm and Perseus Arm are presented. Combining H i data and part of the Outer Arm results, we obtain that the warp structure of both atomic and molecular gas is obvious, while the flare structure only exists in atomic gas in this observing region. In addition, five filamentary giant molecular clouds on the Perseus Arm are identified. Among them, four are newly identified. Their relations with the Milky Way large-scale structure are discussed.

  11. Functional dissection of Streptococcus pyogenes M5 protein: the hypervariable region is essential for virulence.

    Directory of Open Access Journals (Sweden)

    Johan Waldemarsson

    Full Text Available The surface-localized M protein of Streptococcus pyogenes is a major virulence factor that inhibits phagocytosis, as determined ex vivo. Because little is known about the role of M protein in vivo we analyzed the contribution of different M protein regions to virulence, using the fibrinogen (Fg-binding M5 protein and a mouse model of acute invasive infection. This model was suitable, because M5 is required for mouse virulence and binds mouse and human Fg equally well, as shown here. Mixed infection experiments with wild type bacteria demonstrated that mutants lacking the N-terminal hypervariable region (HVR or the Fg-binding B-repeat region were strongly attenuated, while a mutant lacking the conserved C-repeats was only slightly attenuated. Because the HVR of M5 is not required for phagocytosis resistance, our data imply that this HVR plays a major but unknown role during acute infection. The B-repeat region is required for phagocytosis resistance and specifically binds Fg, suggesting that it promotes virulence by binding Fg. However, B-repeat mutants were attenuated even in Fg-deficient mice, implying that the B-repeats may have a second function, in addition to Fg-binding. These data demonstrate that two distinct M5 regions, including the HVR, are essential to virulence during the early stages of an infection. In particular, our data provide the first in vivo evidence that the HVR of an M protein plays a major role in virulence, focusing interest on the molecular role of this region.

  12. Targeted cutaneous delivery of ciclosporin A using micellar nanocarriers and the possible role of inter-cluster regions as molecular transport pathways.

    Science.gov (United States)

    Lapteva, Maria; Santer, Verena; Mondon, Karine; Patmanidis, Ilias; Chiriano, Gianpaolo; Scapozza, Leonardo; Gurny, Robert; Möller, Michael; Kalia, Yogeshvar N

    2014-12-28

    Oral administration of ciclosporin A (CsA) is indicated in the treatment of severe recalcitrant plaque psoriasis. However, CsA is both nephro- and hepatotoxic and its systemic administration also exposes the patient to other severe side effects. Although topical delivery of CsA, targeted directly to psoriatic skin, would offer significant advantages, there are no topical formulations approved for dermatological use. The aim of this work was to formulate CsA loaded polymeric micelles using the biodegradable and biocompatible MPEG-dihexPLA diblock copolymer and to evaluate their potential for delivering the drug selectively into the skin without concomitant transdermal permeation. Micelle formulations were characterised with respect to drug content, size and morphology. Micelle and drug penetration pathways were subsequently visualised with confocal laser scanning microscopy (CLSM) using fluorescein labelled CsA (Fluo-CsA) and Nile-Red (NR) labelled copolymer. Visualisation studies typically use fluorescent dyes as "model drugs"; however, these may have different physicochemical properties to the drug molecule under investigation. Therefore, in this study it was decided to chemically modify CsA and to use this structurally similar fluorescent analogue to visualise molecular distribution and transport pathways. Molecular modelling techniques and experimental determination of log D served as molecular scale and macroscopic methods to compare the lipophilicity of CsA and Fluo-CsA. The spherical, homogeneous and nanometre-scale micelles (with Zav from 25 to 52 nm) increased the aqueous solubility of CsA by 518-fold. Supra-therapeutic amounts of CsA were delivered to human skin (1.4±0.6 μg/cm2, cf. a statistically equivalent 1.1±0.5 μg/cm2 for porcine skin) after application of the formulation with the lowest CsA and copolymer content (1.67±0.03 mg/ml of CsA and 5mg/ml of copolymer) for only 1h without concomitant transdermal permeation. Fluo-CsA was successfully

  13. Enterotoxin Gene Profile and Molecular Characterization of Staphylococcus aureus Isolates from Bovine Bulk Milk and Milk Products of Tigray Region, Northern Ethiopia.

    Science.gov (United States)

    Tarekgne, Enquebaher K; Skjerdal, Taran; Skeie, Siv; Rudi, Knut; Porcellato, Davide; Félix, Benjamin; Narvhus, Judith A

    2016-08-01

    Staphylococcal food poisoning (SFP) is an important foodborne disease worldwide, and milk and milk products are commonly associated with SFP outbreaks. The objectives of this study were to investigate the distribution of staphylococcal enterotoxin (se) genes in Staphylococcus aureus from raw cow's milk and milk products and to assess their genetic background with the spa typing method. Of the 549 samples (297 bulk milk and 162 milk product samples) collected from Tigray region, Northern Ethiopia, 160 (29.1%) were positive for S. aureus, of which 82 (51%) were found to harbor se genes by a modified multiplex PCR. Nine se genes were identified: sea (n = 12), seb (n = 3), sec (n = 3), sed(n = 4), seg (n = 49), seh (n = 2), sei (n = 40), sej (n = 1), and tsst-1 (n = 24). The classical type of genes accounted for 27%. Of the 82 enterotoxigenic isolates, 41.5 and 12.4% harbored two or more se genes, respectively. The highest gene association was observed between sei and seg, whereas sea and seb were always found together with the new types of se genes. Altogether, 18 genotypes of toxin genes were identified, and 33% of the samples contained > 5 log CFU ml(-1) S. aureus. spa typing identified 22 spa types and three novel spa sequences, which showed the high genetic diversity of the isolates. No apparent relationship was observed between spa type and se genes. Of the 25 spa types, 13 (52%) were from raw milk, 3 (12%) from milk products, and 9 (36%) from both types of sample. Types t314 (20.7%,n = 17), t458 (18.3%, n = 15), and t6218 (9.8%, n= 8) were the most common spa types identified and were widely distributed in three of the eight studied localities. This is the first study from the Tigray region to report the high distribution of enterotoxigenic S. aureus with a diversified genetic background from dairy food. The study may provide valuable data for microbial food safety risk assessment, molecular epidemiology, and phylogenetic studies of S. aureus in Ethiopia.

  14. Biodegraded Oil and Its High Molecular Weight (C35+) n-alkanes in the Qianmiqiao Region in the Bohai Bay Basin, Northern China

    Institute of Scientific and Technical Information of China (English)

    WANG Tieguan; ZHU Dan; LU Hong; ZHANG Zhihuan; YANG Chiyin

    2004-01-01

    With a production of 208.2 m3/d, heavy oil was produced by drill stem test (DST) from three shallow reservoirs in Sand Group Nos. Ⅰ and Ⅲ of the Neogene Guantao Formation (Ng1 and NgⅢ) and the Eogene Dongying Formation (Ed) in an exploratory well Ban-14-1 within the Qianmiqiao region, Bohai Bay Basin, northern China. Based on the GC and GC-MS data of theNgⅠand NgⅢheavy oil samples, all n-alkanes and most isoprenoid hydrocarbons are lost and the GC baseline appears as an evident "hump", implying a large quantity of unresolved complex mixture (UCM),which typically revealed a result of heavy biodegradation. However, there still is a complete series of C14-C73 n-alkanes in the high-temperature gas chromatograms (HTGC) of the heavy oil, among which, the abundance of C30- n-alkanes are drastically reduced. The C35-C55 high molecular weight (HMW) n-alkanes are at high abundance and show a normal distribution pattern with major peak at C43 and an obvious odd-carbon-number predominance with CPI37-55 and OEP45-49values of 1.17 and 1.16-1.20, respectively. According to GC-MS analysis, the heavy oil is characterized by dual source inputs of aquatic microbes and terrestrial higher plants. Various steranes and tricyclic terpanes indicate an algal origin, and hopane-type triterpanes, C24tetracyclic terpane and drimane series show the bacterial contribution. With the odd-carbonnumber preference, HMW n-alkanes provide significant information not only on higher plant source input and immaturity,but also on the strong resistibility to biodegradation.

  15. Regionalism, Regionalization and Regional Development

    Directory of Open Access Journals (Sweden)

    Liviu C. Andrei

    2016-03-01

    Full Text Available Sustained development is a concept associating other concepts, in its turn, in the EU practice, e.g. regionalism, regionalizing and afferent policies, here including structural policies. This below text, dedicated to integration concepts, will limit on the other hand to regionalizing, otherwise an aspect typical to Europe and to the EU. On the other hand, two aspects come up to strengthen this field of ideas, i.e. the region (al-regionalism-(regional development triplet has either its own history or precise individual outline of terms.

  16. The human intrinsic factor-vitamin B12 receptor, cubilin: molecular characterization and chromosomal mapping of the gene to 10p within the autosomal recessive megaloblastic anemia (MGA1) region

    DEFF Research Database (Denmark)

    Kozyraki, R; Kristiansen, M; Silahtaroglu, A

    1998-01-01

    -5445 on the short arm of chromosome 10. This is within the autosomal recessive megaloblastic anemia (MGA1) 6-cM region harboring the unknown recessive-gene locus of juvenile megaloblastic anemia caused by intestinal malabsorption of cobalamin (Imerslund-Gräsbeck's disease). In conclusion, the present...... molecular and genetic information on human cubilin now provides circumstantial evidence that an impaired synthesis, processing, or ligand binding of cubilin is the molecular background of this hereditary form of megaloblastic anemia. Udgivelsesdato: 1998-May-15...

  17. Effects of special brain area regional cerebral blood flow abnormal perfusion on learning and memory function and its molecular mechanism in rats

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    s To study the effect of special brain area regional cerebral blood flow (rCBF) abnormal perfusion on learning and memory function and its molecular mechanism,64 adult male healthy Spragne-Dawley (SD) rats were randomly divided into two groups,the false operation group (control group) and the operation group (model group).After surgical operation,the operation group undertook bilateral common carotid artery permanent ligation,while the other group did not.Learning and memory function were measured by Y-maze at 4 h,8 h,24 h and 3 d after surgical operation,respectively.The rCBF of the right frontal lobe and hippocampus was also detected by the PerifluxPF model laser Doppler flowmetry,and the expressions of c-fos or c-jun or Bcl-2 and Bax were also measured by immune histochemistry S-P method accordingly.Results showed that the rCBF of the right frontal lobe and hippocampus in the operation group was significantly lower than that in the false operation group (P < 0.05).The learning indexes,error number (EN),day of reach standard and total reaction time (TRT) in the operation group,were significantly higher than that in the false operation group (P< 0.05).However,the initiative evasion rate in the operation group was significantly lower than that in the false operation group.The study also found that the rCBF was relatively more,the indexes (EN,the day of reach standard and TRT) relatively fewer,but the initiative evasion rate and the memory keeping rate were relatively more.The positive expression and the average absorbency of Fos and Jun in the operation group were significantly higher than that in the false operation group (P< 0.05).Furthermore,Bax and Bcl-2 positive cells were all increased over time in the operation group,and the expression ratio of Bax/Bcl-2 in the operation group was significantly higher than that in the false operation group (P<0.01).In conclusion,rCBF decrease can impair the learning and memory function in rats,which may be related to

  18. Molecular analyses reveal an abundant diversity of ticks and rickettsial agents associated with wild birds in two regions of primary Brazilian Atlantic Rainforest.

    Science.gov (United States)

    Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; McIntosh, Douglas

    2017-06-01

    Brazilian wild birds are recognized as frequent and important hosts for immature stages of more than half of the 32 recognized species of Amblyomma ticks recorded in that country. Several species of Amblyomma harbor rickettsial agents, including members of the spotted fever group (SFG). Most studies on this topic relied primarily on morphological characterization and reported large portions of the collected ticks at the genus rather than species level. Clearly, this factor may have contributed to an underestimation of tick diversity and distribution and makes comparisons between studies difficult. The current investigation combined morphological and molecular analyses to assess the diversity of ticks and rickettsial agents associated with wild birds, captured in two regions of native Atlantic rainforest, in the state of Rio de Janeiro, Brazil. A total of 910 birds were captured, representing two orders, 34 families and 106 species, among which 93 specimens (10.2%), were parasitized by 138 immature ticks (60 larvae and 78 nymphs), representing 10 recognized species of the genus Amblyomma; together with two reasonably well classified haplotypes (Amblyomma sp. haplotype Nazaré and Amblyomma sp. strain USNTC 6792). Amplification by PCR and sequencing of rickettsial genes (htrA, gltA, ompA and ompB), demonstrated the presence of Rickettsia DNA in 48 (34%) of the ticks. Specifically, Rickettsia bellii was detected in a single larva and a single nymph of A. aureolatum; R. amblyomatis was found in 16 of 37 A. longirostre and was recorded for the first time in three nymphs of A. calcaratum; R. rhipicephali was detected in 9 (47%) of 19 Amblyomma sp. haplotype Nazaré ticks. The remaining ticks were infected with genetic variants of R. parkeri, namely strain ApPR in 12 A. parkeri and seven Amblyomma sp. haplotype Nazaré ticks, with the strain NOD found in two specimens of A. nodosum. Interestingly, a single larvae of A. ovale was shown to be infected with the emerging

  19. Molecular characterisation of three regions of the nuclear ribosomal DNA unit and the mitochondrial cox1 gene of Sarcocystis fusiformis from water buffaloes (Bubalus bubalis) in Egypt.

    Science.gov (United States)

    Gjerde, Bjørn; Hilali, Mosaad; Mawgood, Sahar Abdel

    2015-09-01

    A total of 33 macroscopically visible (3-11 × 1-5 mm) sarcocysts of Sarcocystis fusiformis were excised from the oesophagus of 12 freshly slaughtered water buffalos in Giza, Egypt. Genomic DNA was extracted from the sarcocysts, and all isolates were characterised at the mitochondrial cytochrome c oxidase subunit I (cox1) gene through PCR amplification and direct sequencing, whereas a few selected isolates were characterised at the 18S and 28S ribosomal (r) RNA genes and the internal transcribed spacer 1 (ITS1) region of the nuclear rDNA unit following cloning. Among the 33 cox1 sequences (1,038-bp long), there was a total of 13 haplotypes, differing from each other by one to seven substitutions and sharing an identity of 99.3-99.9 %. In comparison, the sequence identity was 98.8-99.0 % among eight complete 18S rRNA gene sequences (1,873-1,879-bp long), 98.1-100 % among 28 complete ITS1 sequences (853-864-bp long) and 97.4-99.6 % among five partial 28S rRNA gene sequences (1,607-1,622 bp). At the three nuclear loci, the intraspecific (and intra-isolate) sequence variation was due to both substitutions and indels, which necessitated cloning of the PCR products before sequencing. Some additional clones of the 18S and 28S rRNA genes were highly divergent from the more typical clones, but the true nature of these aberrant clones could not be determined. Sequence comparisons and phylogenetic analyses based on either 18S rRNA gene or cox1 nucleotide sequences, placed S. fusiformis closest to Sarcocystis cafferi from the African buffalo, but only the analyses based on cox1 data separated the two taxa clearly from each other and showed that they were separate species (monophyletic clusters and 93 % sequence identity at cox1 versus interleaved sequences and 98.7-99.1 % sequence identity at the 18S rRNA gene). Two cats experimentally infected with sarcocysts of S. fusiformis started shedding small numbers of sporocysts 8-10 days post-infection (dpi) and were euthanized 15

  20. Molecular fountain.

    Energy Technology Data Exchange (ETDEWEB)

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  1. Molecular and cytogenetic characterization of a recurrent unbalanced translocation (4;21) (p16.3;q22.1): Relevance to the Wolf-Hirschhorn and Down syndrome critical regions

    Energy Technology Data Exchange (ETDEWEB)

    Sebastio, G.; Perone, L.; Guzzetta, V. [Universita Federico II, Naples (Italy)] [and others

    1996-05-17

    We report on an aneuploidy syndrome due to the unbalanced segregation of a familial translocation (4;21)(p16.3;q22.1) causing a partial 4p monosomy and a partial 21q trisomy. The three affected children presented with severe failure to thrive, short stature, microcephaly, profound hypotonia, and mental retardation. The face, very similar in the three children, is characterized by frontal bossing, upslanting of the palpebral fissures, short nose, and deep set ears, giving the overall appearance of the Down syndrome. The molecular study has defined the aneuploid segment on both 4p and 21q. Most of the Down syndrome critical region was found to be trisomic, while only part of the candidate Wolf-Hirschhorn syndrome critical region was deleted, suggesting that this region is not critical for the major malformations characteristic for WHS. 15 refs., 5 figs., 1 tab.

  2. Molecular dissection of the intrinsic factor-vitamin B12 receptor, cubilin, discloses regions important for membrane association and ligand binding

    DEFF Research Database (Denmark)

    Kristiansen, M; Kozyraki, R; Jacobsen, Christian

    1999-01-01

    Cubilin, the receptor for intrinsic factor-vitamin B12, is a novel type of high molecular weight receptor consisting of a 27 CUB (complement components C1r/C1s, Uegf, and bone morphogenic protein-1) domain cluster preceded by 8 epidermal growth factor repeats and a short N-terminal sequence. In a...

  3. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication

    Directory of Open Access Journals (Sweden)

    Bijma Piter

    2008-11-01

    Full Text Available Abstract We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed Fst values greater than 0.15. However, the non-significant difference (P > 0.05 between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.

  4. Molecular Fountain

    Science.gov (United States)

    Cheng, Cunfeng; van der Poel, Aernout P. P.; Jansen, Paul; Quintero-Pérez, Marina; Wall, Thomas E.; Ubachs, Wim; Bethlem, Hendrick L.

    2016-12-01

    The resolution of any spectroscopic or interferometric experiment is ultimately limited by the total time a particle is interrogated. Here we demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiments, ammonia molecules are decelerated and cooled using electric fields, launched upwards with a velocity between 1.4 and 1.9 m/s and observed as they fall back under gravity. A combination of quadrupole lenses and bunching elements is used to shape the beam such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of free fall, while being strongly focused at the detection region. The molecules are in free fall for up to 266 ms, making it possible, in principle, to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theories.

  5. Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study.

    Directory of Open Access Journals (Sweden)

    Hervé Pascalis

    Full Text Available BACKGROUND/OBJECTIVES: Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. METHODOLOGY: We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households. Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. PRINCIPAL FINDINGS: We found that i Reunion pH1N1 sequences stemmed from global "clade 7" but shaped two phylogenetic sub-clades; ii D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v Quasispecies populations were observed within households and individuals of the cohort-study. CONCLUSIONS: Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of

  6. Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing.

    Science.gov (United States)

    Ferdous, M; Friedrich, A W; Grundmann, H; de Boer, R F; Croughs, P D; Islam, M A; Kluytmans-van den Bergh, M F Q; Kooistra-Smid, A M D; Rossen, J W A

    2016-07-01

    Shiga toxin-producing Escherichia coli (STEC) is one of the major causes of human gastrointestinal disease and has been implicated in sporadic cases and outbreaks of diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome worldwide. In this study, we determined the molecular characteristics and phylogenetic relationship of STEC isolates, and their genetic diversity was compared to that of other E. coli populations. Whole genome sequencing was performed on 132 clinical STEC isolates obtained from the faeces of 129 Dutch patients with gastrointestinal complaints. STEC isolates of this study belonged to 44 different sequence types (STs), 42 serogenotypes and 14 stx subtype combinations. Antibiotic resistance genes were more frequently present in stx1-positive isolates compared to stx2 and stx1 + stx2-positive isolates. The iha, mchB, mchC, mchF, subA, ireA, senB, saa and sigA genes were significantly more frequently present in eae-negative than in eae-positive STEC isolates. Presence of virulence genes encoding type III secretion proteins and adhesins was associated with isolates obtained from patients with bloody diarrhoea. Core genome phylogenetic analysis showed that isolates clustered according to their ST or serogenotypes irrespective of stx subtypes. Isolates obtained from patients with bloody diarrhoea were from diverse phylogenetic backgrounds. Some STEC isolates shared common ancestors with non-STEC isolates. Whole genome sequencing is a powerful tool for clinical microbiology, allowing high-resolution molecular typing, population structure analysis and detailed molecular characterization of strains. STEC isolates of a substantial genetic diversity and of distinct phylogenetic groups were observed in this study.

  7. Isolation and molecular characterization of Rhizoctonia-like fungi associated with orchid roots in the Quadrilátero Ferrífero and Zona da Mata regions of the state of Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Ricardo Eustáquio Nogueira

    2014-06-01

    Full Text Available Mycorrhizal associations can be considered required for orchids, which depend on the fungi for germination and establishment in natural conditions. Knowledge of the mycorrhizal fungi is important for programs aimed at the reintroduction, conservation and management of orchid species. The objective of this study was the molecular characterization of Rhizoctonia-like fungi from orchids in the Quadrilátero Ferrífero ("Iron Quadrangle" and Zona da Mata ("Forest Zone" regions of the state of Minas Gerais, Brazil. The affinities of these fungi were studied by comparing the rRNA internal transcribed spacer region with that of other isolates and sequences in GenBank. Three isolates had an affinity for Epulorhiza repens, and one was the holotypeof E. epiphytica.

  8. Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

    DEFF Research Database (Denmark)

    Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

    2004-01-01

    CD163 is the macrophage receptor for endocytosis of haptoglobin.hemoglobin complexes. The extracellular region consisting of nine scavenger receptor cysteine rich (SRCR) domains also circulates in plasma as a soluble protein. By ligand binding analysis of a broad spectrum of soluble CD163...

  9. Molecular characterization of the U.S. Phaseolus acutifolius A. Gray collection using Amplified Fragment Length Polymorphism (AFLP) and Targeted Region Amplification Polymorphism (TRAP) markers.

    Science.gov (United States)

    Tepary bean (Phaseolus acutifolius A. Gray), a truly Native American crop, is a short life-cycle annual desert legume indigenous to northwestern Mexico and the southwestern USA and is considered drought and heat tolerant. The Western Regional Plant Introduction Station currently maintains 211 acce...

  10. Molecular epidemiology over an 11-year period (2000 to 2010) of extended-spectrum β-lactamase-producing Escherichia coli causing bacteremia in a centralized Canadian region

    NARCIS (Netherlands)

    G. Peirano (G.); A.K. van der Bij (Akke); S. Gregson (Simon); J.D.D. Pitout (J. D D)

    2012-01-01

    textabstractA study was designed to assess the importance of sequence types among extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates causing bacteremia over an 11-year period (2000 to 2010) in a centralized Canadian region. A total of 197 patients with incident infections were

  11. Nucleotide sequence analysis of a DNA region involved in capsular polysaccharide biosynthesis reveals the molecular basis of the nontypeability of two Actinobacillus pleuropneumoniae isolates.

    Science.gov (United States)

    Ito, Hiroya; Ogawa, Torata; Fukamizu, Dai; Morinaga, Yuiko; Kusumoto, Masahiro

    2016-11-01

    The aim of our study was to reveal the molecular basis of the serologic nontypeability of 2 Actinobacillus pleuropneumoniae field isolates. Nine field strains of A. pleuropneumoniae, the causative agent of porcine pleuropneumonia, were isolated from pigs raised on the same farm and sent to our diagnostic laboratory for serotyping. Seven of the 9 strains were identified as serovar 15 strains by immunodiffusion tests. However, 2 strains, designated FH24-2 and FH24-5, could not be serotyped with antiserum prepared against serovars 1-15. Strain FH24-5 showed positive results in 2 serovar 15-specific PCR tests, whereas strain FH24-2 was only positive in 1 of the 2 PCR tests. The nucleotide sequence analysis of gene clusters involved in capsular polysaccharide biosynthesis of the 2 nontypeable strains revealed that both had been rendered nontypeable by the action of ISApl1, a transposable element of A. pleuropneumoniae belonging to the IS30 family. The results showed that ISApl1 of A. pleuropneumoniae can interfere with both the serologic and molecular typing methods, and that nucleotide sequence analysis across the capsular gene clusters is the best means of determining the cause of serologic nontypeability in A. pleuropneumoniae. © 2016 The Author(s).

  12. Detection and molecular characterisation of Giardia duodenalis, Cryptosporidium spp. and Entamoeba spp. among patients with gastrointestinal symptoms in Gambo Hospital, Oromia Region, southern Ethiopia.

    Science.gov (United States)

    Flecha, María J; Benavides, Cynthia M; Tissiano, Gabriel; Tesfamariam, Abraham; Cuadros, Juan; de Lucio, Aida; Bailo, Begoña; Cano, Lourdes; Fuentes, Isabel; Carmena, David

    2015-09-01

    To assess the prevalence and genetic diversity of the enteric protozoa species G. duodenalis, Cryptosporidium spp. and Entamoeba histolytica in individuals with gastrointestinal symptoms compatible with infections by these pathogens seeking medical attention in a rural area in southern Ethiopia. A total of 92 stool samples were initially screened by direct microscopy and immunochromatography and further confirmed by molecular methods. G. duodenalis-positive samples were molecularly characterised by multilocus genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. PCR and DNA sequence analysis of the gene encoding the 60-kDa glycoprotein was used for the subtyping of Cryptosporidium isolates. Detection and differential diagnosis of E. histolytica/dispar were conducted by real-time PCR. PCR-based prevalences were 10.9% for G. duodenalis, 1.1% for Cryptosporidium spp. and 3.3% for Entamoeba spp. Seven (four novel and three known) subtypes of G. duodenalis assemblage B were identified at the GDH locus and 5 (one novel and four known) at the BG locus. A novel variant of C. hominis subtype IbA9G3 was also identified. Two Entamoeba isolates were assigned to E. dispar and an additional one to E. histolytica. Although preliminary, our results strongly suggest that giardiasis, cryptosporidiosis and amoebiasis represent a significant burden in Ethiopian rural population. © 2015 John Wiley & Sons Ltd.

  13. Investigation of zoonotic disease pathogens (Aeromonas hydrophila, Pseudomonas fluorescens, Streptococcus iniae) seen in carp farms in the Northern Iraq-Erbil region by molecular methods

    Science.gov (United States)

    Ibraheem, Azad Saber; Önalan, Şükrü; Arabacı, Muhammed

    2017-04-01

    The aim of this study was to determine the zoonotic bacteria in carp farms in the Northern Iraq-Erbil region. Carp is the main fish species cultured in Erbil region. The most common zoonotic bacteria generally seen in carp farms are Aeromonas hydrophila, Pseudomonas fluorescens and Streptococcus iniae. Samples were collected from 25 carp farms in the Northern Iraq-Erbil region. Six carp samples were collected from each carp farm. Head kidney and intestine tissue samples were collected from each carp sample. Then head kidney and intestine tissue samples were pooled separately from each carp farm. Total bacterial DNA had been extracted from the 25 pooled head kidney and 25 intestinal tissue samples. The pathogen Primers were originally designed from 16S RNA gene region. Zoonotic bacteria were scanned in all tissue samples with absent/present analysis by RT-PCR. Furthermore, the capillary gel electrophoresis bands were used for confirmation of amplicon size which was planned during primer designing stage. As a result, thirteen carp farms were positive in the respect to Aeromonas hydrophila, eight carp farms were positive from head kidney and six carp farms were positive from the intestine, only one carp farm was positive from both head kidney and the intestine tissue samples. In the respect to Streptococcus iniae, four carp farms were positive from head kidney and two carp farms were positive from the intestine. Only one carp farm was positive in the respect to Pseudomonas fluorescens from the intestine. Totally, 9 of 25 carp farms were cleared (negative) the zoonotic bacteria. In conclusion, the zoonotic bacteria were high (64 %) in carp farms in the Northern Iraq-Erbil region.

  14. Investigation for zoonotic disease pathogens (Aeromonas hydrophila, Pseudomonas fluorescens, Streptococcus iniae) seen in carp farms in Duhok region of Northern Iraq by molecular methods

    Science.gov (United States)

    Mohammed, Kamiran Abdulrahman; Arabacı, Muhammed; Önalan, Şükrü

    2017-04-01

    The aim of this study was to determine the zoonotic bacteria in carp farms in Duhok region of the Northern Iraq. Carp is the main fish species cultured in the Duhok region. The most common zoonotic bacteria generally seen in carp farms are Aeromonas hydrophila, Pseudomonas fluorescens and Streptococcus iniae. Samples were collected from 20 carp farms in the Duhok Region of the Northern Iraq. Six carp samples were collected from each carp farm. Head kidney tissue samples and intestine tissue samples were collected from each carp sample. Than head kidney and intestine tissue samples were pooled. The total bacterial DNA extraction from the pooled each 20 head kidney tissue samples and pooled each 20 intestinal tissue samples. Primers for pathogens were originally designed from 16S Ribosomal gene region. Zoonotic bacteria were scanned in all tissue samples by absent / present analysis in the RT-PCR. After RT-PCR, Capillary gel electrophoresis bands were used for the confirmation of the size of amplicon which was planned during primer designing stage. As a result, one sample was positive in respect to Aeromonas hydrophila, from intestine and one carp farm was positive in respect to Pseudomonas fluorescens from intestine and two carp farms were positive in respect to Streptococcus iniae. Totally 17 of 20 carp farms were negative in respect to the zoonotic bacteria. In conclusion the zoonotic bacteria were very low (15 %) in carp farms from the Duhok Region in the Northern Iraq. Only in one Carp farms, both Aeromonas hydrophila and Pseudomonas fluorescens were positive. Also Streptococcus inia were positive in two carp farms.

  15. A molecular biological study on identification of common septicemia bacteria using 16s-23s rRNA gene spacer regions

    Institute of Scientific and Technical Information of China (English)

    傅君芬; 虞和永; 尚世强; 洪文澜; 陆淼泉; 李建平

    2002-01-01

    In the search for a rapid and reliable method for identification of bacteria in blood and cerebrospinal fluid , we developed a unified set of primers and used them under polymerase chain reaction(PCR) to amplify the spacer regions between the 16s and 23s genes in the prokaryotic rRNA genetic loci . Spacer regions within these loci showed a significant level of length and sequence polymorphism across most of the species lines. A generic pair of priming sequences was selected from highly conserved sequences in the 16s and 23s genes occurring adjacent to these polymorphic regions. This single set of primers and reaction conditions were used for the amplification of the 16s-23s spacer regions for 61 strains of standard bacteria and corresponding clinical isolates belonging to 20 genera and 27 species, including Listeria, Staphylococcus and Salmonella species, et al. When the spacer amplification products were resolved by electrophoresis, the resulting patterns could be used to distinguish most of the bacteria species within the test group, and the amplification products of the clinical isolates clustered at the standard species level. Some species presenting similar pattern were further analyzed by HinfI or AluI digestion or DNA clone and sequences analysis in order to establish the specific 16s-23s rRNA gene spacer regions map. Analysis of 42 blood specimens from septicemic neonates and 6 CSF specimens from suspected purulent meningitis patients by bacterial culture and PCR-RFLP(Restriction Fregament Length Polymorphism) showed that 15 specimens of blood culture were positive(35.7%) in the 42 septicemic neonates; 27 specimens were positive(64.2%) by PCR, and that the positive rate by PCR was significantly higher than that by blood culture(P<0.01). Among the 6 CSF specimens, one specimen found positive by blood culture was also positive by PCR, two found negative by blood culture showed positive by PCR; all three were S.epidermidis according to the DNA map. One C

  16. Ionic photofragmentation and photoionization of dimethyl ether in the VUV and soft X-ray regions (8.5 80 eV) absolute oscillator strengths for molecular and dissociative photoionization

    Science.gov (United States)

    Feng, Renfei; Cooper, Glyn; Brion, C. E.

    2001-08-01

    The branching ratios for molecular and dissociative photoionization of dimethyl ether (CH 3OCH 3, DME) have been measured in the VUV and soft X-ray regions using dipole (e,e+ion) coincidence spectroscopy (˜1 eV FWHM) at equivalent photon energies from the first ionization threshold up to 80 eV. The absolute partial oscillator strengths (cross-sections) for molecular and dissociative photoionization have been determined from recently published absolute photoabsorption oscillator strength data [R. Feng, G. Cooper, C.E. Brion, Chem. Phys. 260 (2000) 391] together with the photoionization branching ratios and the (multi-dissociative-corrected) photoionization efficiency obtained from time-of-flight mass spectra reported in the present work. No stable multiply charged molecular ion(s) from DME have been found in the present work. However, the fact that the photoionization efficiency has been measured as greater than unity above ˜30 eV indicates the existence of multi-dissociative products from Coulomb explosion of multiply charged ions. Appearance potentials of all ion products from DME are also reported. The presently reported results are compared with the previously published data where possible.

  17. A naturally occurring mutation within the probe-binding region compromises a molecular-based West Nile virus surveillance assay for mosquito pools (Diptera: Culicidae).

    Science.gov (United States)

    Brault, Aaron C; Fang, Ying; Dannen, Maureen; Anishchenko, Michael; Reisen, William K

    2012-07-01

    A naturally occurring mutation was detected within the probe binding region targeting the envelope gene sequence of West Nile virus used in real-time polymerase chain reaction assays to test mosquito pools and other samples. A single C-->T transition 6nt from the 5' end of the 16mer in the envelope gene probe-binding region at genomic position 1,194 reduced assay sensitivity. The mutation first was detected in 2009 and persisted at a low prevalence into 2011. The mutation caused a 0.4% false negative error rate during 2011. These data emphasized the importance of confirmational testing and redundancy in surveillance systems relying on highly specific nucleic acid detection platforms.

  18. Molecular identification of veterinary yeast isolates by use of sequence-based analysis of the D1/D2 region of the large ribosomal subunit.

    Science.gov (United States)

    Garner, Cherilyn D; Starr, Jennifer K; McDonough, Patrick L; Altier, Craig

    2010-06-01

    Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods-traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit-showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population.

  19. MOLECULAR BIOLOGY ANALYSIS OF IL -1Β, IL -4, AND IL -1Β RA GENE POLYMORPHISMS IN ETHNIC BASHKIR PATIENTS WITH RHEUMATOID ARTHRITIS, LIVING IN C HELYABINSK REGION

    Directory of Open Access Journals (Sweden)

    A. L. Burmistrova

    2007-01-01

    Full Text Available Abstract. Common polymorphisms of interleukin-1β, receptor antagonist interleukin-1, and interleukin-4 genes have been studied among the patients with rheumatoid arthritis of Bashkir origin, living in Chelyabinsk Region. As a result of study, an increased frequency of interleukin-1β homozygosity for a high-producer allele was found. An association has been revealed between the homozygosity for 2-repeat allele of interleukin-4, and the age of disease onset.

  20. Sensitive multiplex spectroscopy in the molecular fingerprint 2.4 μm region with a Cr2+:ZnSe femtosecond laser

    Science.gov (United States)

    Sorokin, E.; Sorokina, I. T.; Mandon, J.; Guelachvili, G.; Picqué, N.

    2010-01-01

    An ultrashort-pulse Cr2+:ZnSe laser is a novel broadband source for sensitive high resolution molecular spectroscopy. A 130-fs pulse allows covering of up to 380 cm−1 spectral domain around 2.4 μm which is analyzed simultaneously with a 0.12 cm−1 (3.6 GHz) resolution by a Fourier-transform spectrometer. Recorded in 13 s, from 70-cm length absorption around 4150 cm−1, acetylene and ammonia spectra exhibit a 3800 signal-to-noise ratio and a 2.4·10−7 cm−1·Hz−1/2 noise equivalent absorption coefficient at one second averaging per spectral element, suggesting a 0.2 ppbv detection level for HF molecule. With the widely practiced classical tungsten lamp source instead of the laser, identical spectra would have taken more than one hour. PMID:19550944

  1. Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora.

    Science.gov (United States)

    Qiu, Ying-Xiong; Fu, Cheng-Xing; Comes, Hans Peter

    2011-04-01

    The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-)temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences

  2. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  3. Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions.

    Science.gov (United States)

    He, Zhen; Li, Wenfeng; Yasaka, Ryosuke; Huang, Yingkun; Zhang, Zhixiang; Ohshima, Kazusato; Li, Shifang

    2014-05-01

    Sequences of the protein 1 (P1) and coat protein (CP) coding regions of 22 sugarcane streak mosaic virus (SCSMV) isolates were determined. Phylogenetic analysis showed that SCSMV had at least three major lineages, and the lineages seemed to reflect geographical origin. The sudden expansions of the Chinese and Indian subpopulations were supported by calculations showing deviations from the neutral equilibrium model for the individual lineages with an overall lack of nucleotide diversity. Our study shows that Chinese and Indian SCSMV isolates are part of a distinct population, and the subpopulations probably reflect founder effects.

  4. Molecular epidemiological study on pre-X region of hepatitis B virus and identification of hepatocyte proteins interacting with whole-X protein by yeast two-hybrid

    Institute of Scientific and Technical Information of China (English)

    Qian Yang; Jun Cheng; Jing Dong; Jian Zhang; Shu-Lin Zhang

    2005-01-01

    AIM: To identify the pre-X region in hepatitis B virus (HBV)genome and to study the relationship between the genotype and the pre-X region. To investigate the biological function of whole-X (pre-X plus X) protein, we performed yeast two-hybrid to screen proteins in liver interacting with whole-X protein.METHODS: The pre-X region of HBV was amplified by polymerase chain reaction (PCR) method, and was cloned to pGEM Teasy vector. After the target region was sequenced, Vector 8.0 software was used to analyze the sequences. The whole-X bait plasmid was constructed by using yeast two-hybrid system 3. Yeast strain AH109 was transformed. After expression of the whole-X protein in AH109 yeast strains was proved, yeast two-hybrid screening was performed by mating AH109 with Y187 containing liver cDNA library plasmid. The mated yeast was plated on quadruple dropout medium and assayed for α-gal activity. The interaction between whole-X protein and the protein obtained from positive colonies was further confirmed by repeating yeast two-hybrid. After extracting and sequencing of plasmid from blue colonies, we carried out analysis by bioinformatics. RESULTS: After sequencing, 27 of 45 clones (60%) were found encoding the pre-X peptide. Eighteen of twenty-seven clones (66.7%) of pre-X coding sequences were found from genotype C. Five positive colonies that interacted with whole-X protein were obtained and sequenced; namely, fetuin B, UDP glycosyltransferase 1 family-polypeptide A9, mannose-P-dolichol utilization defect 1, fibrinogen-B beta polypeptide, transmembrane 4 superfamily member 4CD81 (TM4SF4).CONCLUSION: The pre-X gene exists in HBV genome.Genes of proteins interacting with whole-X protein in hepatocytes were successfully cloned. These results brought some new clues for studying the biological functions of whole-X protein.

  5. Molecular characterization of Staphylococcus aureus isolates from skin and soft tissue infections samples and healthy carriers in the Central Slovenia region.

    Science.gov (United States)

    Svent-Kucina, Natasa; Pirs, Mateja; Kofol, Romina; Blagus, Rok; Smrke, Dragica Maja; Bilban, Marjan; Seme, Katja

    2016-04-01

    Staphylococcus aureus is among the most important human pathogens. It is associated with different infections and is a major cause of skin and soft tissue infections (SSTIs). The aim of our study was to compare S. aureus isolates associated with SSTIs with isolates obtained from healthy carriers in the Central Slovenia region in terms of antimicrobial susceptibility, genetic diversity by clonal complex (CC)/sequence type, spa type, and by toxin gene profiling. In total, 274 S. aureus isolates were collected prospectively by culturing wound samples from 461 SSTI patients and nasal samples from 451 healthy carriers. We have demonstrated high heterogeneity in terms of CCs and spa type in both groups of isolates. The main clone among SSTI strains was Panton-Valentine leukocidin gene (pvl) positive CC121, whereas the main clone among carrier strains was CC45 carrying a large range of toxin genes. The main spa type in both groups was t091. Pvl was more frequently present in SSTI strains (31.2% SSTI vs 3.6% carrier strains) and staphylococcal enterotoxin C was more frequently present in carrier strains (1.6% SSTI vs 17.0% carrier strains). We have also demonstrated that methicillin-resistant S. aureus was a rare cause (2.8%) of SSTIs in our region.

  6. Molecular findings from influenza A(H1N1pdm09 detected in patients from a Brazilian equatorial region during the pandemic period

    Directory of Open Access Journals (Sweden)

    Maria José Couto Oliveira

    2014-11-01

    Full Text Available After the World Health Organization officially declared the end of the first pandemic of the XXI century in August 2010, the influenza A(H1N1pdm09 virus has been disseminated in the human population. In spite of its sustained circulation, very little on phylogenetic data or oseltamivir (OST resistance is available for the virus in equatorial regions of South America. In order to shed more light on this topic, we analysed the haemagglutinin (HA and neuraminidase (NA genes of influenza A(H1N1pdm09 positive samples collected during the pandemic period in the Pernambuco (PE, a northeastern Brazilian state. Complete HA sequences were compared and amino acid changes were related to clinical outcome. In addition, the H275Y substitution in NA, associated with OST resistance, was investigated by pyrosequencing. Samples from PE were grouped in phylogenetic clades 6 and 7, being clustered together with sequences from South and Southeast Brazil. The D222N/G HA gene mutation, associated with severity, was found in one deceased patient that was pregnant. Additionally, the HA mutation K308E, which appeared in Brazil in 2010 and was only detected worldwide the following year, was identified in samples from hospitalised cases. The resistance marker H275Y was not identified in samples tested. However, broader studies are needed to establish the real frequency of resistance in this Brazilian region.

  7. Molecular Cloning of Spergen-4, Encoding a Spermatogenic Cell-Specific Protein Associated with Sperm Flagella and the Acrosome Region in Rat Spermatozoa.

    Science.gov (United States)

    Howida, Ali; Salaheldeen, Elsaid; Iida, Hiroshi

    2016-04-01

    We used a differential display in combination with complementary DNA (cDNA) cloning approach to isolate a novel rat gene LOC690919 with an open reading frame of 1227-length nucleotides encoding a protein of 409 amino acids. This gene was designated as Spergen-4 (a spermatogenic cell-specific gene-4). Spergen-4 mRNA was highly expressed in testis, and its expression was detected in rat testis starting at three weeks of postnatal development and persisting up to adulthood. Mouse and human orthologs, which lack N-terminal 77 amino acid residues of rat Spegen-4, were found in the database. Immunofluorescence microscopy and immunoblot analysis demonstrated that Spergen-4 was not expressed in spermatogonia, spermatocytes, and round spermatids, but was restrictedly detected at sperm head, cytoplasm, and developing flagella of elongated spermatids in rat testis. In mature spermatozoa, Spergen-4 was detected at the acrosome region as well as the principal piece of flagella. Spergen-4 immunosignal disappeared from sperm heads on acrosome reaction induced by progesterone. These data suggest that Spergen-4 integrated into elongated spermatids during spermiogenesis serves as a constituent for acrosome region and flagella of rat spermatozoa.

  8. The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria.

    Science.gov (United States)

    Tramuto, Fabio; Orsi, Andrea; Maida, Carmelo Massimo; Costantino, Claudio; Trucchi, Cecilia; Alicino, Cristiano; Vitale, Francesco; Ansaldi, Filippo

    2016-04-13

    Molecular epidemiology of influenza B virus remained poorly studied in Italy, despite representing a major contributor to seasonal epidemics. This study aimed to reconstruct the phylogenetic relationships and genetic diversity of the hemagglutinin gene sequences of 197 influenza B strains circulating in both Southern (Sicily) and Northern (Liguria) Italy between 2010 and 2015. Upper respiratory tract specimens of patients displaying symptoms of influenza-like illness were screened by real-time RT-PCR assay for the presence of influenza B virus. PCR-positive influenza B samples were further analyzed by sequencing. Neighbor-joining phylogenetic trees were constructed and the amino-acid alignments were analyzed. Phylogenetic analysis showed clusters in B/Victoria clade 1A/1B (n = 29, 14.7%), and B/Yamagata clades 2 (n = 112, 56.8%) and 3 (n = 56, 28.4%). Both influenza B lineages were found to co-circulate during the study period, although a lineage swap from B/Victoria to B/Yamagata occurred in Italy between January 2011 and January 2013. The most represented amino-acid substitutions were N116K in the 120-loop (83.9% of B/Yamagata clade 3 strains) and I146V in the 150-loop (89.6% of B/Victoria clade 1 strains). D197N in 190-helix was found in almost all viruses collected. Our findings provide further evidence to support the adoption of quadrivalent influenza vaccines in our country.

  9. The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010–2015: The Experience of Sicily and Liguria

    Directory of Open Access Journals (Sweden)

    Fabio Tramuto

    2016-04-01

    Full Text Available Molecular epidemiology of influenza B virus remained poorly studied in Italy, despite representing a major contributor to seasonal epidemics. This study aimed to reconstruct the phylogenetic relationships and genetic diversity of the hemagglutinin gene sequences of 197 influenza B strains circulating in both Southern (Sicily and Northern (Liguria Italy between 2010 and 2015. Upper respiratory tract specimens of patients displaying symptoms of influenza-like illness were screened by real-time RT-PCR assay for the presence of influenza B virus. PCR-positive influenza B samples were further analyzed by sequencing. Neighbor-joining phylogenetic trees were constructed and the amino-acid alignments were analyzed. Phylogenetic analysis showed clusters in B/Victoria clade 1A/1B (n = 29, 14.7%, and B/Yamagata clades 2 (n = 112, 56.8% and 3 (n = 56, 28.4%. Both influenza B lineages were found to co-circulate during the study period, although a lineage swap from B/Victoria to B/Yamagata occurred in Italy between January 2011 and January 2013. The most represented amino-acid substitutions were N116K in the 120-loop (83.9% of B/Yamagata clade 3 strains and I146V in the 150-loop (89.6% of B/Victoria clade 1 strains. D197N in 190-helix was found in almost all viruses collected. Our findings provide further evidence to support the adoption of quadrivalent influenza vaccines in our country.

  10. Caracterización molecular de 15 aislamientos de Beauveria bassiana asociados con Cosmopolites y Metamasius en plátano y banano en tres regiones de Colombia

    Directory of Open Access Journals (Sweden)

    Muñoz Flórez Jaime Eduardo

    2008-09-01

    Full Text Available Se colectaron picudos de Cosmopolites y Metamasius en municipios del Valle del Cauca, Caldas y Quindío. Se obtuvieron cultivos monospóricos con diluciones de 10-10 y 10-11. Los aislamientos fueron almacenados a -80°C con glicerol al 10% y el ADN a –20°C. Los marcadores moleculares RAM generaron 82 fragmentos de los cuales 67% fueron polimórficos con una heterocigocidad de 0.24, que indica diversidad media a alta. A un índice de similitud 0.84 se formaron 5 grupos: uno con 11 aislamientos y 4 con un solo aislamiento. En el gran grupo se detectó un duplicado y se encontró diversidad del hongo en los sitios muestreados. No se encontró relación entre aislamientos sobre Cosmopolites y Metamasius o zona geográfica en la formación de grupos genéticos.

  11. Qualitative analysis of Adenomatous Polyposis Coli promoter: Hypermethylation, engagement and effects on survival of patients with esophageal cancer in a high risk region of the world, a potential molecular marker

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    Nasseri Negin

    2009-01-01

    Full Text Available Abstract Background Squamous cell carcinoma of esophagus (SCCE occurs at a high incidence rate in certain parts of the world. This feature necessitates that different aspects of the disease and in particular genetic characteristics be investigated in such regions. In addition, such investigations might lead to achievement of molecular markers helpful for early detection, successful treatment and follow up of the disease. Adenomatous Polyposis Coli (APC promoter hypermethylation has been shown to be a suitable marker for both serum and solid tumors of adenocarcinoma of esophagus. We investigated the status of APC promoter hypermethylation in Iranian patients, compared the results with the former studies, and evaluated its applicability as a candidate molecular marker by examining association between survival of SCCE patients and APC promoter methylation. Methods For evaluating the status of APC promoter hypermethylation and its association with SCCE, a qualitative methylation specific PCR (MSP was used. DNA was extracted and digested with an appropriate restriction enzyme, treated with sodium bisulfite in agarose beads and amplified in two-step PCR reaction by applying either methylated or unmethylated promoter specific primers. Universally methylated DNA and methylase treated blood DNA of healthy donors were used as positive controls as well. Survival of patients was followed up for two years after treatment and survival rate of patients with methylated APC promoter was compared with that of unmethylated patients. Results Assessment of APC promoter methylation revealed that normal tissues were unmethylated, while twenty out of forty five (44.4% tumor tissues were hypermethylated either in one or both alleles of APC. Among the tissues in which methylation was detected, seven were hypermethylated in both alleles while the other thirteen were hypermethylated in one of the two alleles of APC. Analyzing two-year survival rate of patients with respect

  12. [Molecular characterisation and phenotypic description of two patients with reciprocal chromosomal aberrations in the region of the 3q29 microdeletion/microduplication syndromes].

    Science.gov (United States)

    Quintela, I; Barros-Angueira, F; Perez-Gay, L; Dacruz, D; Castro-Gago, M; Carracedo, A; Eiris-Punal, J

    2015-09-16

    Introduccion. Los sindromes de microdelecion y microduplicacion 3q29 se caracterizan por una marcada heterogeneidad fenotipica, y el retraso del desarrollo y la discapacidad intelectual de grado leve-moderado son las manifestaciones clinicas mas frecuentes. Casos clinicos. Dos pacientes con aberraciones cromosomicas reciprocas en la region 3q29. La paciente con la microdelecion 3q29 presenta dificultades de aprendizaje, microcefalia limite, dismorfismo facial leve, deficit atencional e impulsividad, y rasgos ansiosos y obsesivos. El paciente con la microduplicacion 3q29 reciproca presenta dificultades de aprendizaje, dismorfismo facial leve y un perfil conductual disruptivo no asociado previamente con esta duplicacion. Conclusion. Se comparan los fenotipos de estos pacientes y se revisa la bibliografia de pacientes pediatricos con microdeleciones y microduplicaciones 3q29.

  13. Molecular cloning and recombinant expression of the VP28 carboxyl-terminal hydrophilic region from a brazilian white spot syndrome virus isolate

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    Patricia Braunig

    2011-04-01

    Full Text Available In the present study, a fragment of the VP28 coding sequence from a Brazilian WSSV isolate (BrVP28 was cloned, sequenced and expressed in E. coli BL21(DE3 pLysS strain in order to produce the VP28 carboxyl-terminal hydrophilic region. The expression resulted in a protein of about 21 kDa, which was purified under denaturing conditions, resulting in a final highly purified BrVP28 preparation. The recombinant protein obtained can be used in several biotechnology applications, such as the production of monoclonal antibodies which could be used in the development of diagnostic tools as well as in the studies on the characterization of white spot syndrome virus (WSSV isolated in Brazil.

  14. The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.

    Directory of Open Access Journals (Sweden)

    Eva Hřibová

    Full Text Available Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

  15. Molecular assays reveal the presence of Theileria spp. and Babesia spp. in Asian water buffaloes (Bubalus bubalis, Linnaeus, 1758) in the Amazon region of Brazil.

    Science.gov (United States)

    Silveira, Júlia A G; de Oliveira, Cairo H S; Silvestre, Bruna T; Albernaz, Tatiana T; Leite, Rômulo C; Barbosa, José D; Oliveira, Carlos M C; Ribeiro, Múcio F B

    2016-07-01

    Approximately 50% of buffalo herds in Brazil are located in Pará state in northern Brazil. There are several properties where cattle and buffalo live and graze together, and thus, buffalo pathogens may threaten the health of cattle and vice versa. Therefore, knowledge of infectious agents of buffalo is essential for maintaining healthy livestock. Clinical disease caused by Theileria and Babesia parasites in the Asian water buffalo is not common, although these animals may act as reservoir hosts, and the detection of these hemoparasites in buffaloes is as important as it is in cattle. Studies of the infection of buffaloes by hemoparasites in Brazil are scarce. The objective of the present study was to investigate the occurrence of Piroplasmida parasites in Asian water buffaloes in the state of Pará in the Amazon region of Brazil using nested PCR assays and phylogenetic analysis. The 18S rRNA gene and ITS complete region were amplified from DNA extracted from blood samples collected from 308 apparently healthy buffaloes bred on six properties in the state of Pará, Brazil. The prevalence of positive buffalo samples was 4.2% (13/308) for Theileria spp., 3.6% (11/308) for Babesia bovis and 1% (3/308) for Babesia bigemina. Animals infected with Theileria were detected in 50% (3/6) of the assessed properties. Phylogenetic analyses indicated that the Theileria species detected in this study were closely related to Theileria buffeli, Theileria orientalis and Theileria sinensis. To our knowledge, this is the first report of Theileria in Asian water buffaloes in the Americas. The majority of Theileria-positive buffaloes (11/13) belong to a property that has a history of animals presenting lymphoproliferative disease of unknown etiology. Therefore, the present research suggests that this disorder can be associated with Theileria infection in this property. Our results provide new insights on the distribution and biological aspects of hemoparasites transmissible from

  16. Molecular effects of lithium are partially mimicked by inositol-monophosphatase (IMPA)1 knockout mice in a brain region-dependent manner.

    Science.gov (United States)

    Damri, O; Sade, Y; Toker, L; Bersudsky, Y; Belmaker, R H; Agam, G; Azab, A N

    2015-03-01

    We have previously shown that homozygote knockout (KO) of inositol-monophosphatase1 (IMPA1) results in lithium (Li)-like behavior. We now aimed to find out whether Li-treated mice and IMPA1 KO mice exhibit neurochemical similarity at the gene- and protein-expression level. Hippocampal and frontal cortex B-cell lymphoma (Bcl-2), Bcl-2-associated X protein (BAX), P53, Perodoxin2 (PRDX2), myristoylated alanine-rich C kinase substrate (MARCKS) and neuropeptide Y (NPY) mRNA levels, and hippocampal, frontal cortex and hypothalamic cytokine levels, all previously reported to be affected by lithium treatment, were measured in three groups of mice: wildtype (WT) on regular-food (RF), WT on Li-supplemented food (Li-treated) and IMPA1-KOs. Hippocampal and frontal cortex Bcl-2 and MARCKS were the only genes commonly affected (downregulated) by Li and IMPA1 KO; Bcl-2 - by 28% and 19%, respectively; MARCKS - by about 20% in both regions. The effect of Li and of IMPA1 KO on cytokine levels differed among the three brain areas studied. Only in the hippocampus both interventions exerted similar effects. Frontal cortex cytokine levels were unaffected neither by Li nor by IMPA1 KO. Similar changes in Bcl-2 and MARCKS but not in PRDX2 and NPY following both Li-treatment and IMPA1 KO suggest a mechanism different than inositol-monophosphatase1 inhibition for Li׳s effect on the latter genes. The cytokine levels results suggest that the mechanism mediating Li׳s effect on the inflammatory system differs among brain regions. Only in the hippocampus the results favor the involvement of the phosphatidylinositol (PI) cycle. Copyright © 2014 Elsevier B.V. and ECNP. All rights reserved.

  17. Characterization of feline T cell receptor gamma (TCRG) variable region genes for the molecular diagnosis of feline intestinal T cell lymphoma.

    Science.gov (United States)

    Moore, Peter F; Woo, Jennifer C; Vernau, William; Kosten, Sandra; Graham, Petra S

    2005-07-15

    A diagnosis of intestinal lymphoma is currently made on the basis of clinical and morphologic criteria. This can prove problematic for many reasons that include inadequate sample size, the coexistence of lymphoma and inflammation, and the inability to assess architectural integrity of all tissue compartments in biopsy specimens obtained endoscopically. The detection of a clonal population of cells in a lymphoproliferative lesion represents an important criterion for the diagnosis of neoplasia, but this has not been assessed in feline intestinal lymphoma. T cell receptor gamma (TCRG) gene rearrangement analysis using polymerase chain reaction (PCR) is a methodology that can be used to detect clonality in T cell populations. The basis of this assay depends on the assessment of the junctional diversity that results from rearrangement of TCRG V (variable) and J (joining) gene segments. Feline TCRG transcripts from normal small intestine and spleen were obtained using a rapid amplification of cDNA ends (5'RACE) method. Limited diversity of TCRG V and J gene segments was observed. The high degree of sequence homology in the TCRG V and J gene segments was exploited to develop a PCR test for the assessment of TCRG V--J junctional diversity and hence clonality determination of T cell populations in cats. Molecular clonality determination was applied to feline intestinal lymphoplasmacytic inflammatory bowel disease (IBD) (9 cats), and transmural and mucosal T cell lymphoma (28 cats). Clonal rearrangement of the TCRG V--J junction was detected in 22 of 28 intestinal T cell lymphomas, and oligoclonality was detected in 3 intestinal T cell lymphomas. This contrasted with the detection of polyclonal rearrangement in normal intestinal tissues (3 cats) and in lymphoplasmacytic IBD (9 cats). It is proposed that assessment of TCRG V--J junctional diversity for the detection of clonality represents an important adjunctive tool for the diagnosis of T cell lymphoma in the cat.

  18. Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.

    Science.gov (United States)

    Klein, Gracjana; Müller-Loennies, Sven; Lindner, Buko; Kobylak, Natalia; Brade, Helmut; Raina, Satish

    2013-03-22

    It is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This was shown by chemical and structural analyses. Furthermore, the gene whose product is responsible for the addition of this sugar was identified in all Escherichia coli core types and in Salmonella and was designated waaH. Its deduced amino acid sequence exhibits homology to glycosyltransferase family 2. The transcription of the waaH gene is positively regulated by the PhoB/R two-component system in a growth phase-dependent manner, which is coordinated with the transcription of the ugd gene explaining the genetic basis of this modification. Glucuronic acid modification was observed in E. coli B, K12, R2, and R4 core types and in Salmonella. We also show that the phosphoethanolamine (P-EtN) addition on heptose I in E. coli K12 requires the product of the ORF yijP, a new gene designated as eptC. Incorporation of P-EtN is also positively regulated by PhoB/R, although it can occur at a basal level without a requirement for any regulatory inducible systems. This P-EtN modification is essential for resistance to a variety of factors, which destabilize the outer membrane like the addition of SDS or challenge to sublethal concentrations of Zn(2+).

  19. Southwest Alaska Regional Geothermal Energy Project

    Energy Technology Data Exchange (ETDEWEB)

    Holdmann, Gwen [Univ. of Alaska, Fairbanks, AK (United States)

    2015-04-30

    The village of Elim, Alaska is 96 miles west of Nome, on the Seward Peninsula. The Darby Mountains north of the village are rich with hydrothermal systems associated with the Darby granitic pluton(s). In addition to the hot springs that have been recorded and studied over the last 100 years, additional hot springs exist. They are known through a rich oral history of the region, though they are not labeled on geothermal maps. This research primarily focused on Kwiniuk Hot Springs, Clear Creek Hot Springs and Molly’s Hot Springs. The highest recorded surface temperatures of these resources exist at Clear Creek Hot Springs (67°C). Repeated water sampling of the resources shows that maximum temperatures at all of the systems are below boiling.

  20. Molecular Scanning of β-Thalassemia in the Southern Region of Central Java, Indonesia; a Step Towards a Local Prevention Program.

    Science.gov (United States)

    Rujito, Lantip; Basalamah, Muhammad; Mulatsih, Sri; Sofro, Abdul Salam M

    2015-01-01

    Thalassemia is the most prevalent genetic blood disorder worldwide, and particularly prevalent in Indonesia. The purpose of this study was to determine the spectrum of β-thalassemia (β-thal) mutations found in the southern region of Central Java, Indonesia. The subjects of the study included 209 β-thal Javanese patients from Banyumas Residency, a southwest region of Central Java Province. DNA analysis was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), amplification refractory mutation system (ARMS), and the direct sequencing method. The results showed that 14 alleles were found in the following order: IVS-I-5 (G > C) (HBB: c.92 + 5G > C) 43.5%, codon 26 (Hb E; HBB: c.79G > A) 28.2%, IVS-I-1 (G > A) (HBB: c.92 + 1G > A) 5.0%, codon 15 (TGG > TAG) (HBB: c.47G > A) 3.8%, IVS-I-1 (G > T) (HBB: c.92 + 1G > T) 3.1%, codon 35 (-C) (HBB: c.110delC) 2.4%. The rest, including codons 41/42 (-TTCT) (HBB: c.126_129delCTTT), codons 8/9 (+G) (HBB: c.27_28insG), codon 19 (AAC > AGC) (HBB: c.59A > G), codon 17 (AAG > TAG) (HBB: c.52A > T), IVS-I-2 (T > C) (HBB: c.92 + 2T > C), codons 123/124/125 (-ACCCCACC) (HBB: c.370_378delACCCCACCA), codon 40 (-G) (HBB: c.123delG) and Cap +1 (A > C) (HBB: c.-50A > C), accounted for up to 1.0% each. The most prevalent alleles would be recommended to be used as part of β-thal screening for the Javanese, one of the major ethnic groups in the country.

  1. [Molecular characterization and phylogenetic analysis of enteroviruses inducing the outbreaks and seasonal rises of morbidity in different regions of the Republic of Belarus].

    Science.gov (United States)

    Amvros'eva, T V; Poklonskaia, N V; Bezruchko, A A; Fisenko, E G

    2006-01-01

    As shown by the results of the analysis, viruses ECHO 30 circulating over the period of the last 8 years in Belarus, belonged to 3 different genetic subtypes which earlier or simultaneously circulated in other European states. The outbreaks of enterovirus infections (EVI) were facilitated by the appearance of a genetic viral subtype, relatively "new" for human population, and which had not earlier circulated on this territory. Thus, the development of outbreak morbidity in 2003 was caused by a change in the dominating subtype of virus ECHO 30, which caused the outbreak of 1997. The relatively "soft" rise of morbidity in 2004 was due to the continued circulation of the same subtype of virus ECHO 30, that in 2003. The largest outbreaks of EVI in the Republic of Belarus had a number of considerable differences: the outbreak of 1997 in Gomel was characterized by the genetic heterogeneity of infective agents, being simultaneously geographically localized within the limits of one city. However, during the outbreaks of 2003 the circulation of genetically closely related viruses of the one subtype among the population of geographically remote regions of the country was registered.

  2. Molecular epidemiology of Mycobacterium avium subspecies paratuberculosis: IS900 PCR identification and IS1311 polymorphism analysis from ruminants in the Punjab region of India.

    Science.gov (United States)

    Kaur, P; Filia, G; Singh, S V; Patil, P K; Ravi Kumar, G V P P S; Sandhu, K S

    2011-03-01

    Johne's disease is chronic granulomatous infectious enteritis of animals caused by Mycobacterium avium subspecies paratuberculosis. A total of 153 animals from 19 dairy farms, 2 gaushalas (unproductive-animal rehabilitation centers), 2 goat and 2 sheep farms from different districts of the Punjab region were selected on the basis of clinical signs of disease. All samples from cattle (n=86), buffalo (n=34), goat (n=25) and sheep (n=26) were subjected to Ziehl-Neelsen staining and DNA extraction by a freeze and thaw method. Ziehl-Neelsen staining detected 71% samples positive for acid-fast bacilli whereas IS900 PCR detected 55% positive for Map DNA. IS1311 PCR-REA analysis of IS900 positive samples revealed 'Bison' type as the most prevalent (82%) genotype of Map, infecting all domestic ruminants. 'Cattle' type was present in a minority of cases (15%) from cattle, buffaloes and goats. This is the first report of 'Cattle' type Map from buffalo and goat species in India. Copyright © 2010 Elsevier Ltd. All rights reserved.

  3. Molecular analysis of the 16S-23S rDNA internal spacer region (ISR) and truncated tRNA(Ala) gene segments in Campylobacter lari.

    Science.gov (United States)

    Hayashi, K; Tazumi, A; Nakanishi, S; Nakajima, T; Matsubara, K; Ueno, H; Moore, J E; Millar, B C; Matsuda, M

    2012-06-01

    Following PCR amplification and sequencing, nucleotide sequence alignment analyses demonstrated the presence of two kinds of 16S-23S rDNA internal spacer regions (ISRs), namely, long length ISRs of 837-844 base pair (bp) [n = six for urease-negative (UN) Campylobacter lari isolates, UN C. lari JCM2530(T), RM2100, 176, 293, 299 and 448] and short length ISRs of 679-725 bp [n = six for UN C. lari: n = 14 for urease-positive thermophilic Campylobacter (UPTC) isolates]. The analyses also indicated that the short length ISRs mainly lacked the 156 bp sequence from the nucleotide positions 122-277 bp in long length ISRs for UN C. lari JCM2530(T). The 156 bp sequences shared 94.9-96.8 % sequence similarity among six isolates. Surprisingly, atypical tRNA(Ala) gene segment (5' end 35 bp), which was extremely truncated, occurred within the 156 bp sequences in the long length ISRs, as an unexpected tRNA(Ala) pseudogene. An order of the intercistronic tRNA genes within the short nucleotide spacer of 5'-16S rDNA-tRNA(Ala)-tRNA(Ile)-23S rDNA-3' occurred in all the C. lari isolates examined.

  4. Molecular evidence of Anaplasma phagocytophilum and Babesia microti co-infections in Ixodes ricinus ticks in central-eastern region of Poland.

    Science.gov (United States)

    Sytykiewicz, Hubert; Karbowiak, Grzegorz; Hapunik, Joanna; Szpechciński, Adam; Supergan-Marwicz, Marta; Goławska, Sylwia; Sprawka, Iwona; Czerniewicz, Paweł

    2012-01-01

    The aim of the study was to elucidate the distribution of Anaplasma phagocytophilum and Babesia microti co-infection in Ixodes ricinus populations within the central-eastern region of Poland. The prevalence of analysed tick-borne human pathogens in single and polymicrobial infections in I. ricinus ticks were analysed using the conventional and nested PCR techniques. A total number of 1,123 questing tick individuals (291 females, 267 males and 565 nymphs) were collected at different ecosystems (municipal parks, suburban forests, and woodlands). In the presented study, 95 samples of ticks (8.5%) were infected with A.phagocytophilum, 3.1% (n=35) with B. microti, whereas the co-existence status of these human pathogens was detected in 1.8% (n=20) of all tested samples. It has been demonstrated that the prevalence of co-infection status was the highest among females of I. ricinus (11 samples, 3.8%), whereas the lowest within tested nymphs (5 samples, 0.9%). Ticks collected at city parks in Warsaw and suburban areas of this town characterized the highest prevalence of co-infections (3.3 and 4.8%, respectively). Furthermore, it was established that co-infection rates of ticks inhabiting woodlands within Kampinos National Park and Nadbużański Landscape Park were similar and reached the levels of 1.4% (n=5) and 1.1% (n=4), respectively.

  5. Seroprevalence of Rickettsia spp. in Equids and Molecular Detection of 'Candidatus Rickettsia amblyommii' in Amblyomma cajennense Sensu Lato Ticks From the Pantanal Region of Mato Grosso, Brazil.

    Science.gov (United States)

    Alves, Alvair Da S; Melo, Andréia L T; Amorim, Marcus V; Borges, Alice M C M; Gaíva E Silva, Lucas; Martins, Thiago F; Labruna, Marcelo B; Aguiar, Daniel M; Pacheco, Richard C

    2014-11-01

    The aim of the study was to evaluate exposure of equids to rickettsial agents (Rickettsia rickettsii, Rickettsia parkeri, 'Candidatus Rickettsia amblyommii', Rickettsia rhipicephali, and Rickettsia bellii) and rickettsial infection in ticks of a Pantanal region of Brazil. Sera of 547 equids (500 horses and 47 donkeys) were evaluated by indirect immunofluorescence assay. In total, 665 adults and 106 nymphal pools of Amblyomma cajennense F. sensu lato, 10 Dermacentor nitens Neumann ticks, and 88 larval pools of Amblyomma sp. were tested by polymerase chain reaction (PCR). Overall, 337 (61.6%) equids were reactive (titer ≥64) to at least one antigen of Rickettsia spp. The prevalence values for Rickettsia were 66%, and the highest endpoint titers were observed for 'Ca. R. amblyommii'. By PCR 3 (0.45%) A. cajennense s.l. females were positive for 'Ca. R. amblyommii'. Minimum infection rates of 0.75% for nymphs and 0.34% for larvae were calculated. Positive samples of ticks have had a fragment of the 16S mitochondrial rRNA gene sequenced and sequences showed 99% identity to Amblyomma sculptum Berlese. This study reports a wide exposure of equids to Rickettsia agents, and PCR evidence of infection with 'Ca. R. amblyommii', for the first time, in A. sculptum.

  6. Double differential cross sections for proton induced electron emission from molecular analogues of DNA constituents for energies in the Bragg peak region

    Science.gov (United States)

    Rudek, Benedikt; Bennett, Daniel; Bug, Marion U.; Wang, Mingjie; Baek, Woon Yong; Buhr, Ticia; Hilgers, Gerhard; Champion, Christophe; Rabus, Hans

    2016-09-01

    For track structure simulations in the Bragg peak region, measured electron emission cross sections of DNA constituents are required as input for developing parameterized model functions representing the scattering probabilities. In the present work, double differential cross sections were measured for the electron emission from vapor-phase pyrimidine, tetrahydrofuran, and trimethyl phosphate that are structural analogues to the base, the sugar, and the phosphate residue of the DNA, respectively. The range of proton energies was from 75 keV to 135 keV, the angles ranged from 15° to 135°, and the electron energies were measured from 10 eV to 200 eV. Single differential and total electron emission cross sections are derived by integration over angle and electron energy and compared to the semi-empirical Hansen-Kocbach-Stolterfoht (HKS) model and a quantum mechanical calculation employing the first Born approximation with corrected boundary conditions (CB1). The CB1 provides the best prediction of double and single differential cross section, while total cross sections can be fitted with semi-empirical models. The cross sections of the three samples are proportional to their total number of valence electrons.

  7. Molecular phylogenetics of the species-rich angiosperm genus Goniothalamus (Annonaceae) inferred from nine chloroplast DNA regions: Synapomorphies and putative correlated evolutionary changes in fruit and seed morphology.

    Science.gov (United States)

    Tang, Chin Cheung; Thomas, Daniel C; Saunders, Richard M K

    2015-11-01

    A phylogenetic study of the genus Goniothalamus (Annonaceae) is presented using maximum parsimony, maximum likelihood and Bayesian approaches, with 65 species sampled (48.5% of the genus) based on sequences of nine chloroplast DNA regions (11,214 aligned positions). The resultant phylogeny clearly indicates that Goniothalamus is monophyletic. Preliminary research initially focused on identifying synapomorphies and estimating the phylogenetic signal of selected morphological characters based on parsimony and likelihood ancestral character state reconstructions. This prescreening of characters enabled 40 to be selected for further study, and of these 15 are shown here to demonstrate significant phylogenetic signal and to provide clear synapomorphies for several infrageneric clades. Although floral structure in Goniothalamus is comparatively uniform, suggesting a common basic pattern of pollination ecology, fruit and seed morphology in the genus is very diverse and is presumably associated with different patterns of frugivory. The present study assesses correlations amongst fruit and seed characters which are putatively of functional importance with regard to frugivory and dispersal. One-way phylogenetic ANOVA indicates significant phylogenetically independent correlation between the following fruit and seed characters: fruits borne on older branches and/or on the main trunk have larger monocarps than fruits borne on young branches; and monocarps that contain seeds with a hairy testa are larger than those with glabrous seeds. We discuss fruit morphologies and potential explanations for the inferred correlations, and suggest that they may be the result of adaptation to different frugivores (birds, larger non-volant animal and primate seed dispersers, respectively).

  8. Molecular analysis of Brazilian strains of bovine coronavirus (BCoV) reveals a deletion within the hypervariable region of the S1 subunit of the spike glycoprotein also found in human coronavirus OC43.

    Science.gov (United States)

    Brandão, P E; Gregori, F; Richtzenhain, L J; Rosales, C A R; Villarreal, L Y B; Jerez, J A

    2006-09-01

    Bovine coronavirus (BCoV) causes enteric and respiratory dis- orders in calves and dysentery in cows. In this study, 51 stool samples of calves from 10 Brazilian dairy farms were analysed by an RT-PCR that amplifies a 488-bp fragment of the hypervariable region of the spike glycoprotein gene. Maximum parsimony genealogy with a heuristic algorithm using sequences from 15 field strains studied here and 10 sequences from GenBank and bredavirus as an outgroup virus showed the existence of two major clusters (1 and 2) in this viral species, the Brazilian strains segregating in both of them. The mean nucleotide identity between the 15 Brazilian strains was 98.34%, with a mean amino acid similarity of 98%. Strains from cluster 2 showed a deletion of 6 amino acids inside domain II of the spike protein that was also found in human coronavirus strain OC43, supporting the recent proposal of a zoonotic spill- over of BCoV. These results contribute to the molecular characterization of BCoV, to the prediction of the efficiency of immunogens, and to the definition of molecular markers useful for epidemiologic surveys on coronavirus-caused diseases.

  9. Molecular characterization of gap region in 28S rRNA molecules in brine shrimp Artemia parthenogenetica and planarian Dugesia japonica.

    Science.gov (United States)

    Sun, Shuhong; Xie, Hui; Sun, Yan; Song, Jing; Li, Zhi

    2012-04-01

    In most insects and some other protostomes, a small stretch of nucleotides can be removed from mature 28S rRNA molecules, which could create two 28S rRNA subunits (28Sα and 28Sβ). Thus, during electrophoresis, the rRNA profiles of these organisms may differ significantly from the standard benchmark since the two subunits co-migrate with the 18S rRNA. To understand the structure and mechanism of the atypical 28S rRNA molecule, partial fragments of 28Sα and 28Sβ in brine shrimp Artemia parthenogenetica and planarian Dugesia japonica were cloned using a modified technology based on terminal transferase. Alignment with the corresponding sequences of 28S rDNAs indicates that there are 41 nucleotides in A. parthenogenetica and 42 nucleotides in D. japonica absent from the mature rRNAs. The AU content of the gap sequences of D. japonica and A. parthenogenetica is high. Both the gaps may form stem-loop structure. In D. japonica a UAAU cleavage signal is identified in the loop, but it is absent in A. parthenogenetica. Thus, it is proposed that the gap processing of 28S rRNA was a late enzyme-dependent cleavage event in the rRNA maturational process based on the AU rich gap sequence and the formation of the stem-loop structure to expose the processing segment, while the deletion of the gap region would not affect the structure and function of the 28S rRNA molecule.

  10. Standardization and Optimization of mtDNA Isolation and Molecular Genetic Analysis of D-loop Region in Animal Natural Fibres

    Directory of Open Access Journals (Sweden)

    Priyanka P. Rane

    2011-01-01

    Full Text Available Increase in demand for animal natural fibres in recent years for the production of high quality textile products has resulted in the adulteration and false declaration of these fibres causing heavy financial loss. Fibres are expensive due to limited feedstock and less fibre production. To keep up with the demand these fibres are adulterated with less expensive fibres viz., wool to give special effect to the fabric. To control false declaration, there is a need for fibre identification and to ascertain blend composition. Though Scanning Electron Microscopy is generally used for fibre analysis but this method is time consuming, expensive and the reliability of results depend on the expertise of the microscopist. Hence, there is a need for reliable and economical method to characterize these fibres and to study composition of each animal fibre in blends. The aim of the present study was mitochondrial DNA extraction from animal natural fibres in untreated and blends. The modified protocol includes addition of Proteinase K, Dithioerythritol individually in each tube and final extraction with phenol: chloroform: isoamyl alcohol, amplification of D-loop region using species specific and mammalian specific primers. We observed that with species specific primers, it was possible to study inter species variation but the blends could be detected if there was prior knowledge about the fibres in blends. With mammalian specific primers we could study blends and differentiate between fibres from sheep breeds but inter species variation was difficult. It can be concluded that mtDNA analysis can be used to differentiate animal fibres and control adulteration.

  11. Molecular detection of human noroviruses in influent and effluent samples from two biological sewage treatment plants in the region of Monastir, Tunisia.

    Science.gov (United States)

    Hassine-Zaafrane, Mouna; Sdiri-Loulizi, Khira; Kaplon, Jérôme; Ben Salem, Imen; Pothier, Pierre; Aouni, Mahjoub; Ambert-Balay, Katia

    2014-06-01

    Noroviruses (NoVs) are responsible for numerous cases of waterborne and foodborne gastroenteritis every year. They are released in the sewage and their detection in this environment can reflect the epidemiology of the viral strains circulating in the community. A three-year (2007-2010) survey was conducted in order to evaluate the presence of human NoVs using RT-PCR in 518 sewage samples collected at the entrance and exit of two biological sewage treatment plants located in Monastir region, Tunisia. In this study, we aimed to genetically characterize the most prevalent GI and GII NoV strains, in order to obtain a rough estimate of the efficacy of disinfection treatments and to compare the results with clinical data documented in the same area during the same period. This work confirms the wide circulation and the genetic diversity of NoVs in Tunisia and the widespread distribution of NoV variants in both raw and treated wastewater. Indeed, NoV was detected in 192 (37.1%) sewage samples, among them mixed infections with group A rotavirus were detected in 125 (65.1%) cases. The genotypes of the GI NoVs were GI.1, GI.2, GI.4, GI.5, and GI of unassigned genotype (GI.UA), and the genotypes of the GII NoVs were all GII.12. This study enhances the currently poor environmental virological data gathered in Tunisia, demonstrates the benefit of environmental surveillance as a tool to determine the epidemiology of NoVs circulating in a given community, and underlines the need for the design and support of similar long-term studies in our country, in order to compensate for the absence of a national surveillance system for gastroenteric viruses.

  12. Genetic diversity and phylogenetic analysis of Citrus (L from north-east India as revealed by meiosis, and molecular analysis of internal transcribed spacer region of rDNA

    Directory of Open Access Journals (Sweden)

    Marlykynti Hynniewta

    2014-12-01

    Full Text Available The north-eastern region of India is reported to be the center of origin and rich in diversity of Citrus (L. species, where some wild and endangered species namely Citrus indica, Citrus macroptera, Citrus latipes, Citrus ichagensis and Citrus assamensis exist in their natural and undisturbed habitat. In order to have comprehensive information about the extent of genetic variability and the occurrence of cryptic genomic hybridity between and within various Citrus species, a combined approach involving morphological, cytogenetical and molecular approaches were adopted in the present study. Cytogenetic approaches are known to resolve taxonomic riddles in a more efficient manner, by clearly delineating taxa at species and sub species levels. Male meiotic studies revealed a gametic chromosome number of n = 9, without any evidence of numerical variations. Bivalents outnumbered all other types of associations in pollen mother cells (PMCs analyzed at diplotene, diakinesis and metaphase I. Univalents were frequently encountered in nine species presently studied, though their presence appropriately did not influence the distributional pattern of the chromosomes at anaphases I and II. The molecular approaches for phylogenetic analysis based on sequence data related to ITS 1, ITS 2 and ITS 1 + 5.8 s + ITS 2 of rDNA using maximum parsimony method and Bayesian inference have thrown light on species inter-relationship and evolution of Citrus species confirming our cytogenetical interpretations. The three true basic species i.e. Citrus medica, Citrus maxima and Citrus reticulata with their unique status have been resolved into distinct clades with molecular approaches as well. C. indica which occupies a unique position in the phylogenetic ladder of the genus Citrus has been resolved as a distinct clade and almost behaving as an out-group. The presences of quadrivalents in C. indica also echo and support its unique position. From our study it is amply

  13. Isolation of Microsporum gypseum in soil samples from different geographical regions of brazil, evaluation of the extracellular proteolytic enzymes activities (keratinase and elastase) and molecular sequencing of selected strains

    Science.gov (United States)

    Giudice, Mauro Cintra; Reis-Menezes, Adriana Araújo; Rittner, Glauce Mary Gomes; Mota, Adolfo José; Gambale, Walderez

    2012-01-01

    A survey of Microsporum gypseum was conducted in soil samples in different geographical regions of Brazil. The isolation of dermatophyte from soil samples was performed by hair baiting technique and the species were identified by morphology studies. We analyzed 692 soil samples and the recuperating rate was 19.2%. The activities of keratinase and elastase were quantitatively performed in 138 samples. The sequencing of the ITS region of rDNA was performed in representatives samples. M. gypseum isolates showed significant quantitative differences in the expression of both keratinase and elastase, but no significant correlation was observed between these enzymes. The sequencing of the representative samples revealed the presence of two teleomorphic species of M. gypseum (Arthroderma gypseum and A. incurvatum). The enzymatic activities may play an important role in the pathogenicity and a probable adaptation of this fungus to the animal parasitism. Using the phenotypical and molecular analysis, the Microsporum identification and their teleomorphic states will provide a useful and reliable identification system. PMID:24031904

  14. Diagnóstico y caracterización molecular de aislamientos de Mycosphaerella sp. Provenientes de plantaciones de banano y plátano de diferentes regiones de Colombia.

    Directory of Open Access Journals (Sweden)

    Perea Arango Irene

    2003-12-01

    Full Text Available Mycosphaerella fijiensis Morelet, agente causal de la Sigatoka negra, afecta dramáticamente la producción comercial de banano y plátano en la mayoría de las regiones productoras del mundo. En Colombia, la sigatoka negra se observó por primera vez en 1981 en la zona bananera del Urabá y desde entonces se disemino a todas las regiones, Atlantico, Pacifico, Centro y Oriente del país. En el 2000 la enfermedad fue encontrada en el Choco, zona del Pacifico Colombiano cubierta completamente por selva y que presenta cultivos de plátano en pequeñas parcelas al borde del rio Atrato, la única vía de acceso a la región. En este trabajo se realizó una prueba molecular de diagnóstico a 21 cepas de Mycosphaerella spp. Aisladas de diferentes zonas y se estudió la diversidad genética del patógeno en algunas regiones de Colombia utilizando marcadores RAPD’s. En total se obtuvieron 26 bandas polimórficas con los cebadores OPM01, OPM5 Y OPM20. El análisis de distancias genéticas sugiere que las cepas del Choco provienen de la zona del Urabá antioqueño y que en la zona de Santa Marta se presenta una subpoblación del patógeno diferente de las cepas del resto del país.

  15. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  16. A conservative region of the mercuric reductase gene (merA as a molecular marker of bacterial mercury resistance Região conservada do gene da mercúrio redutase (merA como marcador molecular da resistência bacteriana ao mercúrio

    Directory of Open Access Journals (Sweden)

    Adriana Sotero-Martins

    2008-06-01

    Full Text Available The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II to Hg0, which is dependent of the mercuric reductase enzyme (MerA activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains.O mecanismo de resistência bacteriana ao mercúrio mais comum é baseada na redução do Hg(II a Hg0, através da atividade da enzima mercúrio redutase (MerA. O uso do fragmento de 431 pb amplificado de uma região conservada do gene merA, que codifica a enzima MerA,foi utilizado como marcador molecular deste mecanismo, permitindo a identificação de bactérias resistentes ao mercúrio.

  17. Caracterización molecular de 15 aislamientos de Beauveria bassiana asociados con Cosmopolites y Metamasius en plátano y banano en tres regiones de Colombia Molecular characterization of 15 isolations of Beauveria bassiana related to Cosmopolites and Metamasius in plantain and banana in three regions of Colombia

    Directory of Open Access Journals (Sweden)

    Diego Fernando Marmolejo

    2008-10-01

    Full Text Available Se colectaron picudos de Cosmopolites y Metamasius en municipios del Valle del Cauca, Caldas y Quindío. Se obtuvieron cultivos monospóricos con diluciones de 10-10 y 10-11. Los aislamientos fueron almacenados a -80°C con glicerol al 10% y el ADN a -20°C. Los marcadores moleculares RAM generaron 82 fragmentos de los cuales 67% fueron polimórficos con una heterocigocidad de 0.24, que indica diversidad media a alta. A un índice de similitud 0.84 se formaron 5 grupos: uno con 11 aislamientos y 4 con un solo aislamiento. En el gran grupo se detectó un duplicado y se encontró diversidad del hongo en los sitios muestreados. No se encontró relación entre aislamientos sobre Cosmopolites y Metamasius o zona geográfica en la formación de grupos genéticos.Weevils Cosmopolites and Metamasius in municipalities of the Valle del Cauca, Caldas and Quindío departaments of Colombia were collected. Monosporic cultures were obtained from10-10 and 10-11 dilutions of Beauveria bassiana. Isolates were kept at -80°C with 10% glycerol and DNA stored at -20°C. RAMs molecular markers generated a total of 82 fragments of which 67% were polymorphic. A heterozygosity value of 0.24 indicated a medium - high diversity. Five groups were formed which have a similarity value of 0.84 and one big group with 11 isolates and four groups with only one isolate. In the big group was detected a duplicate and fungi genetic diversity in the sampled places. Neither relationship among isolates of Cosmopolites and Metamasius nor geographical zone related to the formation of genetic groups.

  18. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Science.gov (United States)

    Asadzadeh, Mohammad; Ahmad, Suhail; Hagen, Ferry; Meis, Jacques F; Al-Sweih, Noura; Khan, Ziauddin

    2015-01-01

    Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A

  19. MUSCLE W49 : A Multi-Scale Continuum and Line Exploration of the Most Luminous Star Formation Region in the Milky Way. I. Data and The Mass Structure of the Giant Molecular Cloud

    CERN Document Server

    Galvan-Madrid, R; Zhang, Z -Y; Pineda, J E; Peng, T -C; Zhang, Q; Keto, E R; Ho, P T P; Rodriguez, L F; Zapata, L; Peters, T; De Pree, C G; .,

    2013-01-01

    The Multi-Scale Continuum and Line Exploration of W49 (MUSCLE W49) is a comprehensive gas and dust survey of the parental giant molecular cloud (GMC) of W49A, the most luminous (L~10^7 Lsun) star-formation region in the Milky Way. Observations cover the entire GMC at different scales and angular resolutions. In this paper we present: 1) a multiconfiguration SMA mosaic covering the central ~3x3 arcmin (~10 pc, known as W49N), where most of the embedded massive stars reside; and 2) PMO-14m observations covering the entire GMC with maps of up to ~35x35 arcmin in size (~113 pc). We also make use of archival data from the VLA, JCMT-SCUBA, IRAM 30m, and the CSO BOLOCAM Galactic Plane Survey. Our main findings are: 1) The W49 GMC is one of the most massive in the Galaxy with a total mass Mgas~1.1x10^6 Msun within a radius of 60 pc, and Mgas~2x10^5 Msun within a radius of 6 pc. The W49 GMC has a mass reservoir sufficient to form several young massive clusters (YMCs), or even a globular cluster. 2) The mass of the GMC...

  20. Identification of Staphylococcus saprophyticus isolated from patients with urinary tract infection using a simple set of biochemical tests correlating with 16S-23S interspace region molecular weight patterns.

    Science.gov (United States)

    Ferreira, Adriano Martison; Bonesso, Mariana Fávero; Mondelli, Alessandro Lia; da Cunha, Maria de Lourdes Ribeiro de Souza

    2012-12-01

    The emergence of Staphylococcus spp. not only as human pathogens, but also as reservoirs of antibiotic resistance determinants, requires the development of methods for their rapid and reliable identification in medically important samples. The aim of this study was to compare three phenotypic methods for the identification of Staphylococcus spp. isolated from patients with urinary tract infection using the PCR of the 16S-23S interspace region generating molecular weight patterns (ITR-PCR) as reference. All 57 S. saprophyticus studied were correctly identified using only the novobiocin disk. A rate of agreement of 98.0% was obtained for the simplified battery of biochemical tests in relation to ITR-PCR, whereas the Vitek I system and novobiocin disk showed 81.2% and 89.1% agreement, respectively. No other novobiocin-resistant non-S. saprophyticus strain was identified. Thus, the novobiocin disk is a feasible alternative for the identification of S. saprophyticus in urine samples in laboratories with limited resources. ITR-PCR and the simplified battery of biochemical tests were more reliable than the commercial systems currently available. This study confirms that automated systems are still unable to correctly differentiate CoNS species and that simple, reliable and inexpensive methods can be used for routine identification.

  1. The Dark Molecular Gas

    CERN Document Server

    Wolfire, Mark G; McKee, Christopher F

    2010-01-01

    The mass of molecular gas in an interstellar cloud is often measured using line emission from low rotational levels of CO, which are sensitive to the CO mass, and then scaling to the assumed molecular hydrogen H_2 mass. However, a significant H_2 mass may lie outside the CO region, in the outer regions of the molecular cloud where the gas phase carbon resides in C or C+. Here, H_2 self-shields or is shielded by dust from UV photodissociation, where as CO is photodissociated. This H_2 gas is "dark" in molecular transitions because of the absence of CO and other trace molecules, and because H_2 emits so weakly at temperatures 10 K < T < 100 K typical of this molecular component. This component has been indirectly observed through other tracers of mass such as gamma rays produced in cosmic ray collisions with the gas and far-infrared/submillimeter wavelength dust continuum radiation. In this paper we theoretically model this dark mass and find that the fraction of the molecular mass in this dark component ...

  2. Molecular Plasmonics

    Science.gov (United States)

    Wilson, Andrew J.; Willets, Katherine A.

    2016-06-01

    In this review, we survey recent advances in the field of molecular plasmonics beyond the traditional sensing modality. Molecular plasmonics is explored in the context of the complex interaction between plasmon resonances and molecules and the ability of molecules to support plasmons self-consistently. First, spectroscopic changes induced by the interaction between molecular and plasmonic resonances are discussed, followed by examples of how tuning molecular properties leads to active molecular plasmonic systems. Next, the role of the position and polarizability of a molecular adsorbate on surface-enhanced Raman scattering signals is examined experimentally and theoretically. Finally, we introduce recent research focused on using molecules as plasmonic materials. Each of these examples is intended to highlight the role of molecules as integral components in coupled molecule-plasmon systems, as well as to show the diversity of applications in molecular plasmonics.

  3. Molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ladd, A.J.C.

    1988-08-01

    The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

  4. Molecular pharmacognosy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    This article analyzes the background and significance of molecular pharmacognosy,including the molecular identification of medicinal raw materials,phylogenetic evolution of medicinal plants and animals,evaluation and preservation of germplasm resources for medicinal plants and animals,etiology of endangerment and protection of endangered medicinal plants and animals,biosynthesis and bioregulation of active components in medicinal plants,and characteristics and the molecular bases of top-geoherbs.

  5. Molecular Spintronics

    OpenAIRE

    Shiraishi, Masashi; Ikoma, Tadaaki

    2011-01-01

    Molecular spintronics is recognized to as an attractive new research direction in a field of spintronics, following to metallic spintronics and inorganic semiconductor spintronics, and attracts many people in recent decades. The purpose of this manuscript is to describe the history of molecular spintronics by introducing important achievements and to show the current status of this field. In addition, the authors briefly introduce several theories for implementing studies in molecular spintro...

  6. MUSCLE W49: A multi-scale continuum and line exploration of the most luminous star formation region in the Milky Way. I. Data and the mass structure of the giant molecular cloud

    Energy Technology Data Exchange (ETDEWEB)

    Galván-Madrid, R.; Pineda, J. E.; Peng, T.-C. [European Southern Observatory, Karl-Schwarzschild-Str. 2, D-85748 Garching (Germany); Liu, H. B.; Ho, P. T. P. [Academia Sinica Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 106, Taiwan (China); Zhang, Z.-Y. [Max-Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Zhang, Q.; Keto, E. R. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Rodríguez, L. F.; Zapata, L. [Centro de Radioastronomía y Astrofísica, UNAM, A.P. 3-72 Xangari, Morelia 58089 (Mexico); Peters, T. [Institut für Theoretische Physik, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich (Switzerland); De Pree, C. G. [Department of Physics and Astronomy, Agnes Scott College, Decatur, GA 30030 (United States)

    2013-12-20

    The Multi-scale Continuum and Line Exploration of W49 is a comprehensive gas and dust survey of the giant molecular cloud (GMC) of W49A, the most luminous star-formation region in the Milky Way. The project covers, for the first time, the entire GMC at different scales and angular resolutions. In this paper, we present (1) an all-configuration Submillimeter Array mosaic in the 230 GHz (1.3 mm) band covering the central ∼3' × 3' (∼10 pc, known as W49N), where most of the embedded massive stars reside and (2) Purple Mountain Observatory 14 m telescope observations in the 90 GHz band, covering the entire GMC with maps of up to ∼35' × 35' in size, or ∼113 pc. We also make use of archival data from the Very Large Array, JCMT-SCUBA, the IRAM 30 m telescope, and the Caltech Submillimeter Observatory BOLOCAM Galactic Plane Survey. We derive the basic physical parameters of the GMC at all scales. Our main findings are as follows. (1) The W49 GMC is one of the most massive in the Galaxy, with a total mass M {sub gas} ∼ 1.1 × 10{sup 6} M {sub ☉} within a radius of 60 pc. Within a radius of 6 pc, the total gas mass is M {sub gas} ∼ 2 × 10{sup 5} M {sub ☉}. At these scales, only ∼1% of the material is photoionized. The mass reservoir is sufficient to form several young massive clusters (YMCs) as massive as a globular cluster. (2) The mass of the GMC is distributed in a hierarchical network of filaments. At scales <10 pc, a triple, centrally condensed structure peaks toward the ring of HC H II regions in W49N. This structure extends to scales from ∼10 to 100 pc through filaments that radially converge toward W49N and its less-prominent neighbor W49S. The W49A starburst most likely formed from global gravitational contraction with localized collapse in a 'hub-filament' geometry. (3) Currently, feedback from the central YMCs (with a present mass M {sub cl} ≳ 5 × 10{sup 4} M {sub ☉}) is still not enough to entirely disrupt

  7. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Directory of Open Access Journals (Sweden)

    Mohammad Asadzadeh

    Full Text Available Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp, C. orthopsilosis (109 bp, C. metapsilosis (217 bp and L. elongisporus (258 bp were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380 by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study was performed by amplified fragment length polymorphism (AFLP analysis. Phenotypically identified C. parapsilosis isolates (n = 380 were identified as C. parapsilosis sensu stricto (n = 361, C. orthopsilosis (n = 15, C. metapsilosis (n = 1 and L. elongisporus (n = 3 by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1 comprising 11 isolates recovered from 10

  8. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model

  9. Molecular geometry

    CERN Document Server

    Rodger, Alison

    1995-01-01

    Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

  10. Molecular Haeckel.

    Science.gov (United States)

    Elinson, Richard P; Kezmoh, Lorren

    2010-07-01

    More than a century ago, Ernst Haeckel created embryo drawings to illustrate the morphological similarity of vertebrate early embryos. These drawings have been both widely presented and frequently criticized. At the same time that the idea of morphological similarity was recently attacked, there has been a growing realization of molecular similarities in the development of tissues and organs. We have surveyed genes expressed in vertebrate embryos, and we have used them to construct drawings that we call Molecular Haeckels. The Molecular Haeckels emphasize that, based on gene expression, there is a greater similarity among vertebrate embryos than even Haeckel might have imagined. (c) 2010 Wiley-Liss, Inc.

  11. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  12. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    ) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  13. [Molecular imaging].

    Science.gov (United States)

    Turetschek, K; Wunderbaldinger, P

    2002-01-01

    The disclosure of the human genoma, the progress in understanding of diseases on molecular and cellular levels, the discovery of new disease-specific targets, and the development of new medications will revolutionize our understanding of the etiology and the treatment of many disease entities. Radiologists are faced with a paradigm shift from unspecific to specific molecular imaging techniques as well as with enormous speed in the development of new methods and should be enrolled actively in this field of medicine.

  14. Variantes moleculares en el gen L1 del virus del papiloma humano tipo 16, y regiones de la proteína L1 probablemente involucradas en la interacción virus-célula epitelial

    Directory of Open Access Journals (Sweden)

    María Mercedes Bravo

    2004-03-01

    Full Text Available

    La infección con virus del papiloma humano de alto riesgo es considerada como el principal factor de riesgo en el desarrollo del cáncer de cuello uterino. Entre los HPV de alto riesgo, el tipo 16 es el más frecuente tanto en mujeres con citología normal, como en mujeres con lesiones premalignas y en cáncer invasivo. Se ha demostrado la existencia de variaciones en la secuencia del genoma de HPV16, estos polimorfismos se han agrupado en cinco ramas filogenéticas denominadas según su distribución geográfica: Europeas (E, Asiaticas-Americanas (AA, Asiáticas (As, Africanas (Af y Norteamericanas (NA; determinadas por sustituciones nucleotídicas en los genes E6, L1 y L2 y la región larga de control.

    Varios estudios han sugerido que las variantes no Europeas son más agresivas que las Europeas, esto puede ser el reflejo de una interacción diferente con el huésped y por tanto implicar diferencias en el resultado final de la infección (mayor persistencia o mayor oncogenicidad.

    Particularmente se ha demostrado que las variaciones en la secuencia de aminoácidos de la proteína L1, la proteína principal de la cápside viral, pueden modificar las epítopes neutralizantes del virus afectando la efectividad de la respuesta inmune, también estas variaciones pueden afectar la capacidad de ensamble de las cápsides y la afinidad por receptores a nivel epitelial.

    El propósito de este estudio fue identificar las variaciones moleculares del gen L1 de HPV16 en aislamientos provenientes de cepillados cervicales de mujeres colombianas con citología normal y con cáncer de cuello uterino, con el fin de analizar si existen variaciones que alteren las regiones

  15. Molecular physics

    CERN Document Server

    Demtröder, Wolfgang

    2008-01-01

    The richly illustrated book comprehensively explains the important principles of diatomic and polyatomic molecules and their spectra in two separate, distinct parts. The first part concentrates on the theoretical aspects of molecular physics, such as the vibration, rotation, electronic states, potential curves, and spectra of molecules. The different methods of approximation for the calculation of electronic wave functions and their energy are also covered. The introduction of basics terms used in group theory and their meaning in molecular physics enables an elegant description of polyatomic

  16. Molecular pathways

    DEFF Research Database (Denmark)

    Cox, Thomas R; Erler, Janine Terra

    2014-01-01

    that 45% of deaths in the developed world are linked to fibrotic disease. Fibrosis and cancer are known to be inextricably linked; however, we are only just beginning to understand the common and overlapping molecular pathways between the two. Here, we discuss what is known about the intersection...... of fibrosis and cancer, with a focus on cancer metastasis, and highlight some of the exciting new potential clinical targets that are emerging from analysis of the molecular pathways associated with these two devastating diseases. Clin Cancer Res; 20(14); 3637-43. ©2014 AACR....

  17. Molecular modeling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-01-01

    Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

  18. Molecular gastronomy

    Science.gov (United States)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  19. Molecular farming

    NARCIS (Netherlands)

    Merck, K.B.; Vereijken, J.M.

    2006-01-01

    Molecular Farming is a new and emerging technology that promises relatively cheap and flexible production of large quantities of pharmaceuticals in genetically modified plants. Many stakeholders are involved in the production of pharmaceuticals in plants, which complicates the discussion on the poss

  20. Molecular characteristics of dengue virus outbreak in China-Myanmar border region, Yunnan province, 2015%云南省中缅边境2015年一起登革热暴发的分子特征分析

    Institute of Scientific and Technical Information of China (English)

    郭晓芳; 杨明东; 姜进勇; 李华昌; 朱崇革; 桂琴; 卜力群; 周红宁

    2016-01-01

    Objective To understand the molecular characteristics of a dengue virus outbreak in China-Myanmar border region,Yunnan province,2015 and provide etiological evidence for the disease control and prevention.Methods Semi-nested RT-PCR was conducted to detect the capsid pre-membrane (CprM) gene of RNA of dengue virus by using dengue virus NS1 positive serum samples collected in Mengdin township,Gengma county,Yunnan province in July,2015.Some positive samples were then detected by using PCR with specific primers to amplify the full E gene.The positive PCR products were directly sequenced.Then sequences generated in this study were BLAST in NCBI website and aligned in Megalign in DNAstar program.Multiple sequence alignments were carried out by using Mega 5.05 software based on the sequences generated in this study and sequences downloaded from GenBank,including the representative strains from different countries and regions.Phylogenetic trees were constructed by using Neighbor-Joining tree methods with Mega 5.05 software.Results Twenty one of 25 local cases and 10 of 14 imported cases from Myanmar were positive for DENV-1.Eight serum samples were negative for dengue virus.A total of 13 strains with E gene (1 485 bp),including 8 local strains and 5 imported strains,were sequenced,which shared 100% nucleotide sequence identities.Twelve strains with CprM gene (406 bp) from 9 local cases and 3 imported cases shared 100% nucleotide sequence identities.Phylogenetic analyses based on E gene showed that the new 13 strains clustered in genotype Ⅰ of dengue virus and formed a distinct lineage.Conclusions This outbreak was caused by genotype Ⅰ of DENV-1,which had the closest phylogenetic relationships with dengue virus from neighboring Burma area.Comprehensive measures of prevention and control of dengue fever should be strengthened to prevent the spread of dengue virus.%目的 对2015年云南省中缅边境一起登革热暴发查明病因,对流行的登革病毒(DENV)

  1. Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations.

    Science.gov (United States)

    Deggim-Messmer, Vanessa; Bloemberg, Guido V; Ritter, Claudia; Voit, Antje; Hömke, Rico; Keller, Peter M; Böttger, Erik C

    2016-07-01

    Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1-2days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods.

  2. H.E.S.S. detection of TeV emission from the interaction region between the supernova remnant G349.7+0.2 and a molecular cloud

    NARCIS (Netherlands)

    Abramowski, A.; et al., [Unknown; Balzer, A.; Berge, D.; Bryan, M.; Salek, D.; Vink, J.

    2015-01-01

    G349.7+0.2 is a young Galactic supernova remnant (SNR) located at the distance of 11.5 kpc and observed across the entire electromagnetic spectrum from radio to high energy (HE; 0.1 GeV molecular clo

  3. Effect of dark, hard, and vitreous kernel content on protein molecular weight distribution and on milling and breadmaking quality characteristics for hard spring wheat samples from diverse growing regions

    Science.gov (United States)

    Kernel vitreousness is an important grading characteristic for segregation of sub-classes of hard red spring (HRS) wheat in the U.S. This research investigated the protein molecular weight distribution (MWD), and flour and baking quality characteristics of different HRS wheat market sub-classes. T...

  4. Structure of Hot Molecular Cores

    OpenAIRE

    Rolffs, Rainer

    2011-01-01

    High-mass stars form deeply embedded in dense molecular gas, which they heat up and ionize due to their high energy output. During an early phase, the ionization is confined to small regions, and the stellar radiation is absorbed by dust. The high temperatures lead to the evaporation of ice mantles around dust grains, and many highly excited and complex molecules can be observed in these Hot Molecular Cores. At later stages, the whole molecular cloud is ionized and disrupted, and a...

  5. Grand canonical Molecular Dynamics Simulations

    CERN Document Server

    Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K

    2011-01-01

    For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.

  6. Caracterização molecular do HTLV-1/2 em doadores de sangue em Belém, Estado do Pará: primeira descrição do subtipo HTLV-2b na região Amazônica Molecular characterization of HTLV-1/2 among blood donors in Belém, State of Pará: first description of HTLV-2b subtype in the Amazon region

    Directory of Open Access Journals (Sweden)

    Ethienne Lobato dos Santos

    2009-06-01

    Full Text Available Este trabalho objetivou a caracterização molecular do vírus linfotrópico de células T humanas infectando doadores de sangue atendidos na Fundação Centro de Hemoterapia e Hematologia do Pará. Amostras de DNA de 79 indivíduos soropositivos para o vírus linfotrópico de células T humanas foram analisadas por meio da reação em cadeia da polimerase para as regiões genômicas pX, env e 5'LTR, de polimorfismos de comprimento de fragmentos de restrição e do seqüenciamento da região 5LTR, com posterior análise filogenética, definindo o tipo e o subtipo do HTLV circulante na população estudada. Observou-se uma maior prevalência de HTLV-1 (71% em relação ao HTLV-2 (29%. As amostras de HTLV-1 sequenciadas foram classificadas como pertencentes ao subtipo Cosmopolita, subgrupo Transcontinental, sendo as de HTLV-2 identificadas como HTLV-2c. A análise de polimorfismos de comprimento de fragmentos de restrição da região env e do sequenciamento da região 5'LTR, identificou, pela primeira vez na Amazônia Brasileira, uma amostra de HTLV-2b, enfatizando a necessidade de estudos moleculares contínuos na região para melhor entendimento da epidemiologia de transmissão do HTLV na população e permitir a vigilância epidemiológica da emergência de novos tipos e subtipos.This study aimed to perform molecular characterization on the human T-cell lymphotropic virus (HTLV infecting blood donors attended at the Hematology and Hemotherapy Center-Foundation of Pará. DNA samples from 79 HTLV-seropositive individuals were analyzed by means of the polymerase chain reaction on the pX, env and 5'LTR genomic regions; restriction fragment length polymorphism analysis; and sequencing of the 5'LTR region with subsequent phylogenetic analysis. From this, the HTLV types and subtypes circulating in the study population were defined. There was higher prevalence of HTLV-1 (71% than of HTLV-2 (29%. HTLV-1 samples were classified as belonging to the

  7. Molecular ion photofragment spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O/sub 2//sup +/(/sup 4/..pi../sub u/) metastable state which is found to consist of two main components: the /sup 4/..pi../sub 5/2/ and /sup 4/..pi../sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the /sup 4/..pi../sub 3/2/ and /sup 4/..pi../sub 1/2/ spin components having a short lifetime (approx. 6 ms).

  8. Molecular cytogenetics.

    Science.gov (United States)

    Carpenter, N J

    2001-09-01

    In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

  9. Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-12-01

    Full Text Available

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important
    tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and
    the exponential growth of the knowledge of protein structures have made it possible for organic compounds to tailored to
    decrease harmful side effects and increase the potency. This article provides a detailed description of the techniques
    employed in molecular modeling. Molecular modelling is a rapidly developing discipline, and has been supported from
    the dramatic improvements in computer hardware and software in recent years.

  10. Regional Competition in Maghreb Region

    Institute of Scientific and Technical Information of China (English)

    EL AMOURI ALLAL

    2016-01-01

    Great powers focus on cooperation instead of competition in their regions in order to maintain stability and develop the economy of their regions and the world in general. The United States for example created the North American Free Trade Agreement (NAFT

  11. Molecular Rotors

    Science.gov (United States)

    2006-10-31

    Molecular Dipolar Rotors on Insulating Surfaces," Salamanca , Spain. Trends in Nanotechnology Conference. September 5-9, 2003 [86] Laura I. Clarke, Mary Beth...Horansky at the Trends in Nanotechnology Conference, Salamanca , Spain (September 5-9, 2003). [145] Michl, J. “Unusual Molecules: Artificial Surface...temperature and frequency for difluorophenylene rotor crystal. Figure JP6. Monte Carlo results for the local potential asymmetry at

  12. Molecular scale

    Directory of Open Access Journals (Sweden)

    Christopher H. Childers

    2016-03-01

    Full Text Available This manuscript demonstrates the molecular scale cure rate dependence of di-functional epoxide based thermoset polymers cured with amines. A series of cure heating ramp rates were used to determine the influence of ramp rate on the glass transition temperature (Tg and sub-Tg transitions and the average free volume hole size in these systems. The networks were comprised of 3,3′-diaminodiphenyl sulfone (33DDS and diglycidyl ether of bisphenol F (DGEBF and were cured at ramp rates ranging from 0.5 to 20 °C/min. Differential scanning calorimetry (DSC and NIR spectroscopy were used to explore the cure ramp rate dependence of the polymer network growth, whereas broadband dielectric spectroscopy (BDS and free volume hole size measurements were used to interrogate networks’ molecular level structural variations upon curing at variable heating ramp rates. It was found that although the Tg of the polymer matrices was similar, the NIR and DSC measurements revealed a strong correlation for how these networks grow in relation to the cure heating ramp rate. The free volume analysis and BDS results for the cured samples suggest differences in the molecular architecture of the matrix polymers due to cure heating rate dependence.

  13. Africa Region

    African Journals Online (AJOL)

    Impact of HIV/AIDS on» Gross Domestic Product (GGP) in the WHO. Africa Region ... methods) and for economic evaluations of treatment, prevention and promotion. , programmes. ..... develop new products), for which we could not find data ...

  14. Regional odontodysplasia.

    Science.gov (United States)

    Mehta, D N; Bailoor, D; Patel, B

    2011-01-01

    Regional odontodysplasia is an unusual developmental anomaly in which ectodermal and mesodermal tooth components are affected. We present a rare case of a developmental anomaly called regional odontodysplasia or 'ghost teeth' in a 12-year-old Indian girl. The anomaly affected right maxillary permanent teeth. The mandibular teeth were unaffected. The clinical, radiographic and histological features are reviewed. The management of affected patients is discussed.

  15. Regional odontodysplasia

    Directory of Open Access Journals (Sweden)

    D N Mehta

    2011-01-01

    Full Text Available Regional odontodysplasia is an unusual developmental anomaly in which ectodermal and mesodermal tooth components are affected. We present a rare case of a developmental anomaly called regional odontodysplasia or ′ghost teeth′ in a 12-year-old Indian girl. The anomaly affected right maxillary permanent teeth. The mandibular teeth were unaffected. The clinical, radiographic and histological features are reviewed. The management of affected patients is discussed.

  16. Molecular photodissociation

    CERN Document Server

    van Dishoeck, Ewine F

    2011-01-01

    Photodissociation is the dominant removal process of molecules in any region exposed to intense ultraviolet (UV) radiation. This includes diffuse and translucent interstellar clouds, dense photon-dominated regions, high velocity shocks, the surface layers of protoplanetary disks, and cometary and exoplanetary atmospheres. The rate of photodissociation depends on the cross sections for absorption into a range of excited electronic states, as well as on the intensity and shape of the radiation field at each position into the region of interest. Thus, an acccurate determination of the photodissociation rate of even a simple molecule like water or carbon monoxide involves many detailed considerations ranging from its electronic structure to its dissociation dynamics and the specifics of the radiation field that the molecule is exposed to. In this review chapter, each of these steps in determining photodissociation rates is discussed systematically and examples are provided.

  17. Molecular plasmonics

    CERN Document Server

    Fritzsche, Wolfgang

    2014-01-01

    Adopting a novel approach, this book provides a unique ""molecular perspective"" on plasmonics, concisely presenting the fundamentals and applications in a way suitable for beginners entering this hot field as well as for experienced researchers and practitioners. It begins by introducing readers to the optical effects that occur at the nanoscale and particularly their modification in the presence of biomolecules, followed by a concise yet thorough overview of the different methods for the actual fabrication of nanooptical materials. Further chapters address the relevant nanooptics, as well as

  18. Molecular nanomagnets

    CERN Document Server

    Gatteschi, Dante; Villain, Jacques

    2006-01-01

    Nanomagnetism is a rapidly expanding area of research which appears to be able to provide novel applications. Magnetic molecules are at the very bottom of the possible size of nanomagnets and they provide a unique opportunity to observe the coexistence of classical and quantum properties. The discovery in the early 90's that a cluster comprising twelve manganese ions shows hysteresis of molecular origin, and later proved evidence of quantum effects, opened a new research area whichis still flourishing through the collaboration of chemists and physicists. This book is the first attempt to cover

  19. Molecular spintronics.

    Science.gov (United States)

    Sanvito, Stefano

    2011-06-01

    The electron spin made its debut in the device world only two decades ago but today our ability of detecting the spin state of a moving electron underpins the entire magnetic data storage industry. This technological revolution has been driven by a constant improvement in our understanding on how spins can be injected, manipulated and detected in the solid state, a field which is collectively named Spintronics. Recently a number of pioneering experiments and theoretical works suggest that organic materials can offer similar and perhaps superior performances in making spin-devices than the more conventional inorganic metals and semiconductors. Furthermore they can pave the way for radically new device concepts. This is Molecular Spintronics, a blossoming research area aimed at exploring how the unique properties of the organic world can marry the requirements of spin-devices. Importantly, after a first phase, where most of the research was focussed on exporting the concepts of inorganic spintronics to organic materials, the field has moved to a more mature age, where the exploitation of the unique properties of molecules has begun to emerge. Molecular spintronics now collects a diverse and interdisciplinary community ranging from device physicists to synthetic chemists to surface scientists. In this critical review, I will survey this fascinating, rapidly evolving, field with a particular eye on new directions and opportunities. The main differences and challenges with respect to standard spintronics will be discussed and so will be the potential cross-fertilization with other fields (177 references).

  20. Molecular Aggregation in Disodium Cromoglycate

    Science.gov (United States)

    Singh, Gautam; Agra-Kooijman, D.; Collings, P. J.; Kumar, Satyendra

    2012-02-01

    Details of molecular aggregation in the mesophases of the anti-asthmatic drug disodium cromoglycate (DSCG) have been studied using x-ray synchrotron scattering. The results show two reflections, one at wide angles corresponding to π-π stacking (3.32 å) of molecules, and the other at small angles which is perpendicular to the direction of molecular stacking and corresponds to the distance between the molecular aggregates. The latter varies from 35 - 41 å in the nematic (N) phase and 27 -- 32 å in the columnar (M) phase. The temperature evolution of the stack height, positional order correlations in the lateral direction, and orientation order parameter were determined in the N, M, and biphasic regions. The structure of the N and M phases and the nature of the molecular aggregation, together with their dependence on temperature and concentration, will be presented.

  1. Molecular characterization of tat gene and long terminal repeat region of human immunodeficiency virus type-1 detected among the injecting drug users (IDUs) of Manipur, India: identification of BC recombinants.

    Science.gov (United States)

    Mullick, Ranajoy; Sengupta, Satarupa; Sarkar, Kamalesh; Chakrabarti, Sekhar

    2010-02-01

    The tat gene of human immunodeficiency virus type-1 (HIV-1) is responsible for the initiation and elongation of viral transcription through the LTR (long terminal repeat) transactivation process. Our study included structural and functional analyses of the tat gene and LTR region of 35 injecting drug users (IDUs) from Manipur (a north-eastern state in India and a potential source of HIV-1 recombinants) in order to search for the recombinants and variation in the transactivation process if any due to recombination. Analysis showed prevalence of subtype C with few BC recombinants for the tat gene showing identical recombination breakpoints. Phylogenetic analysis of the LTR region of those IDU strains showed strong resemblance to Indian subtype C forming a completely separate cluster from the other global C LTR sequences. The TAR element (transactivator response region) in all the LTR sequences was fairly conserved. Further study of the transactivation rate of the C and BC tat for the Manipur C LTR showed almost equal transactivity in both the cases. This is the first report of characterisation of tat gene and LTR region of HIV-1 samples among IDUs from north-eastern India.

  2. The California Molecular Cloud

    CERN Document Server

    Lada, Charles J; Alves, Joao F

    2009-01-01

    We present an analysis of wide-field infrared extinction maps of a region in Perseus just north of the Taurus-Auriga dark cloud complex. From this analysis we have identified a massive, nearby, but previously unrecognized, giant molecular cloud (GMC). From comparison of foreground star counts with Galactic models we derive a distance of 450 +/- 23 parsecs to the cloud. At this distance the cloud extends over roughly 80 pc and has a mass of approximately 10^5 solar masses, rivaling the Orion (A) Molecular Cloud as the largest and most massive GMC in the solar neighborhood. Although surprisingly similar in mass and size to the more famous Orion Molecular Cloud (OMC) the newly recognized cloud displays significantly less star formation activity with more than an order of magnitude fewer young stellar objects than found in the OMC, suggesting that both the level of star formation and perhaps the star formation rate in this cloud are an order of magnitude or more lower than in the OMC. Analysis of extinction maps ...

  3. a Molecular Fountain

    Science.gov (United States)

    Cheng, Cunfeng; van der Poel, Aernout P. P.; Ubachs, Wim; Bethlem, Hendrick

    2017-06-01

    The resolution of any spectroscopic experiment is limited by the coherent interaction time between the probe radiation and the particle that is being studied. The introduction of cooling techniques for atoms and ions has resulted in a dramatic increase of interaction times and accuracy, it is hoped that molecular cooling techniques will lead to a similar increase. Here we demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiment, beams of ammonia molecules are decelerated, trapped and cooled using inhomogeneous electric fields and subsequently launched. Using a combination of quadrupole lenses and buncher elements, the beam is shaped such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of less than 10μK and a longitudinal temperature of less than 1μK) while the molecules are in free fall, but strongly focused at the detection region. The molecules are in free fall for up to 266 milliseconds, making it possible, in principle, to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theories.

  4. Molecular-beam scattering

    Science.gov (United States)

    Vernon, M. F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N2 from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HC1 (FEMALE) NAC1 + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2(2)P/sub 3/2/) and Na(3(2)P/sub 3/2) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  5. Molecular-beam scattering

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, M.F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N/sub 2/ from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HCl ..-->.. NaCl + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2/sup 2/P/sub 3/2/) and Na(3/sup 2/P/sub 3/2/) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  6. Lack of consistence between morphological and molecular genetic ...

    African Journals Online (AJOL)

    tdtzeng

    2011-02-14

    Feb 14, 2011 ... 454-bp at 5' end of mitochondrial DNA control region were conducted. ..... Molecular Evolutionary Genetics Analysis and sequence alignment. ... substitutions in the control region of mitochondrial DNA in humans.

  7. Molecular cloning of the interleukin-1 gene cluster: Construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13

    Energy Technology Data Exchange (ETDEWEB)

    Nothwang, H.G.; Strahm, B.; Denich, D. [Freiburg Univ. (Germany)] [and others

    1997-05-01

    Genes of the interleukin-1 (IL-1) gene cluster localized on chromosome 2q13 are implicated in many physiological and pathophysiological processes. We present here a high-resolution physical map of this region between markers D2S2008 and D2S43/PAX8. An integrated YAC/PAC contig and a partial transcriptional map were constructed by STS-content mapping using the CEPH YAC library and three PAC libraries. A total of 3 YACs, 34 PACs, and 56 STSs were integrated: 33 newly generated probes to PAC end sequences, 9 polymorphic and 4 nonpolymorphic markers, 5 known genes, 4 expressed sequence tags, and 1 pseudogene. Within the map, a complete PAC contig of > 1 Mb encompasses the IL-1 gene cluster and PAX8, a paired-box-containing gene. This allowed us to define the transcriptional orientation of GLVR1, IL1B, and IL1RN and to show that PAX8 is localized outside the IL-1 gene cluster. FISH analysis localized PAC clones containing the IL-1 gene cluster to 2q12-q13. The data provide the basis for further characterization of the IL-1 gene cluster and for the construction of a sequence-ready PAC contig of this region. 45 refs., 2 figs., 2 tabs.

  8. H.E.S.S. detection of TeV emission from the interaction region between the supernova remnant G349.7+0.2 and a molecular cloud

    CERN Document Server

    ,

    2014-01-01

    G349.7+0.2 is a young Galactic supernova remnant (SNR) located at the distance of 11.5 kpc and observed across the entire electromagnetic spectrum from radio to high energy (HE) Gamma-rays. Radio and infrared observations indicate that the remnant is interacting with a molecular cloud. In this paper, the detection of very high energy (VHE) Gamma-ray emission coincident with this SNR with the High Energy Stereoscopic System (H.E.S.S.) is reported. An integral flux F(E>400GeV)=(6.5 +-1.1stat +-1.3syst) x 10^{-13} ph/cm/s corresponding to 0.7% of that of the Crab Nebula and to a luminosity of 10^34 erg/s above the same energy threshold, and a steep photon index Gamma_VHE = 2.8 +-0.27stat +-0.20syst are measured. The analysis of more than 5 yr of Fermi-LAT data towards this source shows a power-law like spectrum with a best-fit photon index Gamma_HE = 2.2 +-0.04stat +0.13-0.31syst. The combined Gamma-ray spectrum of G349.7+0.2 can be described by either a broken power-law (BPL) or a power-law with exponential (or...

  9. Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O 139 outbreak based on the inter-genomic heterogeneity of the 16S-23S rRNA intergenic spacer regions.

    Science.gov (United States)

    Ghatak, Atreyi; Majumdar, Anasuya; Ghosh, Ranajit K

    2005-12-01

    We have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eight rrn operons (rrna-rrnh) of Vibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O 139 outbreak. ISR classes 'a' and 'g' were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O 139 serogroup and post-O 139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

  10. Regional odontodysplasia

    Directory of Open Access Journals (Sweden)

    Thimma Reddy B

    2010-01-01

    Full Text Available Regional odontodysplasia (ROD is a rare developmental anomaly involving both mesodermal and ectodermal components in a group of contiguous teeth. It affects the primary and permanent dentitions in the maxilla and the mandible or both, however, the maxilla is frequently involved. Although the etiology of the ROD is uncertain, it has been suggested that numerous other factors play a role. The treatment plan should be based on the degree of involvement as well as the functional and esthetic needs in each case. This article reports the case of a 5-year-old boy presenting a rare anomaly on the right side of the maxillary arch. The treatment performed was rehabilitation with temporary partial acrylic denture and periodic checkups. The extraction was followed by rehabilitation with dental implants. The main aim of this article is to provide valuable information to pediatric dentists about the review and treatment alternatives for ROD.

  11. Vortex, Molecular Spin and Nanovorticity An Introduction

    CERN Document Server

    McCormack, Percival

    2012-01-01

    The subject of this book is the physics of vortices. A detailed analysis of the dynamics of vortices will be presented. The important topics of vorticity and molecular spin will be dealt with, including the electromagnetic analogy and quantization in superfluids. The effect of molecular spin on the dynamics of molecular nano-confined fluids using the extended Navier-Stokes equations will also be covered –especially important to the theory and applicability of nanofluidics and associated devices. The nanoscale boundary layer and nanoscale vortex core are regions of intense vorticity (molecular spin). It will be shown, based on molecular kinetic theory and thermodynamics, that the macroscopic (solid body) rotation must be accompanied by internal rotation of the molecules. Electric polarization of the internal molecular rotations about the local rotation axis –the Barnett effect – occurs. In such a spin aligned system, major changes in the physical properties of the fluid result.

  12. Molecular surveillance for drug-resistant Plasmodium falciparum in clinical and subclinical populations from three border regions of Burma/Myanmar: cross-sectional data and a systematic review of resistance studies

    Science.gov (United States)

    2012-01-01

    health workers can contribute to molecular surveillance of drug resistance in remote areas of Myanmar. Marginal and displaced populations under-represented among previous resistance investigations can and should be included in resistance surveillance efforts, particularly once genetic markers of artemisinin-delayed parasite clearance are identified. Subclinical infections may contribute to the epidemiology of drug resistance, but determination of gene amplification from desiccated filter samples requires further validation when DNA concentration is low. PMID:22992214

  13. Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O139 outbreak based on the intergenomic heterogeneity of the 16S-23S rRNA intergenic spacer regions

    Indian Academy of Sciences (India)

    Atreyi Ghatak; Anasuya Majumdar; Ranajit K Ghosh

    2005-12-01

    We have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eight rrn operons (rrna-rrnh) of Vibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O139 outbreak. ISR classes ‘a’ and ‘g’ were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O139 serogroup and post-O139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

  14. Study on molecular epidemiology of Borna disease virus in Zunyi regions of Guizhou province%遵义市及周边地区博尔纳病毒感染分子流行病学研究

    Institute of Scientific and Technical Information of China (English)

    王长明; 徐平; 葛均江; 郭振元

    2008-01-01

    Objective In order to study the epidemiology of Borna disease virus (BDV) in Zunyi region and its surrounding regions in Guizhou province. Methods p24 fragment of BDV fragments in peripheral blood mononuclear cells (PBMC) from 43 patients with viral encephalitis (VE), 9 cases with multiple sclerosis (MS), 7 cases with Guillain-Barre syndrome (GBS), 5 cases with Parkinson disease (PD), 98 healthy donors and 300 goats were examined by quantitative fluorescence nested reverse transcriptase polymerase chain reaction (PCR). Gene sequence and amino acid sequence were analyzed for positive products. Results The positive rate of BDV p24 fragment in PBMC from VE (13.95 %) and MS (22.22 %) were significantly higher than in healthy donors (0 %, P0.05). Guillain-Barre syndrome and Parkinson disease( PD)were tested negative. The sequence of the BDV p24 fragment from the patients with VE was in conformity with that of the MS. Results presented that 3 situs consistency silent mutation when compared with strain V and its homogeneity was 96.51%. 2 situs consistency silent mutation compared with BDV/MDCK and its homogeneity was 97.67%. 2 situs consistency silent mutation when compared with C6BV and its homogeneity was 97.67 %. Sequences of the BDV p24 fragment from the goats presented 3 situs consistency silent mutation when compared with strain V and its homogeneity was 96.51%. 3 situs consistency silent mutation when compared with BDV/MDCK and its homogeneity was 96.51%. 3 situs consistency silent mutation when compared with C6BV and its homogeneity was 96.51%. However, there were no changes of encoding amino acids in all BDV p24 fragments from neuropsychiatric disorders. Conclusion Our data indicated that the BDV infection was presented in patients with VE, MS and goats from Zunyi region and its surrounding regions of Guizhou province. BDV might play a potential role in the development of VE, MS as well as having correlations with animals.%目的 探讨博尔纳病毒(BDV)在遵

  15. Diagnóstico y caracterización molecular de Mycosphaerella fijiensis mediante la técnica de amplificación aleatoria de polimorfismos (RAPD y análisis de regiones transcriptos internos (ITS´s

    Directory of Open Access Journals (Sweden)

    Chacín Zambrano Christian Andrei

    2010-07-01

    Full Text Available Coming from the foliar sheet it was posible to obtain 12 Mycosphaerella fijiensis isolations originating from the plantain and banana zones of Colombia, establishing monosporic cultures to purify and to avoid overlapping of the fungus. The DNA was estracted from the mycelium and the foliar tissue infected by means of the protocol of Goodwin and Lee and Gilbertson and Dellaporta, by good quality was obtained. The ITS region was amplified though of universal and specific primers showing products of amplification of 233 pb for the ITS A(primer 1 + primer 2, a 360 pb band for the ITS B (primer 3 + primer 4, a 593 pb band for the ITS C (primer 1 + primer 4 and an amplification of 1080 pb with the combination of the specific MF 137 y R635 primers. Simultaneously the genetic variability by the RAPD technique was determined generating products of amplification between 280 pb – 2115 pb and common bands between the obtained isolations. A genetic similarity was determined of the isolations of “Norte de Santander” in Colombia, and the isolation of “Mérida” in Venezuela, at 70% in relation with those of “Santander” and “Antioquia” in Colombia with 48% and 35% each determined respectively.

  16. A molecular fountain

    CERN Document Server

    Cheng, Cunfeng; Jansen, Paul; Quintero-Pérez, Marina; Wall, Thomas E; Ubachs, Wim; Bethlem, Hendrick L

    2016-01-01

    The resolution of any spectroscopic or interferometric experiment is ultimately limited by the total time a particle is interrogated. We here demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiments, ammonia molecules are decelerated and cooled using electric fields, launched upwards with a velocity between 1.4 and 1.9\\,m/s and observed as they fall back under gravity. A combination of quadrupole lenses and bunching elements is used to shape the beam such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of $<$10\\,$\\mu$K and a longitudinal temperature of $<$1\\,$\\mu$K) when the molecules are in free fall, while being strongly focused at the detection region. The molecules are in free fall for up to 266\\,milliseconds, making it possible to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theorie...

  17. Molecular detection of rickettsias DNA in ticks around northeast region of China%东北部分地区蜱携带几种病原立克次体的分子检测

    Institute of Scientific and Technical Information of China (English)

    吴琼; 冯立; 王洪军; 吴益民; 付学奇; 王卓; 张志强

    2012-01-01

    Objective To understand the prevalence of tick-borne rickettsias around northeast region of China. Methods Wild ticks were captured and polymerase chain reaction (PCR) was used to amplify the rickettsias DNA of spotted fever group, human granulocytic ehrlichia and Ehrlichia chaff eensis carried by ticks. Results Ehrlichia chaff eensis DNA was found in I. Persulcatus and D. silvarum with the positive rates of 3.29% and 1.88% respectively. Meanwhile, human granulocytic ehrlichia DNA was amplified from I. Persulcatus with the positive rate of 2. 95%. However spotted fever group Rickettsiae was mainly found in H. concinna, with as high as 6.67% ticks carrying this rickettsiae, higher than that in I. Persulcatus and D. silvarum which were only 1. 69% and 2. 36%. Conclusions 7. Persulcatus and D. silvarum are possibly the main hosts of human granulocytic ehrlichia and Ehrlichia chaff eensis , while H. concinna mainly carries spotted fever group Rickettsiae in northeast region of China, indicating that it might be the natural foci of spotted feve, human granulocytic anaplasma and Ehrlichiosis.%目的 为了解东北地区蜱中携带立克次体的情况.方法 应用人工小时布旗法采集东北部分地区不同生境的游离蜱,采用PCR作斑点热立克次体、查菲埃立克体、人粒细胞无形体DNA检测.结果 从东北地区全沟硬蜱和森林革蜱检出查菲埃立克体DNA,全沟硬蜱平均阳性率为3.29%,森林革蜱为1.88%;从全沟硬蜱检出人粒细胞无形体DNA,平均阳性率为2.98%;从嗜群血蜱检出斑点热立克次体DNA,其平均阳性率(6.67%)明显高于全沟硬蜱(1.69%)和森林革蜱(2.36%).结论 东北地区全沟硬蜱和森林革蜱可能是查菲埃立克体、人粒细胞无形体的主要携带媒介,嗜群血蜱主要携带斑点热立克次体,提示东北地区存在三种蜱媒立克次体病的自然疫源地.

  18. A Spatially Resolved Study of Cold Dust, Molecular Gas, H ii Regions, and Stars in the z = 2.12 Submillimeter Galaxy ALESS67.1

    Science.gov (United States)

    Chen, Chian-Chou; Hodge, J. A.; Smail, Ian; Swinbank, A. M.; Walter, Fabian; Simpson, J. M.; Calistro Rivera, Gabriela; Bertoldi, F.; Brandt, W. N.; Chapman, S. C.; da Cunha, Elisabete; Dannerbauer, H.; De Breuck, C.; Harrison, C. M.; Ivison, R. J.; Karim, A.; Knudsen, K. K.; Wardlow, J. L.; Weiß, A.; van der Werf, P. P.

    2017-09-01

    We present detailed studies of a z = 2.12 submillimeter galaxy, ALESS67.1, using sub-arcsecond resolution ALMA, adaptive optics-aided VLT/SINFONI, and Hubble Space Telescope (HST)/CANDELS data to investigate the kinematics and spatial distributions of dust emission (870 μm continuum), 12CO(J = 3–2), strong optical emission lines, and visible stars. Dynamical modeling of the optical emission lines suggests that ALESS67.1 is not a pure rotating disk but a merger, consistent with the apparent tidal features revealed in the HST imaging. Our sub-arcsecond resolution data set allows us to measure half-light radii for all the tracers, and we find a factor of 4–6 smaller sizes in dust continuum compared to all the other tracers, including 12CO; also, ultraviolet (UV) and Hα emission are significantly offset from the dust continuum. The spatial mismatch between the UV continuum and the cold dust and gas reservoir supports the explanation that geometrical effects are responsible for the offset of the dusty galaxy on the IRX–β diagram. Using a dynamical method we derive an {α }{CO}=1.8+/- 1.0, consistent with other submillimeter galaxies (SMGs) that also have resolved CO and dust measurements. Assuming a single {α }{CO} value we also derive resolved gas and star formation rate surface densities, and find that the core region of the galaxy (≲ 5 kpc) follows the trend of mergers on the Schmidt–Kennicutt relationship, whereas the outskirts (≳ 5 kpc) lie on the locus of normal star-forming galaxies, suggesting different star formation efficiencies within one galaxy. Our results caution against using single size or morphology for different tracers of the star formation activity and gas content of galaxies, and therefore argue the need to use spatially resolved, multi-wavelength observations to interpret the properties of SMGs, and perhaps even for z> 1 galaxies in general.

  19. Molecular Identification and Historic Demography of the Marine Tucuxi (Sotalia guianensis at the Amazon River’s Mouth by Means of Mitochondrial Control Region Gene Sequences and Implications for Conservation

    Directory of Open Access Journals (Sweden)

    Joseph Mark Shostell

    2013-09-01

    Full Text Available In 2005, three fishermen, with artisan fishing vessels and drift gillnets, accidentally captured around 200 dolphins between Vigia and Salinópolis in the Amazon River estuary. The dolphins died and they then prepared their vaginas and penises in order to sell them in the Ver-ao-Peso market in the city of Belem within the Brazilian state of Pará. We randomly sampled a minimal quantity of tissue of these sexual organs from 78 of these 200 dolphins and we determined the following results after sequencing 689 base pairs (bp from the mitochondrial control region gene: (1 96.15% (75/78 of these dolphins belonged to the species Sotalia guianensis. The other species detected were Steno brenadensis, Stenella coeruleoalba and Tursiops truncatus; (2 The levels of gene diversity found in this sample of S. guianensis were high (33 haplotypes, haplotype diversity of 0.917 and nucleotide diversity of 0.0045 compared to gene diversities found in other Brazilian S. guianensis locations; (3 All the population genetics methods employed indicated a clear population expansion in this population. This population expansion could have begun 400,000 years ago; (4 The haplotype divergence within this population could have begun around 2.1 millions of years ago (MYA, with posterior splits around 2.0–1.8 MYA, 1.7–1.8 MYA, 1–1.5 MYA, 0.6–0.8 MYA, 0.4–0.2 MYA and 0.16–0.02 MYA, all during the Pleistocene.

  20. Molecular Detection and Drug Resistance of Mycobacterium tuberculosis Complex from Cattle at a Dairy Farm in the Nkonkobe Region of South Africa: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Blessing Silaigwana

    2012-05-01

    Full Text Available Mycobacterium tuberculosis complex (MTBC causes tuberculosis (TB in humans and animals. We investigated the presence of MTBC in cattle milk and its drug resistance using polymerase chain reaction (PCR. Two hundred samples (100 mL each were obtained from a dairy farm in the Nkonkobe region of South Africa. The samples were processed using the modified Petroff method. DNA was isolated using a Zymo Bacterial DNA kit and amplified using Seeplex® MTB Nested ACE assay. The Genotype® Mycobacterium tuberculosis-multidrug resistantplus (MTBDRplus assay was used to perform drug susceptibility and detection of mutations conferring resistance to isoniazid (INH and rifampicin (RIF. Eleven samples tested positive for MTBC DNA using the Seeplex® MTB Nested ACE assay. The Genotype® MTBDRplus assay showed that 10/11 samples were resistant to both INH and RIF i.e., multi-drug resistant (MDR. The most and least frequent rpoB mutations detected in RIF resistant samples were H526Y (9/10 and D516V (2/10 respectively. None of the INH resistant samples harbored mutations in the katG gene. However, all of them harbored the T8A mutation in the inhA gene. These results have clinical and epidemiological significance and calls for further studies and necessary actions to delineate the situation.

  1. Critical interpretation of CH– and OH– stretching regions for infrared spectra of methanol clusters (CH{sub 3}OH){sub n} (n = 2–5) using self-consistent-charge density functional tight-binding molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yoshifumi [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Lee, Yuan-Pern [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 10617, Taiwan (China); Irle, Stephan [Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Witek, Henryk A., E-mail: hwitek@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (China)

    2014-09-07

    Vibrational infrared (IR) spectra of gas-phase O–H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C–H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C–H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν{sub 3}, ν{sub 9}, and ν{sub 2} C–H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.

  2. On molecular graph comparison.

    Science.gov (United States)

    Melo, Jenny A; Daza, Edgar

    2011-06-01

    Since the last half of the nineteenth century, molecular graphs have been present in several branches of chemistry. When used for molecular structure representation, they have been compared after mapping the corresponding graphs into mathematical objects. However, direct molecular comparison of molecular graphs is a research field less explored. The goal of this mini-review is to show some distance and similarity coefficients which were proposed to directly compare molecular graphs or which could be useful to do so.

  3. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  4. Recombination hot spot in 3.2-kb region of the Charcot-Marie Tooth type 1A repeat sequences: New tools for molecular diagnosis of hereditary neuropathy with liability to pressure palsies and of Charcot-Marie-Tooth type 1A

    Energy Technology Data Exchange (ETDEWEB)

    Lopes, J.; LeGuern, E.; Gouider, R.; Tardieu, S.; Abbas, N. [Hopital de la Salpetriere, Paris (France)] [and others

    1996-06-01

    Charcot-Marie-Tooth type 1A (CMT1A) disease and hereditary neuropathy with liability to pressure palsies (HNPP) are autosomal dominant neuropathies, associated, respectively, with duplications and deletions of the same 1.5-Mb region on 17p11.2-p12. These two rearrangements are the reciprocal products of an unequal meiotic crossover between the two chromosome 17 homologues, caused by the misalignment of the CMT1A repeat sequences (CMT1A-REPs), the homologous sequences flanking the 1.5-Mb CMT1A/HNPP monomer unit. In order to map recombination breakpoints within the CMT1A-REPs, a 12.9-kb restriction map was constructed from cloned EcoRI fragments of the proximal and distal CMT1A-REPs. Only 3 of the 17 tested restriction sites were present in the proximal CMT1A-REP but absent in the distal CMT1A-REP, indicating a high degree of homology between these sequences. The rearrangements were mapped in four regions of the CMT1A-REPs by analysis of 76 CMT1A index cases and 38 HNPP patients, who were unrelated. A hot spot of crossover breakpoints located in a 3.2-kb region accounted for three-quarters of the rearrangements, detected after EcoRI/SacI digestion, by the presence of 3.2-kb and 7.8-kb junction fragments in CMT1A and HNPP patients, respectively. These junction fragments, which can be detected on classical Southern blots, permit molecular diagnosis. Other rearrangements can also be detected by gene dosage on the same Southern blots. 25 refs., 4 figs., 2 tabs.

  5. Molecular clouds. [significance in stellar evolution

    Science.gov (United States)

    Thaddeus, P.

    1977-01-01

    An attempt is made to understand star formation in the context of the dense interstellar molecular gas from which stars are made. Attention is given to how molecular observations (e.g., UV spectroscopy and radio 21-cm and recombination line observations) provide data on the physical state of the dense interstellar gas; observations of H II regions, stellar associations, and dark nebulae are discussed. CO clouds are studied with reference to radial velocity, temperature, density, ionization, magnetic field.

  6. Molecular characterization of Rhodococcus equi isolates of horse breeding farms from an endemic region in South of Brazil by multiplex PCR PCR multiplex para caracterização molecular de isolados de Rhodococcus equi provenientes de haras de uma região endêmica no Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Cristina da Costa Krewer

    2008-03-01

    Full Text Available Rhodococcus equi is a gram-positive coco-bacillus and an intracellular opportunistic pathogen which causes pneumonia in foals. It is widely detected in environment and has been isolated from several sources, as soil, feces and gut from health and sick foals. The goal of this study was to characterize the epidemiological status (endemic, sporadic or no infection of horse breeding farms from Bage County in South of Brazil, using a multiplex PCR. One hundred and eighteen R. equi isolates were identified by biochemical tests and submitted to a specie-specific and vapA multiplex PCR. These isolates were obtained from: three farms where the R. equi infection has been noticed, two farms where the disease has been not reported and one farm where the disease is frequent. All clinical isolates from horse breeding farms where the disease is endemic and/or sporadic were vapA-positive. None environmental isolates were vapA-positive. In three horse breeding farms with sporadic R. equi infection, 11.54% of the isolates from adult horse feces were vapA-positive. The multiplex PCR technique has proven to be effective for the molecular and epidemiological characterization of the R. equi isolates in horse breeding farms. An important finding in this study was the isolation of vapA-positive R. equi from adult horse feces, which is an evidence for other routes of dissemination of this pathogen in the farms.Rhodococcus equi é um coco-bacilo gram positivo que causa pneumonia em potros. Trata-se de um patógeno oportunista amplamente detectado no ambiente e isolado de várias fontes, como solo, fezes e intestino de potros doentes e sadios. O presente estudo visa caracterizar a situação epidemiológica de criatórios eqüinos da região de Bagé, RS, Brasil, pela técnica de PCR multiplex. Cento e dezoito isolados de R. equi foram identificados por testes bioquímicos e, posteriormente, submetidos a um PCR multiplex para caracterização da espécie e da presença do

  7. Multiscale coupling of molecular dynamics and peridynamics

    Science.gov (United States)

    Tong, Qi; Li, Shaofan

    2016-10-01

    We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.

  8. Finding Distant Galactic HII Regions

    CERN Document Server

    Anderson, L D; Johnstone, B M; Bania, T M; Balser, Dana S; Wenger, Trey V; Cunningham, V

    2015-01-01

    The WISE Catalog of Galactic HII Regions contains $\\sim2000$ HII region candidates lacking ionized gas spectroscopic observations. All candidates have the characteristic HII region mid-infrared morphology of WISE $12\\,\\,\\mu\\,m$ emission surrounding $22\\,\\mu\\,m$ emission, and additionally have detected radio continuum emission. We here report Green Bank Telescope (GBT) hydrogen radio recombination line (RRL) and radio continuum detections at X-band (9GHz; 3cm) of 302 WISE HII region candidates (out of 324 targets observed) in the zone $225^{\\circ} > l > -20^{\\circ}$, $|b| \\le 6^{\\circ}$. Here we extend the sky coverage of our HII region Discovery Survey (HRDS), which now contains nearly 800 HII regions distributed across the entire northern sky. We provide LSR velocities for the 302 detections and kinematic distances for 131 of these. Of the 302 new detections, five have ($l, b, v$) coordinates consistent with the Outer Scutum-Centaurus Arm (OSC), the most distant molecular spiral arm of the Milky Way. Due to ...

  9. Molecular outflows in starburst nuclei

    CERN Document Server

    Roy, Arpita; Sharma, Prateek; Shchekinov, Yuri

    2016-01-01

    Recent observations have detected molecular outflows in a few nearby starburst nuclei. We discuss the physical processes at work in such an environment in order to outline a scenario that can explain the observed parameters of the phenomenon, such as the molecular mass, speed and size of the outflows. We show that outflows triggered by OB associations, with $N_{OB}\\ge 10^5$ (corresponding to a star formation rate (SFR)$\\ge 1$ M$_{\\odot}$ yr$^{-1}$ in the nuclear region), in a stratified disk with mid-plane density $n_0\\sim 200\\hbox{--}1000$ cm$^{-3}$ and scale height $z_0\\ge 200 (n_0/10^2 \\, {\\rm cm}^{-3})^{-3/5}$ pc, can form molecules in a cool dense and expanding shell. The associated molecular mass is $\\ge 10^7$ M$_\\odot$ at a distance of a few hundred pc, with a speed of several tens of km s$^{-1}$. We show that a SFR surface density of $10 \\le \\Sigma_{SFR} \\le 50$ M$_\\odot$ yr$^{-1}$ kpc$^{-2}$ favours the production of molecular outflows, consistent with observed values.

  10. Molecular line tracers of high-mass star forming regions

    NARCIS (Netherlands)

    Nagy, Zsofia

    2013-01-01

    Hoge-massa sterren beïnvloeden hun omgeving op diverse manieren waaronder feedback door ver-ultraviolette straling en mechanische feedback via schokken en sterrewinden. Het doordringen van UV-straling in moleculaire wolken creëert zogenaamde foton-gedomineerde gebieden (PDRs) met diverse chemische l

  11. Molecular profiling of midbrain dopamine regions in cocaine overdose victims

    National Research Council Canada - National Science Library

    Tang, Wen‐Xue; Fasulo, Wendy H; Mash, Deborah C; Hemby, Scott E

    2003-01-01

    .... To evaluate whether the alterations in gene expression in cocaine overdose victims are associated with specific dopamine populations in the midbrain, cDNA arrays and western blotting were used...

  12. Molecular characterization of chikungunya virus from three regions of Cameroon

    Institute of Scientific and Technical Information of China (English)

    Demanou Maurice; Sadeuh-Mba Serge Alain; Vanhecke Christophe; Ndikweti Rene; Kouna Tsala Irene; Inais Nsizoa Marthe; Njouom Richard

    2015-01-01

    Dear Editor,Chikungunya virus(CHIKV),a single-stranded RNA virus that belongs to the genus Alphavirus,family Togaviridae,is transmitted by mosquitoes of the genus Aedes(Diptera:Culicidae),predominantly Aedes aegypti and A.albopictus(Staples et al.,2014).CHIKV infection is most often characterized by fever,headache,

  13. Progress in molecular SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Borman, S.

    1987-04-15

    A review of sputtering and molecular ion emission is presented. New derivatization techniques have produced lower detection limits for molecular secondary ion mass spectrometry (SIMS). Spectra of representative organic compounds are presented.

  14. Advancement of Molecular Morphology

    Institute of Scientific and Technical Information of China (English)

    顾江

    2004-01-01

    @@ Molecular morphology is a new discipline of medical science that studies morphology at the molecular level. This includes the investigation of occurrence and distribution of proteins, peptides, DNA and RNA sequences at the tissue, cellular, and ultrastructural levels.

  15. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  16. Physical Chemistry of Molecular

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Established in 2009, the group consists of six researchers and more than 70 research assistants and graduate students from the CAS Key Laboratory of Molecular Nanostructures and Nanotechnologies at the CAS Institute of Chemistry.Its research focuses on the physical chemistry involved in molecular assembly, molecular nanostructures, functional nanomaterials and conceptual nano-devices.

  17. [Molecular variability in the commom shrew Sorex araneus L. from European Russia and Siberia inferred from the length polymorphism of DNA regions flanked by short interspersed elements (Inter-SINE PCR) and the relationships between the Moscow and Seliger chromosome races].

    Science.gov (United States)

    Bannikova, A A; Bulatova, N Sh; Kramerov, D A

    2006-06-01

    Genetic exchange among chromosomal races of the common shrew Sorex araneus and the problem of reproductive barriers have been extensively studied by means of such molecular markers as mtDNA, microsatellites, and allozymes. In the present study, the interpopulation and interracial polymorphism in the common shrew was derived, using fingerprints generated by amplified DNA regions flanked by short interspersed repeats (SINEs)-interSINE PCR (IS-PCR). We used primers, complementary to consensus sequences of two short retroposons: mammalian element MIR and the SOR element from the genome of Sorex araneus. Genetic differentiation among eleven populations of the common shrew from eight chromosome races was estimated. The NP and MJ analyses, as well as multidimensional scaling showed that all samples examined grouped into two main clusters, corresponding to European Russia and Siberia. The bootstrap support of the European Russia cluster in the NJ and MP analyses was respectively 76 and 61%. The bootstrap index for the Siberian cluster was 100% in both analyses; the Tomsk race, included into this cluster, was separated with the bootstrap support of NJ/MP 92/95%.

  18. Molecular methods for biofilms

    KAUST Repository

    Ferrera, Isabel

    2014-08-30

    other cell components into the organic phase. The last step is the purification of nucleic acids, which may dramatically reduce the efficiency of the recovery. The method used should, therefore, result in a compromise between yield and purity. PCR and DNA sequencing: Application of DNA polymerase chain reaction (PCR) amplification and DNA sequencing in order to amplify and determine the DNA of microbial marker genes, allows the understanding of microbial diversity with an ever-increasing resolution and accuracy. This chapter provides an overview over DNA PCR amplification and DNA sequencing methods. It discusses protocols and analysis software as well as potential pitfalls associated with application of these methods. While PCR is a molecular technique to amplify virtually unlimited amounts of a particular DNA sequence from only a few DNA copies of input material, DNA sequencing refers to the actual determination of the sequence of nucleotides of a strand of DNA (or RNA). In phylogeny-based analyses, taxa are operationally defined by relatedness to another sequence in a phylogenetic tree. Similarly to representative operational taxonomic units (OTU) sequences, all sequenced 16S fragments can be assigned to a species or taxon in a database. Community comparison by genetic fingerprinting techniques: This chapter discusses community fingerprinting analyses that can be used to compare multiple microbial communities. It focuses on denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and automated rRNA intergenic spacer analysis (ARISA) methods. DGGE discriminates DNA fragments having different sequences and different AT/GC content. Terminal restriction fragment length polymorphism (T-RFLP) involves the extraction of DNA from environmental samples. The ARISA technique uses the highly variable internal transcribed (ITS) regions of rDNA. All fingerprinting techniques have the advantage of being able to process many samples

  19. Molecular computing origins and promises

    CERN Document Server

    Rambidi, Nicholas G

    2014-01-01

    Molecular Computing explores whether molecular primitives can prove to be real alternatives to contemporary semiconductor means. The text discusses molecular primitives and circuitry for information processing devices.

  20. Molecular Diagnosis of Cystic Fibrosis.

    Science.gov (United States)

    Deignan, Joshua L; Grody, Wayne W

    2016-01-01

    This unit describes a recommended approach to identifying causal genetic variants in an individual suspected of having cystic fibrosis. An introduction to the genetics and clinical presentation of cystic fibrosis is initially presented, followed by a description of the two main strategies used in the molecular diagnosis of cystic fibrosis: (1) an initial targeted variant panel used to detect only the most common cystic fibrosis-causing variants in the CFTR gene, and (2) sequencing of the entire coding region of the CFTR gene to detect additional rare causal CFTR variants. Finally, the unit concludes with a discussion regarding the analytic and clinical validity of these approaches.

  1. Engineering molecular machines

    Science.gov (United States)

    Erman, Burak

    2016-04-01

    Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

  2. Workshop on molecular animation.

    Science.gov (United States)

    Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E

    2010-10-13

    From February 25 to 26, 2010, in San Francisco, the Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for producing high-quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories.

  3. Cellular and Molecular Basis of Cerebellar Development

    Directory of Open Access Journals (Sweden)

    Salvador eMartinez

    2013-06-01

    Full Text Available Historically, the molecular and cellular mechanisms of cerebellar development were investigated through structural descriptions and studying spontaneous mutations in animal models and humans. Advances in experimental embryology, genetic engineering and neuroimaging techniques render today the possibility to approach the analysis of molecular mechanisms underlying histogenesis and morphogenesis of the cerebellum by experimental designs. Several genes and molecules were identified to be involved in the cerebellar plate regionalization, specification and differentiation of cerebellar neurons, as well as the establishment of cellular migratory routes and the subsequent neuronal connectivity. Indeed, pattern formation of the cerebellum requires the adequate orchestration of both key morphogenetic signals, arising from distinct brain regions, and local expression of specific transcription factors. Thus, the present review wants to revisit and discuss these morphogenetic and molecular mechanisms taking place during cerebellar development in order to understand causal processes regulating cerebellar cytoarchitecture, its highly topographically ordered circuitry and its role in brain function.

  4. HIV Molecular Immunology 2015

    Energy Technology Data Exchange (ETDEWEB)

    Yusim, Karina [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Korber, Bette Tina [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Brander, Christian [Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona (Spain); Barouch, Dan [Beth Israel Deaconess Medical Center, Boston, MA (United States). Division of Vaccine Research; de Boer, Rob [Utrecht University, Utrecht (Netherlands). Faculty of Biology; Haynes, Barton F. [Duke Univ., Durham, NC (United States). Duke Human Vaccine Institute and Departments of Medicine, Surgery and Immunology; Koup, Richard [National Inst. of Health (NIH), Bethesda, MD (United States). Vaccine Research Center; Moore, John P. [Cornell Univ., Ithaca, NY (United States). Weill Medical College; Walker, Bruce D. [Ragon Institute, Cambridge, MA (United States); Watkins, David [Wisconsin Regional Primate Research Center, Madison, WI (United States)

    2016-04-05

    The scope and purpose of the HIV molecular immunology database: HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2015 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/ content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins

  5. Molecular biodiversity of Red Sea demosponges.

    Science.gov (United States)

    Erpenbeck, Dirk; Voigt, Oliver; Al-Aidaroos, Ali M; Berumen, Michael L; Büttner, Gabriele; Catania, Daniela; Guirguis, Adel Naguib; Paulay, Gustav; Schätzle, Simone; Wörheide, Gert

    2016-04-30

    Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge diversity in this area is insufficient to recognize, for example, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular biodiversity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of biodiversity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular diversity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge biodiversity of the Red Sea and adjacent waters.

  6. Molecular biodiversity of Red Sea demosponges

    KAUST Repository

    Erpenbeck, Dirk

    2016-01-07

    Sponges are important constituents of coral reef ecosystems, including those around the Arabian Peninsula. Despite their importance, our knowledge on demosponge diversity in this area is insufficient to recognize, for example, faunal changes caused by anthropogenic disturbances. We here report the first assessment of demosponge molecular biodiversity from Arabia, with focus on the Saudi Arabian Red Sea, based on mitochondrial and nuclear ribosomal molecular markers gathered in the framework of the Sponge Barcoding Project. We use a rapid molecular screening approach on Arabian demosponge collections and analyze results in comparison against published material in terms of biodiversity. We use a variable region of 28S rDNA, applied for the first time in the assessment of demosponge molecular diversity. Our data constitutes a solid foundation for a future more comprehensive understanding of sponge biodiversity of the Red Sea and adjacent waters.

  7. Cultural and molecular detection of zoonotic tuberculosis and its ...

    African Journals Online (AJOL)

    Cultural and molecular detection of zoonotic tuberculosis and its public health impacts in selected districts of Tigray region, Ethiopia. ... Besides, livestock owners were interviewed for the evaluation of the zoonotic potential of BTB. On the basis ...

  8. The molecular basis of somatic hypermutation of immunoglobulin genes.

    Science.gov (United States)

    Storb, U

    1996-04-01

    Somatic hypermutation amplifies the variable region repertoire of immunoglobulin genes. Recent experimental evidence has thrown light on various molecular models of somatic hypermutation. A link between somatic hypermutation and transcription coupled DNA repair is shaping up.

  9. Desenvolvimento regional: a diversidade regional como potencialidade

    Directory of Open Access Journals (Sweden)

    José Odim Degrandi

    2013-04-01

    Full Text Available Throughout the second half of the twentieth century the debate on regional development in Brazil received special attention, especially among economists and geographers. Two main approaches stand out in the debate: one that understands the promotion of regional development from the reduction / elimination of regional inequalities, and the other proposes the understanding of regional diversity and potentiality for developing regions. The first was and still remains hegemonic, being evidenced both in scientific papers and in documents guiding public policies in the area. The latter is evidenced most clearly from the 1990s on, a period when the concept of region is resumed under a new approach. This paper aims to clarify the meaning of each of these concepts in order to contribute to the qualification of the discussion on regional development.

  10. Desenvolvimento regional: a diversidade regional como potencialidade

    Directory of Open Access Journals (Sweden)

    Virginia Elisabeta Etges

    2013-03-01

    Full Text Available Ao longo da segunda metade do século XX o debate sobre desenvolvimento regional no Brasil recebeu atenção especial, principalmente, entre economistas e geógrafos. Dois enfoques principais se destacam no debate: um, que entende a promoção do desenvolvimento regional a partir da redução/eliminação das desigualdades regionais; outro, que propõe a compreensão da diversidade regional como potencialidade para o desenvolvimento de regiões. O primeiro foi e continua sendo hegemônico, evidenciado tanto em trabalhos científicos quanto em documentos norteadores das políticas públicas na área. Já o segundo evidencia-se mais claramente a partir da década de 1990, período em que o conceito de região é retomado sob um novo enfoque. Neste trabalho pretende-se explicitar o significado de cada uma dessas concepções, no intuito de contribuir para a qualificação da discussão sobre desenvolvimento regional.Palavras-chave | Desenvolvimento regional; diversidade regional; potencialidades; região.Código JEL | O18; R11; R58. REGIONAL DEVELOPMENT: REGIONAL DIVERSITY AS POTENTIALAbstractThroughout the second half of the twentieth century the debate on regional development in Brazil received special attention, especially among economists and geographers. Two main approaches stand out in the debate: one that understands the promotion of regional development from the reduction / elimination of regional inequalities, and the other proposes the understanding of regional diversity and potentiality for developing regions. The first was and still remains hegemonic, being evidenced both in scientific papers and in documents guiding public policies in the area. The latter is evidenced most clearly from the 1990s on, a period when the concept of region is resumed under a new approach. This paper aims to clarify the meaning of each of these concepts in order to contribute to the qualification of the discussion on regional development.Keywords | Regional

  11. Time-resolved vibrational spectroscopy of a molecular shuttle

    NARCIS (Netherlands)

    Panman, M.R.; Bodis, P.; Shaw, D.J.; Bakker, B.H.; Newton, A.C.; Kay, E.R.; Leigh, D.A.; Buma, W.J.; Brouwer, A.M.; Woutersen, S.

    2012-01-01

    Time-resolved vibrational spectroscopy is used to investigate the inter-component motion of an ultraviolet-triggered two-station molecular shuttle. The operation cycle of this molecular shuttle involves several intermediate species, which are observable in the amide I and amide II regions of the mid

  12. Analysis of the 3' Cmu region of the rabbit Ig heavy chain locus.

    Science.gov (United States)

    Lanning, Dennis K; Zhai, Shi-Kang; Knight, Katherine L

    2003-05-08

    The immunoglobulin D (IgD) antibody class was, for many years, identified only in primates, rodents and teleost fish. The limited distribution of IgD among vertebrates suggested that IgD is a functionally redundant antibody class that has been lost by many vertebrate species during evolution. The recent identification of IgD in artiodactyls, however, suggests that IgD might be more widely expressed among vertebrates than previously thought, possibly serving a unique role in immunity. IgD expression has been searched for but not detected in rabbits. In order to search directly for a rabbit Cdelta locus encoding the constant region of IgD, we determined the nucleotide sequence of 13.5 kb of genomic DNA downstream of the rabbit Cmu locus. We did not find a rabbit Cdelta locus in this region, but found instead that this region is densely populated by repetitive elements, including a long interspersed DNA element repeat, six C repeats, and two processed pseudogenes. We conclude that the rabbit probably does not express IgD because there is no Cdelta locus immediately downstream of the rabbit Cmu locus.

  13. Molecular modelling and molecular dynamics of CFTR.

    Science.gov (United States)

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  14. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  15. Sober Topological Molecular Lattices

    Institute of Scientific and Technical Information of China (English)

    张德学; 李永明

    2003-01-01

    A topological molecular lattice (TML) is a pair (L, T), where L is a completely distributive lattice and r is a subframe of L. There is an obvious forgetful functor from the category TML of TML's to the category Loc of locales. In this note,it is showed that this forgetful functor has a right adjoint. Then, by this adjunction,a special kind of topological molecular lattices called sober topological molecular lattices is introduced and investigated.

  16. Exercises in molecular computing.

    Science.gov (United States)

    Stojanovic, Milan N; Stefanovic, Darko; Rudchenko, Sergei

    2014-06-17

    CONSPECTUS: The successes of electronic digital logic have transformed every aspect of human life over the last half-century. The word "computer" now signifies a ubiquitous electronic device, rather than a human occupation. Yet evidently humans, large assemblies of molecules, can compute, and it has been a thrilling challenge to develop smaller, simpler, synthetic assemblies of molecules that can do useful computation. When we say that molecules compute, what we usually mean is that such molecules respond to certain inputs, for example, the presence or absence of other molecules, in a precisely defined but potentially complex fashion. The simplest way for a chemist to think about computing molecules is as sensors that can integrate the presence or absence of multiple analytes into a change in a single reporting property. Here we review several forms of molecular computing developed in our laboratories. When we began our work, combinatorial approaches to using DNA for computing were used to search for solutions to constraint satisfaction problems. We chose to work instead on logic circuits, building bottom-up from units based on catalytic nucleic acids, focusing on DNA secondary structures in the design of individual circuit elements, and reserving the combinatorial opportunities of DNA for the representation of multiple signals propagating in a large circuit. Such circuit design directly corresponds to the intuition about sensors transforming the detection of analytes into reporting properties. While this approach was unusual at the time, it has been adopted since by other groups working on biomolecular computing with different nucleic acid chemistries. We created logic gates by modularly combining deoxyribozymes (DNA-based enzymes cleaving or combining other oligonucleotides), in the role of reporting elements, with stem-loops as input detection elements. For instance, a deoxyribozyme that normally exhibits an oligonucleotide substrate recognition region is

  17. 真鲷(Pagrus major)vasa基因5′端启动子克隆及表达载体构建%MOLECULAR CLONING AND CONSTRUCTION OF THE 5' FLANKING REGION EXPRESSION VECTOR OF THE vasa GENE OF RED SEABREAM (PAGRUS MAJOR)

    Institute of Scientific and Technical Information of China (English)

    林帆; 刘清华; 李军; 隋娟; 肖志忠; 徐世宏; 马道远; 肖永双

    2011-01-01

    采用染色体步移(Genome walking)的方法克隆了真鲷vasa基因5′侧翼序列,采用生物信息学方法分析潜在的顺式作用元件,并与斑马鱼核心启动子进行比对,在此基础上构建了绿色荧光蛋白表达载体。序列分析结果显示:克隆得到的真鲷vasa基因5′侧翼序列序列长度为2762bp,其中包括TATA-box、CAAT-box、SP-1、GAGA-1、OCT-1、v-Myb、Sox-5、SRY、HNF等可能对vasa基因转录调控起重要作用的顺式作用元件。潜在的核心启动子区与斑马鱼核心启动子具有同源性(61.1%)%Red seabream (Pagrus major) is a commercially important marine species in China. With the rapid development of marine aquaculture industry, resource conservation and identification of red seabream is increasingly important. Although sperm cryopreservation of the red seabream is relatively successful, little progress has made on embryo cryopreservation. Primordial germ cell (PGC) is the progenitor of the germ cell lineage, giving rise to either egg or sperm, with the potential to create complete individual organisms after fertilization. Cryopreservation of PGCs provides a new way for resource conservation. Vasa, a member of DEAD-box gene family, is strictly expressed in germ cell lineage. It is widely used as a molecular marker to study origin, migration and differentiation of PGCs. The objective of this study is to inves- tigate potential cis-acting elements that involve in the transcription regulation of vasa gene in red seabream and set up a basis for further research on promoter efficiency and isolation of PGCs with GFP special expression. As the vasa 5'UTR reported (GenBank: AB378581) is not long enough to design three nested primers, we first amplified the first intron to get enough information. Next, 5' flanking region of red seabream vasa was amplified from genomic DNA by Genome Walking. Potential transcript factor binding sites were analyzed by bioinformatics

  18. HIV Molecular Immunology 2014

    Energy Technology Data Exchange (ETDEWEB)

    Yusim, Karina [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Barouch, Dan [Beth Israel Deaconess Medical Center, Boston, MA (United States); Koup, Richard [Vaccine Research Center National Institutes of Health (United States); de Boer, Rob [Utrecht Univ. (Netherlands). Dept. of Biology; Moore, John P. [Cornell Univ., Ithaca, NY (United States). Weill Medical College; Brander, Christian [Institucioi Catalana de Recerca i Estudis Avancats (ICREA), Barcelona (Spain); Haynes, Barton F. [Duke Univ., Durham, NC (United States). Duke Human Vaccine Institute and Departments of Medicine, Surgery and Immunology; Walker, Bruce D. [Ragon Institute of Massachusetts General Hospital, Cambridge, MA (United States); Harvard Univ., Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2015-02-03

    HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

  19. Atomic and molecular supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.

    1997-12-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  20. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  1. Molecular cloning, construction of the expression vector and detection of transcription activity of vasa regulatory regions in half-smooth tongue sole (Cynoglossus semilaevis)%半滑舌鳎vasa调控区的克隆、表达载体构建及其驱动活性检测

    Institute of Scientific and Technical Information of China (English)

    黄进强; 陈松林; 邵长伟; 刘洋; 林帆; 李亚亚; 王娜

    2015-01-01

    为研究半滑舌鳎(Cynoglossus semilaevis) vasa(Csvasa)基因调控区的功能,在已克隆的Csvasa 基因编码序列的基础上,采用基因组步移和PCR扩增的方法克隆得到Csvasa调控区,通过生物信息学方法分析vasa基因5′区,并构建了含Csvasa 基因调控区的绿色荧光蛋白(GFP)表达载体(pCsvasa-GFP-T),进一步通过显微注射技术初步验证调控区的驱动活性。结果表明,通过基因组步移和PCR扩增获得Csvasa 5′区5166 bp和3′区1655 bp,利用在线生物信息学软件对5′区序列进行分析,发现在转录起始点上游26 b p处存在保守的TATA框,以及潜在的转录因子结合点如 SRY、Oct-1、Sox-5、CREB、GATA、AP-1、C/EBP、Sp-1、c-Myc、HNF、NKX2-5、V-Myb 等。通过显微注射技术,将所构建的 pCsvasa-GFP-T 鳉表达载体注射于青(Oryzias latipes)受精卵并进行培养观测,发现Csvasa调控区能够驱动GFP在青鳉胚胎内表达,荧光表达率为81%。将有荧光的胚胎培养为成鱼,检测外源基因的整合率为11.5%。这些结果为进一步研究半滑舌鳎原始生殖细胞(PGCs)的标记、追踪和操作研究以及半滑舌鳎的性别控制等奠定了基础。%The Vasa gene is an excellent candidate molecular marker for studying primordial germ cells (PGCs) because of its specific expression in germ cell lineages. PGCs can be labeled by a reporter gene driven by regula-tory regions of the vasa gene. Half-smooth tongue sole (Cynoglossus semilaevis) is an economically important flatfish in China, and the females of this species grow two to four times bigger than males. Sex reversal is common in this fish and females cannot guarantee egg production by natural spawning under artificial culture conditions. Therefore, transplantation of PGCs and surrogate broodstock production might be employed to improve the pro-duction of this fish. Promoter choice in transgenic research is important for regulating expression of a foreign gene

  2. 寿光地区感病辣椒TYLCV的分子鉴定和病毒DNA-A序列分析%Molecular Identification and DNA-A Gene Sequence Analysis of Tomato Yellow Leaf Curl Virus on Pepper( Capsicum annuum )in Shouguang Region

    Institute of Scientific and Technical Information of China (English)

    刘春香; 刘彩云; 李会平; 曹京

    2012-01-01

    由于TYLCV的宿主广泛,本试验对山东寿光地区的感病毒病辣椒进行了TYLCV感染的分子鉴定,发现寿光地区的辣椒感染了TYLCV病毒,且感染率较高.通过对病毒基因组DNA-A序列的克隆和序列分析发现,寿光感病辣椒的TYLCV序列与临沂和德州的TYLCV亲缘关系最近,并对具体突变点进行了分析.进化树分析显示,克隆得到的辣椒病毒与墨西哥的TYLCV病毒同源性较高,而与危害辣椒较严重的TYLCSV的遗传距离较远.%Molecular identification were done on tomato yellow leaf curl virus ( TYLCV) isolated from pepper plants showing TYLCV symptoms in Shouguang region because TYLCV have more hosts. The result showed peppers in Shouguang infected TYLCV with high efficiency among detected plants. The isolate was the most close to the TYLCV Linyi isolate and Dezhou isolate, and the detail point mutation of Shouguang TYLCV genome compared with Linyi were analyzed. Phylogenetic tree analysis indicated that TYLCV of mexico were found to show high sequence i-dentity with that we cloned, and with relatively low similarity to TYLCSV strains which damaged pepper seriously.

  3. Central Region Regionally Ecological Significant Areas

    Data.gov (United States)

    Minnesota Department of Natural Resources — This is an analysis of regionally significant Terrestrial and Wetland Ecological Areas in the seven county metropolitan area. Individual forest, grassland and...

  4. Terahertz molecular resonance of cancer DNA

    Science.gov (United States)

    Cheon, Hwayeong; Yang, Hee-Jin; Lee, Sang-Hun; Kim, Young A.; Son, Joo-Hiuk

    2016-11-01

    Carcinogenesis involves the chemical and structural alteration of biomolecules in cells. Aberrant methylation of DNA is a well-known carcinogenic mechanism and a common chemical modification of DNA. Terahertz waves can directly observe changes in DNA because the characteristic energies lie in the same frequency region. In addition, terahertz energy levels are not high enough to damage DNA by ionization. Here, we present terahertz molecular resonance fingerprints of DNA methylation in cancer DNA. Methylated cytidine, a nucleoside, has terahertz characteristic energies that give rise to the molecular resonance of methylation in DNA. Molecular resonance is monitored in aqueous solutions of genomic DNA from cancer cell lines using a terahertz time-domain spectroscopic technique. Resonance signals can be quantified to identify the types of cancer cells with a certain degree of DNA methylation. These measurements reveal the existence of molecular resonance fingerprints of cancer DNAs in the terahertz region, which can be utilized for the early diagnosis of cancer cells at the molecular level.

  5. Vibrational energy transfer in shocked molecular crystals.

    Science.gov (United States)

    Hooper, Joe

    2010-01-07

    We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state.

  6. NGC 3503 and its molecular environment

    CERN Document Server

    Duronea, N U; Cappa, C E; Corti, M; Arnal, E M

    2011-01-01

    We present a study of the molecular gas and interstellar dust distribution in the environs of the HII region NGC 3503 associated with the open cluster Pis 17 with the aim of investigating the spatial distribution of the molecular gas linked to the nebula and achieving a better understanding of the interaction of the nebula and Pis 17 with their molecular environment. We based our study in ^{12}CO(1-0) observations of a region of ~0.6 deg. in size obtained with the 4-m NANTEN telescope, unpublished radio continuum data at 4800 and 8640 MHz obtained with the ATCA telescope, radio continuum data at 843 MHz obtained from SUMSS, and available IRAS, MSX, IRAC-GLIMPSE, and MIPSGAL images. We found a molecular cloud (Component 1) having a mean velocity of -24.7 km s^{-1}, compatible with the velocity of the ionized gas, which is associated with the nebula and its surroundings. Adopting a distance of 2.9 +/- 0.4 kpc the total molecular mass and density yield (7.6 +/- 2.1) x 10^3 Msun and 400 +/- 240 cm^{-3}, respectiv...

  7. Molecular Typing and Differentiation

    Science.gov (United States)

    In this chapter, general background and bench protocols are provided for a number of molecular typing techniques in common use today. Methods for the molecular typing and differentiation of microorganisms began to be widely adopted following the development of the polymerase chai...

  8. Advancement of Molecular Morphology

    Institute of Scientific and Technical Information of China (English)

    顾江

    2004-01-01

    Molecular morphology is a new discipline of medical science that studies morphology at the molecular level. This includes the investigation of occurrence and distribution of proteins, peptides, DNA and RNA sequences at the tissue, cellular, and uhrastructural levels. Morphology is defined as a field of science investigating the shape,

  9. Molecular Stirrers in Action

    NARCIS (Netherlands)

    Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

    2014-01-01

    A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity. Quantitat

  10. Multifunctionality in molecular magnetism.

    Science.gov (United States)

    Pinkowicz, Dawid; Czarnecki, Bernard; Reczyński, Mateusz; Arczyński, Mirosław

    2015-01-01

    Molecular magnetism draws from the fundamental ideas of structural chemistry and combines them with experimental physics resulting in one of the highest profile current topics, namely molecular materials that exhibit multifunctionality. Recent advances in the design of new generations of multifunctional molecular magnets that retain the functions of the building blocks and exhibit non-trivial magnetic properties at higher temperatures provide promising evidence that they may be useful for the future construction of nanoscale devices. This article is not a complete review but is rather an introduction into thefascinating world of multifunctional solids with magnetism as the leitmotif. We provide a subjective selection and discussion of the most inspiring examples of multifunctional molecular magnets: magnetic sponges, guest-responsive magnets, molecular magnets with ionic conductivity, photomagnets and non-centrosymmetric and chiral magnets.

  11. Hamiltonian adaptive resolution simulation for molecular liquids.

    Science.gov (United States)

    Potestio, Raffaello; Fritsch, Sebastian; Español, Pep; Delgado-Buscalioni, Rafael; Kremer, Kurt; Everaers, Ralf; Donadio, Davide

    2013-03-08

    Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well-defined statistical ensembles can be generated making use of all standard molecular dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.

  12. Molecular complexes of phenols with DDQ

    Indian Academy of Sciences (India)

    T Vinod Kumar; T Veeraiah; G Venkateshwarlu

    2000-04-01

    Molecular complexes of phenols with DDQ have been studied spectrophotometrically in the temperature range of 10-30°C in a solvent (CHCl3) of low polarity under low donor concentrations. All the complexes exhibit one CT band each in the wavelength region where acceptor and donor do not have any absorption. The complexes are inferred to be of the - type and have y configuration in which the donor molecular orbital encompasses the substituent. The ionization potentials of the donors, the stability constants and thermodynamic parameters of the complexes have been evaluated.

  13. The current state of molecular cytogenetics in cancer diagnosis.

    Science.gov (United States)

    Liehr, Thomas; Othman, Moneeb A K; Rittscher, Katharina; Alhourani, Eyad

    2015-04-01

    Cytogenetics and molecular cytogenetics are and will continue to be indispensable tools in cancer diagnostics. Leukemia and lymphoma diagnostics are still emphases of routine (molecular) cytogenetics and corresponding studies of solid tumors gain more and more prominence. Here, first a historical perspective of molecular tumor cytogenetics is provided, which is followed by the basic principles of the fluorescence in situ hybridization (FISH) approach. Finally the current state of molecular cytogenetics in cancer diagnostics is discussed. Nowadays routine diagnostics includes basic FISH approaches rather than multicolor-FISH. The latter together with modern high-throughput methods have their impact on research to identify new tumor-associated genomic regions.

  14. The Regional Dimension

    DEFF Research Database (Denmark)

    Eskjær, Mikkel Fugl

    2013-01-01

    is largely dependent on regional media systems, yet the role this regional dimension plays has been largely overlooked. This article presents a comparative study of climate-change coverage in three geo-cultural regions, The Middle East, Scandinavia, and North America, and explores the link between global...... climate-change communication and regional media systems. It finds that regional variations in climate-change communication carry important communicative implications concerning perceptions of climate change's relevance and urgency...

  15. EVALUATING FUNCTIONAL REGIONS

    Directory of Open Access Journals (Sweden)

    Samo Drobne

    2012-12-01

    Full Text Available In the paper, we suggest an approach to evaluate the number and composition of functional regions. Suggested approach is based on basic characteristics of functional regions, that are (1 more intensive intra-regional than the inter-regional interactions and (2 internal social and economic heterogeneity. Those characteristics are measured by factors estimated in spatial interaction model. The approach to evaluate functional regions was applied to Slovenia for three time periods.

  16. Magnetic Splitting of Molecular Lines in Sunspot

    Science.gov (United States)

    Berdyugina, S. V.; Frutiger, C.; Solanki, S. K.

    A study of molecular lines in sunspots is of particular interest because of their high temperature and pressure sensitivity. Many of them are also magnetically sensitive, but this was not yet widely investigated. With high-resolution, high signal-to-noise Fourier spectroscopy in four Stokes parameters now available, the use of molecular lines for studying the structure of sunspots brings real gains. One is the extension of spot models, including magnetic field, up to layers, where atomic lines suffer from NLTE effects but molecules can still be treated in the LTE approximation. Equally important is the fact that since molecular lines are extremely temperature sensitive they can be used to probe the thermal and magnetic structure of the coolest parts of sunspots. We present calculations of splitting and the Stokes parameters for a number of molecular lines in the visible and near-infrared regions. Our first selections are the green system of MgH A2Π-X2σ and the TiO triplet α, γ' and γ systems as the most studied band systems in the sunspot spectrum. The calculations involve different regimes of the molecular Zeeman effect, up to the complete Paschen-Back effect for individual lines. We look for molecular lines which can be used along with atomic lines to derive magnetic, thermal and dynamic properties of the umbra.

  17. Tidally-disrupted Molecular Clouds falling to the Galactic Center

    CERN Document Server

    Tsuboi, Masato; Uehara, Kenta; Miyawaki, Ryosuke; Miyazaki, Atsushi

    2016-01-01

    We found a molecular cloud connecting from the outer region to the "Galactic Center Mini-spiral (GCMS)" which is a bundle of the ionized gas streams adjacent to Sgr A*. The molecular cloud has a filamentary appearance which is prominent in the CS J=2-1 emission line and is continuously connected with the GCMS. The velocity of the molecular cloud is also continuously connected with that of the ionized gas in the GCMS observed in the H42alpha recombination line. The morphological and kinematic relations suggest that the molecular cloud is falling from the outer region to the vicinity of Sgr A*, being disrupted by the tidal shear of Sgr A* and ionized by UV emission from the Central Cluster. We also found the SiO J=2-1 emission in the boundary area between the filamentary molecular cloud and the GCMS. There seems to exist shocked gas in the boundary area.

  18. Molecular Mechanism of Somite Development

    Directory of Open Access Journals (Sweden)

    Gulfidan Coskun

    2013-06-01

    Full Text Available From third week of gestation, notochord and the neural folds begin to gather at the center of the embryo to form the paraxial mesoderm. Paraxial mesoderm separates into blocks of cells called somitomers at the lateral sides of the neural tube of the head region. At the beginning of the third week somitomeres take ring shapes and form blocks of somites from occipital region to caudal region. Although somites are transient structures, they are extremely important in organizing the segmental pattern of vertebrate embryos. Somites give rise to the cells that form the vertebrae and ribs, the dermis of the dorsal skin, the skeletal muscles of the back, and the skeletal muscles of the body wall and limbs. Somitogenesis are formed by a genetic mechanism that is regulated by cyclical expression of genes in the Notch, Wnt and fibroblast growth factor signaling pathways. The prevailing model of the mechanism governing somitogenesis is the “clock and wave front”. Somitogenesis has components of periodicity, separation, epithelialization and axial specification. According to this model, the clock causes cells to undergo repeated oscillations, with a particular phase of each oscillation defining the competency of cells in the presomitic mesoderm to form a somite. Any disruption in this mechanism can be cause of severe segmentation defects of the vertebrae and congenital anomalies. In this review, we discuss the molecular mechanisms underlying the somitogenesis which is an important part of morphogenesis. [Archives Medical Review Journal 2013; 22(3.000: 362-376

  19. Molecular Population Genetics

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-01-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

  20. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  1. Annulation of tetrathiafulvalene to the bay region of perylenediimide.

    Science.gov (United States)

    Jaggi, Michael; Blum, Carmen; Marti, Basil S; Liu, Shi-Xia; Leutwyler, Samuel; Decurtins, Silvio

    2010-03-19

    A tetrathiafulvalene donor has been annulated to the bay region of perylenediimide affording a new pi-conjugated molecular dyad. Various electronic excited charge-transfer states are generated in different oxidation states, leading to almost full absorption in the visible to near-IR region with a high extinction coefficient.

  2. Modeling of molecular properties

    CERN Document Server

    Comba, Peter

    2011-01-01

    Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. The modeling covered in this book ranges from methods for small chemical to large biological molecules and materials. With its comprehensive coverage of important research fields in molecular and materials science, this is a must-have for all organic, inorganic and biochemists as well as materials scientists interested in applied theoretical and computational chemistry. The 28

  3. Molecularly Imprinted Membranes

    Directory of Open Access Journals (Sweden)

    Fabrizio Caldera

    2012-07-01

    Full Text Available Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed.

  4. Molecular heat pump.

    Science.gov (United States)

    Segal, Dvira; Nitzan, Abraham

    2006-02-01

    We propose a molecular device that pumps heat against a thermal gradient. The system consists of a molecular element connecting two thermal reservoirs that are characterized by different spectral properties. The pumping action is achieved by applying an external force that periodically modulates molecular levels. This modulation affects periodic oscillations of the internal temperature of the molecule and the strength of its coupling to each reservoir resulting in a net heat flow in the desired direction. The heat flow is examined in the slow and fast modulation limits and for different modulation wave forms, thus making it possible to optimize the device performance.

  5. Regional Alternative Transportation Evaluation, Region 6

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Region 6 (Colorado, Kansas, Montana, Nebraska, North Dakota, South Dakota, Utah, and Wyoming) RATE found that visitors to many stations enjoy activities that...

  6. ALMA view of the Galactic Center 50km/s molecular cloud

    CERN Document Server

    Uehara, Kenta; Kitamura, Yoshimi; Miyawaki, Ryosuke; Miyazaki, Atsushi

    2016-01-01

    We have observed the Galactic Center 50km/s molecular cloud (50MC) with ALMA to search for filamentary structures. In the CS J=2-1 emission line channel maps, we succeeded in identifying 27 molecular cloud filaments using the DisPerSE algorithm. This is the first attempt of "filament-finding" in the Galactic Center Region. These molecular cloud filaments strongly suggest that the molecular cloud filaments are also ubiquitous in the molecular clouds of the Galactic Center Region.

  7. ALMA view of the Galactic Center 50km/s molecular cloud

    Science.gov (United States)

    Uehara, Kenta; Tsuboi, Masato; Kitamura, Yoshimi; Miyawaki, Ryosuke; Miyazaki, Atsushi

    2017-01-01

    We have observed the Galactic Center 50km/s molecular cloud (50MC) with ALMA to search for filamentary structures. In the CS J=2-1 emission line channel maps, we succeeded in identifying 27 molecular cloud filaments using the DisPerSE algorithm. This is the first attempt of filament-finding in the Galactic Center Region. These molecular cloud filaments strongly suggest that the molecular cloud filaments are also ubiquitous in the molecular clouds of the Galactic Center Region.

  8. Molecular cloud complex associated with ON 1

    Energy Technology Data Exchange (ETDEWEB)

    Israel, F.P.; Wooten, H.A.

    1983-03-15

    Observations of CO with different resolutions near the compact H ii region/maser source ON 1 are presented, as well as new H/sub 2/CO and HCO/sup +/ observations. ON 1 is part of an extended molecular cloud complex with overall dimensions of 25 x 60 pc at a distance of 1.4 kpc; it appears to be the only site of star formation in at least the western part of the complex. ON 1 coincides with a compact and dense molecular cloud core (size 0.8 pc) that shows little sign of disruption indicating that ON 1 has only recently turned on. The isolation and apparent youth of ON 1 suggest that we observe here the very beginning of the star formation phase of a molecular cloud complex.

  9. Molecular chemistry and the missing mass problem in PNe

    CERN Document Server

    Kimura, Rafael K; Aleman, Isabel; 10.1051/0004-6361/201118429

    2012-01-01

    Detections of molecular lines, mainly from H2$ and CO, reveal molecular material in planetary nebulae. Observations of a variety of molecules suggest that the molecular composition in these objects differs from that found in interstellar clouds or in circumstellar envelopes. The success of the models, which are mostly devoted to explain molecular densities in specific planetary nebulae, is still partial, however. The present study aims at identifying the influence of stellar and nebular properties on the molecular composition of planetary nebulae by means of chemical models. A comparison of theoretical results with those derived from the observations may provide clues to the conditions that favor the presence of a particular molecule. A self-consistent photoionization numerical code was adapted to simulate cold molecular regions beyond the ionized zone. The code was used to obtain a grid of models and the resulting column densities are compared with those inferred from observations. Our models show that the i...

  10. A Study of the Molecular Cloud S64 with Multiple Lines of CO Isotopes

    Institute of Scientific and Technical Information of China (English)

    Lei Zhu; Yue-Fang Wu; Yue Wei

    2006-01-01

    We report on a study of the molecular cloud S64 with observations at millimeter wavelengths of multiple molecular lines of CO isotopes. A weak outflow is found, and its physical parameters are estimated. The departure of the core of S64 from the S64 HⅡ region indicates that there are still other star formation activities in that region.

  11. Molecular electronic junction transport

    DEFF Research Database (Denmark)

    Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

    2012-01-01

    Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...

  12. The Molecular Foundry (TMF)

    Data.gov (United States)

    Federal Laboratory Consortium — Founded in 2006 by the Department of Energy (DOE), the Molecular Foundry is a critical part of the DOE's National Nanotechnology Initiative, a multi-agency framework...

  13. Are there molecular signatures?

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  14. Mistakes and Molecular Evolution.

    Science.gov (United States)

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  15. Molecular Mechanisms of Preeclampsia

    OpenAIRE

    N. Vitoratos; D. Hassiakos; Iavazzo, C.

    2012-01-01

    Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

  16. Molecular marker databases.

    Science.gov (United States)

    Lai, Kaitao; Lorenc, Michał Tadeusz; Edwards, David

    2015-01-01

    The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

  17. Atomic & Molecular Interactions

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  18. Nonequilibrium molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))

    1990-11-01

    The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

  19. Molecular Imaging of Huntington's Disease.

    Science.gov (United States)

    Ciarmiello, Andrea; Giovacchini, Giampiero; Giovannini, Elisabetta; Lazzeri, Patrizia; Borsò, Elisa; Mannironi, Antonio; Mansi, Luigi

    2017-08-01

    The onset and the clinical progression of Huntington Disease (HD) is influenced by several events prompted by a genetic mutation that affects several organs tissues including different regions of the brain. In the last decades years, Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) helped to deepen the knowledge of neurodegenerative mechanisms that guide to clinical symptoms. Brain imaging with PET represents a tool to investigate the physiopathology occurring in the brain and it has been used to predict the age of onset of the disease and to evaluate the therapeutic efficacy of new drugs. This article reviews the contribution of PET and MRI in the research field on Huntington's disease, focusing in particular on some most relevant achievements that have helped recognize the molecular changes, the clinical symptoms and evolution of the disease. J. Cell. Physiol. 232: 1988-1993, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. [Molecular diagnosis of mycobacterial infections].

    Science.gov (United States)

    Fend, F; Langer, R; Hann von Weyhern, C W; Schulz, S; Miethke, T

    2007-01-01

    Tuberculosis remains a leading cause of morbidity and mortality worldwide. A rapid and reliable diagnosis and discrimination from infections with nontuberculous mycobacteria (NTM) is critical. Frequently, formalin-fixed, paraffin-embedded (FFPE) tissues remain the only source for detection of micro-organisms in suspected cases of mycobacterial infection. Recently, numerous methods, including PCR assays, in situ hybridization and immunohistochemistry have been developed for detection of mycobacteria in FFPE samples. PCR-based assays are directed either against M.tbc.-specific sequences, such as IS6110, or amplify regions common to many mycobacterial species, e.g. the 65 kDa antigen, and then require sequencing or restriction fragment length polymorphism for species identification. Whereas the detection of DNA of M.tbc. in the correct setting is always of clinical relevance, the presence of various NTM species has to be interpreted with great caution due to their ubiquitous nature. However, the routine application of molecular tests has demonstrated that NTM infections are more common than previously thought, even in non-immunosuppressed hosts. The introduction of real-time PCR technology allows precise quantification of mycobacterial DNA and can be used for species identification through melting point analysis or appropriate DNA probes. Application of these assays originally developed for clinical microbiology offer a great opportunity for diagnostic improvement in molecular pathology as compared to qualitative PCR, mainly due to an increased specificity and a lower risk of contamination. Given the clinical impact of a positive molecular result for M. tbc., future efforts have to be aimed at standardization and quality control.