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Sample records for molecular cloud-3 region

  1. A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

    NASA Technical Reports Server (NTRS)

    Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

    1995-01-01

    In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

  2. Molecular Regionalization of the Diencephalon

    PubMed Central

    Martinez-Ferre, Almudena; Martinez, Salvador

    2012-01-01

    The anatomic complexity of the diencephalon depends on precise molecular and cellular regulative mechanisms orchestrated by regional morphogenetic organizers at the neural tube stage. In the diencephalon, like in other neural tube regions, dorsal and ventral signals codify positional information to specify ventro-dorsal regionalization. Retinoic acid, Fgf8, BMPs, and Wnts signals are the molecular factors acting upon the diencephalic epithelium to specify dorsal structures, while Shh is the main ventralizing signal. A central diencephalic organizer, the zona limitans intrathalamica (ZLI), appears after neurulation in the central diencephalic alar plate, establishing additional antero-posterior positional information inside diencephalic alar plate. Based on Shh expression, the ZLI acts as a morphogenetic center, which cooperates with other signals in thalamic specification and pattering in the alar plate of diencephalon. Indeed, Shh is expressed first in the basal plate extending dorsally through the ZLI epithelium as the development proceeds. Despite the importance of ZLI in diencephalic morphogenesis the mechanisms that regulate its development remain incompletely understood. Actually, controversial interpretations in different experimental models have been proposed. That is, experimental results have suggested that (i) the juxtaposition of the molecularly heterogeneous neuroepithelial areas, (ii) cell reorganization in the epithelium, and/or (iii) planar and vertical inductions in the neural epithelium, are required for ZLI specification and development. We will review some experimental data to approach the study of the molecular regulation of diencephalic regionalization, with special interest in the cellular mechanisms underlying planar inductions. PMID:22654731

  3. Molecular emission in regions of star formation

    NASA Astrophysics Data System (ADS)

    Gusdorf, Antoine

    2008-11-01

    Recent observations show that young stars being formed eject matter at several tens of kilometers per second, in the form of 'jets' that impact the matter whose collapse is at the origin of the formation of the star. The supersonic impact between this jet and the parent interstellar cloud of the star generates a shock front, in the form of a bow-shock, which propagates in the collapsing interstellar gas, and also an inverse shock that propagates along the jet itself. The structure of these shocks depends on their velocity as well as on the physical properties of the gas in which they propagate, and specially on the value of the local magnetic field. Numerical MagnetoHydroDynamical simulations of the propagation of such shocks are a way to constrain the physical and chemical properties of the gas in which molecular lines are emitted. Interstellar shocks are modelled, both in stationary and non stationary ways, and grids of models are built for various ranges of input, preshock parameters (shock velocity, preshock density, magnetic field, and shock age for non stationary models). The case of molecular hydrogen is investigated first. Because of its particular importance (due to its large density and crucial role as a gas coolant or as a collision partner for molecular species), its level populations are solved within the shock code, as well as its population transfer. The shock wave modifies the chemical composition of the gas, partially or totally dissociating the molecular hydrogen, which is the main coolant of the gas. In the regions where molecular hydrogen still remains, H2 is collisionally excited, generating rovibrational and purely rotational transitions emission. These emissions are actually observed, from the ground in Infrared region, by ISO (Infrared Space Observatory) and Spitzer satellites. Excitation diagrams are used to compare the models with existing observations in the L1157 outflow around a young, Class 0 proto-star, confirming that non

  4. Molecular Outflows in Massive Star Forming Regions

    NASA Astrophysics Data System (ADS)

    Cunningham, Nichol

    2015-11-01

    This thesis presents millimetre continuum and molecular line observations exploring the properties of molecular outflows towards massive star forming regions. Massive stars produce some of the most energetic phenomena in the Galaxy, yet we still do not have a comprehensive understanding of how they actually form. Outflows are known to play a key role in this formation process and their properties, particularly how they change depending on the mass, luminosity and evolution of the driving source can shed light on how massive stars actually form. This thesis presents observations at both high (SMA 3 arcsecond) and low (JCMT 15 arcsecond) spatial resolution of the known jet/outflow tracers, SiO and 12CO, towards a sample massive star forming region drawn from the RMS survey. Furthermore, the presence of infall signatures is explored through observations of HCO+ and H13CO+, and the hot core nature of the regions is probed using tracers such as CH3CN, HC3N and CH3OH. SiO is detected towards approximately 50% of the massive young stellar objects and HII regions in the JCMT sample. The detection of SiO appears to be linked to the age of the RMS source, with the likely younger sources showing a stronger dependence with SiO. The presence of SiO also appears to be linked to the CO velocity, with SiO more efficiently tracing sources with higher velocity dispersions. In the MOPRA observations towards a sample of 33 RMS sources, CH3CN is detected towards 66% of the sources, with the redder likely younger sources having the largest rotational temperatures. This thesis presents the first interferometric SiO (5-4) and 12CO (2-1) observations, taken with the SMA, towards the massive star forming region G203.3166/NGC 2264-C. In this intermediate/massive star forming cluster, SiO is again tracing the youngest sources. Both the SiO and 12CO emission trace two bipolar, high velocity outflows towards the mm brightest, IR-dark, likely youngest sources in this reg! ion. In contrast the IR

  5. The magnetic field of cloud 3 in L204

    SciTech Connect

    Cashman, Lauren R.; Clemens, D. P. E-mail: clemens@bu.edu

    2014-10-01

    The L204 dark cloud complex is a nearby filamentary structure in Ophiuchus North that has no signs of active star formation. Past studies show that L204 is interacting with the nearby runaway O star, ζ Oph, and hosts a magnetic field that is coherent across parsec-length scales. Near-infrared H-band (1.6 μm) linear polarization measurements were obtained for 3896 background stars across a 1° × 1.°5 region centered on the dense Cloud 3 in L204, using the Mimir near-infrared instrument on the 1.8 m Perkins Telescope. Analysis of these observations reveals both large-scale properties and small-scale changes in the magnetic field direction in Cloud 3. In the northern and western ζ Oph facing regions of the cloud, the magnetic field appears to be pushed up against the face of the cloud. This may indicate that the UV flux from ζ Oph has compressed the magnetic field on the western edge of L204. The plane-of-sky magnetic field strength is estimated to be ∼11-26 μG using the Chandrasekhar-Fermi method. The polarimetry data also reveal that the polarization efficiency (PE ≡ P {sub H}/A {sub V}) steadily decreases with distance from ζ Oph (–0.09% ± 0.03% mag{sup –1} pc{sup –1}). Additionally, power-law fits of PE versus A {sub V} for localized samples of probe stars show steeper negative indices with distance from ζ Oph. Both findings highlight the importance of external illumination, here from ζ Oph, in aligning dust grains to embedded magnetic fields.

  6. Molecular Hydrogen Line Emission from Photodissociation Regions

    NASA Astrophysics Data System (ADS)

    Chrysostomou, Antonio

    1993-01-01

    The work presented in this thesis is dedicated to the study of the physical properties of photodissociation regions (PDRs), the surface layers of molecular clouds which are irradiated by ultraviolet radiation. The structure of PDRs is investigated with the development of an anlytical model which incorporates the essential heating and cooling mechanisms in a PDR. The main parameters in the model are the density and the incident ulttraviolet radiation field (G0) impinging on the surface which dissociates the molecules in the PDR. It is demonstrated that when the ratio (n / G0) is high (> 100 cm-3) the attenuation of ultraviolet photons is dominated by H2 self shielding, which brings the Hi/H2 transition zone close to the surface of the cloud (Av < 1). When the ratio is of order unity then the attenuation of ultraviolet photons is dominated by dust grains in the PDR. In this case, the Hi / H2 transition zone occurs at a depth of Av ~2-3. Images of the PDR in the northern bar of M17 show that there is a spatial coincidence, accurate to ~1 arcsec, of the H2 and 3.28 micron emission regions (the 3.28 micron emission being a tracer of the hot edge of the PDR delineated by the Hii / Hi transition) placing a lower limit to the density in the clumps of 105 cm-3. This coincidence is also observed in other PDR sources (eg. NGC 2023) and can be readily explained if the sources are clumpy. It is not clear in the northern bar of M17, where G0 ~104, whether shielding by dust or H2 molecules is dominated the attenuation of ultraviolet photons. A uniform, high density PDR model is sufficient to reproduce the observed H2 line intensity, however the images clearly reveal structures at the 2 arcsec level suggesting that a clumpy model is a realistic solution. Long slit K band spectroscopy measurements were taken in the northern bar of M17, where up to 16 H2 lines were identified. Analysis of the data suggests that the emission can only be explained if the H2 molecules are being excited

  7. [Molecular spectral diagnosis of star forming regions].

    PubMed

    Xi, S; Qin, S; Deng, L; Yang, J

    2001-08-01

    Stars are the basic building blocks of our universe, therefore it is one of the most important research topics in astrophysics to understand the origin and the early evolution of these objects. The current picture is that stars are formed during the collapse of a large enough self-gravitating interstellar molecular cloud. The early collapse gives birth to a fetus of a star, which is surrounded by a rotating accretion disk. The proto-star accretes interstellar matter through the disk which in turn transfer the accumulated matter to the central proto-star, then the star gets weight during the process. Observation shows that gorgeous ejection of matter always come along with the accretion process. In the presence of disks, these outflows usually escape from the system along the axis of the disk, forming so called bipolar outflows. Typical tracers of these activities are rich molecules such as CO, SiC2, C3H, C3H2 etc. Observationally, such typical molecular outflows can be detected using Doppler effect by spectroscopic measurements. Using the 13.7 m radio telescope in Delingha station of Purple Mountain Observatory, we performed a survey for 12 low temperature IRAS objects, some of the sources show high velocity properties. Detailed analysis of the Doppler profiles of IRS34 is presented. Star forming activities are clearly seen in this field. PMID:12945260

  8. HCO emission from H II-molecular cloud interface regions.

    PubMed

    Schenewerk, M S; Snyder, L E; Hollis, J M; Jewell, P R; Ziurys, L M

    1988-05-15

    A survey of well-known molecular clouds in the four strongest HCO NK-,K+ = 1(01)-0(00) hyperfine transitions has been carried out to determine the prevalence of HCO and to study its chemistry. HCO emission was observed in seven molecular clouds. Three of these, NGC 2264, W49, and NGC 7538, were not previously known sources of HCO. In addition, NGC 2024 and Sgr B2 were mapped and shown to have extensive HCO emission. The survey results show the HCO abundance to be enhanced in H II-molecular cloud interface regions and support a correlation between C+ and HCO emission. The strength of the HCO emission in NGC 2024 is interpreted in terms of this enhancement and the source structure and proximity to Earth. PMID:11538466

  9. From the H II Region to the Molecular Cloud: Determining Physical Conditions in Star Forming Regions

    NASA Astrophysics Data System (ADS)

    Abel, N. P.

    2004-12-01

    Infrared missions such as Spitzer offer new insights into the chemical evolution and star formation history of the universe. Although objects such as starburst galaxies, which are among the most luminous objects in the universe, are the primary focus, OMC-1, a lower luminosity region with superb spatial resolution, serves as a benchmark to test the physics of newly formed O stars interacting with the surrounding molecular environment. The classical approach in determining conditions in the ionized, photodissociated, and molecular regions is to treat each problem separately. In actuality, however, this is a single continuous phenomenon, linked through the transport of gas and radiation. Here we self-consistently calculate the physical conditions and emission from the hot HII region to the cold, molecular gas as a continuous hydrostatic layer. The ion states of the first 30 elements, along with the abundances of 70 molecules, are determined with the temperature and electron density. The grain physics is treated self-consistently, with grain charge transfer, single photon heating, and PAH effects all included. Additionally, level populations of all the rotational/vibrational levels of the ground electronic state of molecular hydrogen are determined (see the dissertation talk of Gargi Shaw). As a benchmark, we consider the physical conditions through OMC-1 1' west of the Trapezium, where emission-line observations of the HII region and the PDR/molecular cloud all exist. Accurately interpreting this spectrum will give us confidence that we can apply our calculations to more luminous and distant starburst galaxies. We predict the sometimes significant contribution of the HII region to important PDR emission-line diagnostics. This has consequences for the interpretation of IR observations, the deduced values of n(H) and G0 in PDRs, and hence the overall conditions in star forming regions. All calculations were developed with the spectral synthesis code Cloudy, which is

  10. Molecular characterization of a strong candidate region for schizophrenia

    SciTech Connect

    Karayiorgou, M. |; Housman, D.E.; Morrow, B.

    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.

  11. Observations of the Ionized, Neutral, and Molecular Components Associated with an Expanding H II Region

    NASA Astrophysics Data System (ADS)

    Lebrón, Mayra E.; Rodríguez, Luis F.; Lizano, Susana

    2001-10-01

    We present H92α, HI 21 cm, NH3 (1, 1) and NH3 (2, 2) lines and radio continuum observations toward the compact HII region G111.61+0.37, located in the region Sharpless 159. The dense molecular gas (traced by the ammonia lines) in the vicinity of G111.61+0.37 is distributed in clumps indicating considerable inhomogeneity in the molecular gas. A warm (Trot=47 K) ammonia clump is located just in front of the head of the cometary HII region. The photodissociated region associated to this compact HII region was detected in the HI 21 cm line. The neutral region is extended in the direction opposite to the dense molecular gas. The velocity distribution of the neutral gas suggests that the HI region is expanding in a champagne flow resembling that of the HII region, although with much lower velocities.

  12. The Physics of Molecular Shocks in Star-Forming Regions

    NASA Technical Reports Server (NTRS)

    Hollenbach, David; Cuzzi, Jeffrey (Technical Monitor)

    1996-01-01

    Molecular shocks are produced by the impact of the supersonic infall of gas and dust onto protostars and by the interaction of the supersonic outflow from the protostar with the circumstellar material. Infalling gas creates an accretion shock around the circumstellar disk which emits a unique infrared spectrum and which processes the interstellar dust as it enters the disk. The winds and jets from protostars also impact the disk, the infalling material, and the ambient molecular cloud core creating shocks whose spectrum and morphology diagnose the mass loss processes of the protostar and the orientation and structure of the star forming system. We discuss the physics of these shocks, the model spectra derived from theoretical models, and comparisons with observations of H2O masers, H2 emission, as well as other shocks tracers. We show the strong effect of magnetic fields on molecular shock structure, and elucidate the chemical changes induced by the shock heating and compression.

  13. Molecular organization of the human Raf-1 promoter region.

    PubMed Central

    Beck, T W; Brennscheidt, U; Sithanandam, G; Cleveland, J; Rapp, U R

    1990-01-01

    A genomic DNA fragment containing the Raf-1 promoter region was isolated by using a cDNA extension clone. Nucleotide sequencing of genomic DNA clones, primer extension, and S1 nuclease assays have been used to identify the 5' ends of Raf-1 RNAs. Consistent with its ubiquitous expression, the Raf-1 promoter region had features of a housekeeping gene in that it was GC-rich (HTF-like), lacked TATA and CAAT boxes, and contained heterogeneous RNA start sites and four potential binding sites for the transcription factor SP1. In addition, an octamer motif (ATTTCAT), a potential binding site for the octamer family of transcription factors, was located at -734 base pairs. The Raf-1 promoter region drove reporter gene expression 30-fold over the promoterless reporter in Cos 7 cells. Images PMID:1694010

  14. Dense molecular gas tracers in high mass star formation regions

    NASA Astrophysics Data System (ADS)

    Ma, Hong-Jun; Gao, Yu; Wu, Jing-Wen

    2016-02-01

    We report the FCRAO observations that mapped HCN (1-0), CS (2-1), HNC (1-0) and HCO+ (1-0) in ten high-mass star forming cores associated with water masers. We present velocity integrated intensity maps of the four lines for these dense cores, compare their line profiles, and derive physical properties of these cores. We find that these four tracers identify areas with similar properties in these massive dense cores, and in most cases, the emissions of HCN and HCO+ are stronger than those of HNC and CS. We also use the line ratios of HCO+/HCN, HNC/HCN and HNC/HCO+ as the diagnostics to explore the environment of these high-mass star forming regions, and find that most of the cores agree with the model that photodominated regions dominate the radiation field, except for W44, for which the radiation field is similar to an X-ray dominated region.

  15. Cluster Evolution In The Rosette Molecular Cloud Main Core Region

    NASA Astrophysics Data System (ADS)

    Ybarra, Jason E.; Román-Zúñiga, C.; Lada, E. A.; Balog, Z.

    2011-05-01

    Using Spitzer Space Telescope and Chandra X-ray data, we identify YSOs in the RMC main core region. Nearest Neighbor Method (NNM) was employed to analyze the structures and distributions of Class I/0, Class II, and Class III sources. Additionally, we developed a ratio mapping technique to investigate the progression of star formation. We discuss the distribution of YSOs, progression of star formation, and structure of the clusters in this region. This work is based in part on archival data obtained with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA. Support for this work was provided by an award issued by JPL/Caltech, Florida Space Grant Consortium, and a NASA GSRP fellowship.

  16. ROTATION OF THE WARM MOLECULAR GAS SURROUNDING ULTRACOMPACT H II REGIONS

    SciTech Connect

    Klaassen, P. D.; Wilson, C. D.; Keto, E. R.; Zhang, Q.

    2009-10-01

    We present molecular line and 1.4 mm continuum observations toward five massive star-forming regions at arcsecond resolution using the Submillimeter Array. We find that the warm molecular gas surrounding each H II region (as traced by SO{sub 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 H II region and find that this mass, when added to the derived gas mass, is a significant fraction of the dynamical mass for that region.

  17. Two γ-ray bursts from dusty regions with little molecular gas.

    PubMed

    Hatsukade, B; Ohta, K; Endo, A; Nakanishi, K; Tamura, Y; Hashimoto, T; Kohno, K

    2014-06-12

    Long-duration γ-ray bursts are associated with the explosions of massive stars and are accordingly expected to reside in star-forming regions with molecular gas (the fuel for star formation). Previous searches for carbon monoxide (CO), a tracer of molecular gas, in burst host galaxies did not detect any emission. Molecules have been detected as absorption in the spectra of γ-ray burst afterglows, and the molecular gas is similar to the translucent or diffuse molecular clouds of the Milky Way. Absorption lines probe the interstellar medium only along the line of sight, so it is not clear whether the molecular gas represents the general properties of the regions where the bursts occur. Here we report spatially resolved observations of CO line emission and millimetre-wavelength continuum emission in two galaxies hosting γ-ray bursts. The bursts happened in regions rich in dust, but not particularly rich in molecular gas. The ratio of molecular gas to dust (<9-14) is significantly lower than in star-forming regions of the Milky Way and nearby star-forming galaxies, suggesting that much of the dense gas where stars form has been dissipated by other massive stars. PMID:24919918

  18. Molecular Clouds and Star Formation in the Southern H II Regions

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Reiko; Saito, Hiro; Mizuno, Norikazu; Mine, Yoshihiro; Mizuno, Akira; Ogawa, Hideo; Fukui, Yasuo

    1999-12-01

    We have carried out extensive 13CO(J = 1-0) observations toward 23 southern H II regions associated with bright-rimmed clouds. In total, 95 molecular clouds have been identified to be associated with the H II regions. Among the 95, 57 clouds \\ are found to be associated with 204 IRAS point sources which are candidates for young stellar objects. There is a significant increase of star-formation efficiency on the side facing to the H II regions; the luminosity-to-mass ratio, defined as the ratio of the stellar luminosity to the molecular cloud mass, is higher by an order of magnitude on the near side of the H II \\ regions than that on the far side. This indicates that molecular gas facing to the H II regions is more actively forming massive s\\ tars whose luminosity is >~ 103 LO . In addition, the number density of the IRAS point sources increases by a factor of 2 on the near side of the H II regions compared with on the far side. These results strongly suggest that the active formation of massive stars on the near side of the H II regions is due to the effects of the H II regions, such as the compression of molecular material by the ionization/shock fronts. For the whole Galaxy, we estimate that the present star-formation rate under such effects is at least 0.2-0.4 MO yr-1, corresponding to a few 10% by mass.

  19. Molecular Astrophysics

    NASA Astrophysics Data System (ADS)

    Hartquist, T. W.

    2005-07-01

    Part I. Molecular Clouds and the Distribution of Molecules in the Milky Way and Other Galaxies: 1. Molecular clouds in the Milky Way P. Friberg and A. Hjalmarson; 2. Molecules in galaxies L. Blitz; Part II. Diffuse Molecular Clouds: 3. Diffuse cloud chemistry E. F. Van Dishoeck; 4. Observations of velocity and density structure in diffuse clouds W. D. Langer; 5. Shock chemistry in diffuse clouds T. W. Hartquist, D. R. Flower and G. Pineau des Forets; Part III. Quiescent Dense Clouds: 6. Chemical modelling of quiescent dense interstellar clouds T. J. Millar; 7. Interstellar grain chemistry V. Buch; 8. Large molecules and small grains in astrophysics S. H. Lepp; Part IV. Studies of Molecular Processes: 9. Molecular photoabsorption processes K. P. Kirby; 10. Interstellar ion chemistry: laboratory studies D. Smith, N. G. Adams and E. E. Ferguson; 11. Theoretical considerations on some collisional processes D. R. Bates; 12. Collisional excitation processes E. Roueff; 13. Neutral reactions at Low and High Temperatures M. M. Graff; Part V. Atomic Species in Dense Clouds: 14. Observations of atomic species in dense clouds G. J. Melnick; 15. Ultraviolet radiation in molecular clouds W. G. Roberge; 16. Cosmic ray induced photodissociation and photoionization of interstellar molecules R. Gredel; 17. Chemistry in the molecular cloud Barnard 5 S. B. Charnley and D. A. Williams; 18. Molecular cloud structure, motions, and evolution P. C. Myers; Part VI. H in Regions of Massive Star Formation: 19. Infrared observations of line emission from molecular hydrogen T. R. Geballe; 20. Shocks in dense molecular clouds D. F. Chernoff and C. F. McKee; 21. Dissociative shocks D. A. Neufeld; 22. Infrared molecular hydrogen emission from interstellar photodissociation regions A. Sternberg; Part VII. Molecules Near Stars and in Stellar Ejecta: 23. Masers J. M. Moran; 24. Chemistry in the circumstellar envelopes around mass-losing red giants M. Jura; 25. Atoms and molecules in supernova 1987a R

  20. Genetic and Molecular Mapping of Chromosome Region 85a in Drosophila Melanogaster

    PubMed Central

    Jones, W. K.; Rawls-Jr., J. M.

    1988-01-01

    Chromosome region 85A contains at least 12 genetic complementation groups, including the genes dhod, pink and hunchback. In order to better understand the organization of this chromosomal segment and to permit molecular studies of these genes, we have carried out a genetic analysis coupled with a chromosome walk to isolate the DNA containing these genes. Complementation tests with chromosomal deficiencies permitted unambiguous ordering of most of the complementation groups identified within the 85A region. Recombinant bacteriophage clones were isolated that collectively span over 120 kb of 85A DNA and these were used to produce a molecular map of the region. The breakpoint sites of a number of 85A chromosome rearrangements were localized on the molecular map, thereby delimiting regions of the DNA that contain the various genetic complementation groups. PMID:2852138

  1. STUDIES OF MOLECULAR CLOUDS ASSOCIATED WITH H II REGIONS: S175

    SciTech Connect

    Azimlu, Mohaddesseh; Fich, Michel; McCoey, Carolyn

    2009-06-15

    We are studying the impact of H II regions on star formation in their associated molecular clouds. In this paper, we present James Clerk Maxwell Telescope R x A molecular line observations of S175 and environs. This is the first within a sample of 10 H II regions and their surrounding molecular clouds selected for our study. We first make 7' x 7' maps in {sup 12}CO(2-1), which are used to investigate the structure of the cloud and to identify individual clumps. Single point observations were made in {sup 13}CO(2-1) and CS(5-4) at the peak of the {sup 12}CO(2-1) emission within each clump in order to measure the physical properties of the gas. Densities, temperatures, clump masses, peak velocities, and line widths were measured and calculated using these observations. We have identified two condensations (S175A and S175B) in the molecular cloud associated with this H II region. S175A is adjacent to the ionization front and is expected to be affected by the H II region, while S175B is too distant to be disturbed. We compare the structure and gas properties of these two regions to investigate how the molecular gas has been affected by the H II region. S175A has been heated by the H II region and partially compressed by the ionized gas front, but contrary to our expectation it is a quiescent region while S175B is very turbulent and dynamically active. Our investigation for the source of turbulence in S175B resulted in the detection of an outflow within this region.

  2. Molecular evolution of duplicated amylase gene regions in Drosophila melanogaster: evidence of positive selection in the coding regions and selective constraints in the cis-regulatory regions.

    PubMed Central

    Araki, H; Inomata, N; Yamazaki, T

    2001-01-01

    In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. F(st) between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (G'st = -0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5' flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5' flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster. PMID:11156987

  3. Observations of molecular and atomic gas in photodissociation regions. [interstellar chemistry

    NASA Technical Reports Server (NTRS)

    Jaffe, D. T.; Howe, J. E.

    1989-01-01

    Dense gas at the ionized/neutral boundaries of molecular clouds illuminated by far-UV photons plays an important role in the appearance of the neutral interstellar medium. It also is a laboratory for the study of UV-photochemistry and of a number of heating and cooling phenomena not seen elsewhere. Fine structure lines of neutral and low ionization potential species dominate the cooling in the outer part of the photodissociation regions. Observations of these lines show that the regions are dense and highly clumped. Observations of H2 and CO show that heating by UV photons plays a significant role in the excitation of molecular lines near the H II/neutral boundary. Warm CO is more abundant in these regions than predicted by the standard theoretical models. Optical reflection nebulas provide an ideal laboratory for the study of photodissocciation region phenomena.

  4. Molecular emission in dense massive clumps from the star-forming regions S231-S235

    NASA Astrophysics Data System (ADS)

    Ladeyschikov, D. A.; Kirsanova, M. S.; Tsivilev, A. P.; Sobolev, A. M.

    2016-04-01

    The paper is concerned with the study of the star-forming regions S231-S235 in radio lines of molecules of the interstellar medium—carbon monoxide (CO), ammonia (NH3), cyanoacetylene (HC3N), in maser lines—methanol (CH3OH) and water vapor (H2O). The regions S231-S235 belong to the giant molecular cloudG174+2.5. The goal of this paper is to search for new sources of emission toward molecular clumps and to estimate their physical parameters from CO and NH3 molecular lines. We obtained new detections ofNH3 andHC3Nlines in the sources WB89673 and WB89 668 which indicates the presence of high-density gas. From the CO line, we derived sizes, column densities, and masses of molecular clumps. From the NH3 line, we derived gas kinetic temperatures and number densities in molecular clumps. We determined that kinetic temperatures and number densities of molecular gas are within the limits 16-30 K and 2.8-7.2 × 103 cm-3 respectively. The shock-tracing line of CH3OH molecule at a frequency of 36.2 GHz was detected in WB89 673 for the first time.

  5. Star forming regions towards Gum 31: distribution of the molecular gas

    NASA Astrophysics Data System (ADS)

    Vazzano, M. M.; Cappa, C. E.; Vasquez, J.; Rubio, M.

    2015-08-01

    We analyze the distribution of the molecular gas associated with IRAS and 2MASS sources, young stellar objects linked to the Hii region Gum31. We based our studies on observations obtained with the APEX telescope, located in the north of Chile. We used observations of different CO isotopologues, CS(7-6) and HCO(4-3) lines. The sources are located on the edge of the Gum31 Hii region, whose shock front substantially affects the morphology of their molecular environs. The observations revealed that in the surroundings of the sources there is molecular gas associated with the nebula, which is shown by the CO(3-2) emission, with small high density clumps detected in CO(3-2).

  6. SCIENCE RESULTS INTEGRATION. BRINGING MOLECULAR BIOLOGY TECHNIQUES TO REGIONAL WATER MONITORING PROGRAMS

    EPA Science Inventory

    EPA's Office of Research and Development (ORD) develops innovative methods for use in environmental monitoring and assessment by scientists in Regions, states, and Tribes. Molecular-biology-based methods are not yet established in the environmental monitoring "tool box". SRI (Sci...

  7. An Unbiased Search for Molecular Hydrogen Outflows in the Orion B Star Forming Region

    NASA Astrophysics Data System (ADS)

    Froebrich, D.; Ziener, R.; Eislöffel, J.

    The formation of stars is often accompanied by molecular outflows. One possible tracer of these outflows is the shocked emission of molecular hydrogen in the near-infrared. We conducted an unbiased survey for molecular outflows in the Orion B region with MAGIC at the 1.23 m telescope on Calar Alto in the 1-0 S(1) line of molecular hydrogen at 2.212μm and in the K' bandpass (continuum). The observed field was about 2.7 square degrees, including the known outflows of NGC2071, HH19, HH24, HH25, HH26, HH27, HH37, HH67, HH91, HH92, HH93, HH94, HH212, HH247, HH248, HH249 and HH260. In addition to these known H2 flows, we find ten new groups of H2 emission features, and discuss their morphology and possible outflow sources.

  8. Regeneration of reptilian scales after wounding: neogenesis, regional difference, and molecular modules

    PubMed Central

    Wu, Ping; Alibardi, Lorenzo; Chuong, Cheng-Ming.

    2014-01-01

    Lizard skin can produce scales during embryonic development, tail regeneration, and wound healing; however, underlying molecular signaling and extracellular matrix protein expression remains unknown. We mapped cell proliferation, signaling and extracellular matrix proteins in regenerating and developing lizard scales in different body regions with different wound severity. Following lizard tail autotomy (self-amputation), de novo scales regenerate from regenerating tail blastema. Despite topological differences between embryonic and adult scale formation, asymmetric cell proliferation produces the newly formed outer scale surface. Regionally different responses to wounding were observed; open wounds induced better scale regeneration from tail skin than trunk skin. Molecular studies suggest NCAM enriched dermal regions exhibit higher cell proliferation associated with scale growth. β-catenin may be involved in epidermal scale differentiation. Dynamic tenascin-C expression suggests its involvement in regeneration. We conclude that different skin regions exhibit different competence for de novo scale formation. While cellular and morphogenetic paths differ during development and regeneration of lizard scale formation, they share general proliferation patterns, epithelial-mesenchymal interactions and similar molecular modules composed of adhesion and extracellular matrix molecules. PMID:24665362

  9. Molecular characterization of tea mosquito bug from tea growing regions of India.

    PubMed

    Suganthi, M; Chandrashekara, K N; Arvinth, S; Raj Kumar, R

    2016-09-01

    The tea mosquito bug, Helopeltis (Hemiptera: Miridae), is an insidious pest that poses a significant economical threat to tea plantations. As a basic first step to control this pest is authentic identification, but the inability to determine morphological characters of Helopeltis species makes this process very difficult. DNA barcoding is a reliable alternative to traditional morphological identification of this pest. Since tea is cultivated in different parts of the country, an attempt was made to molecular characterization of Helopeltis. This is the first report on molecular identification and diversity characterization of Helopeltis collected from tea growing regions of southern and north India, using cytochrome c oxidase subunit I (COI) gene of mitochondrial (mt) DNA. Beginning with the molecular identification of this pest is essential to start an effective pest management strategy, and will provide basic information for diffusion pattern, population dynamics and chemical application. PMID:26186305

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation

    SciTech Connect

    Lindner, Benjamin; Petridis, Loukas; Schulz, Roland; Smith, Jeremy C

    2013-01-01

    The precipitation of lignin onto cellulose after pretreatment of lignocellulosic biomass is an obstacle to economically viable cellulosic ethanol production. Here, 750 ns nonequilibrium molecular dynamics simulations are reported of a system of lignin and cellulose in aqueous solution. Lignin is found to strongly associate with itself and the cellulose. However, noncrystalline regions of cellulose are observed to have a lower tendency to associate with lignin than crystalline regions, and this is found to arise from stronger hydration of the noncrystalline chains. The results suggest that the recalcitrance of crystalline cellulose to hydrolysis arises not only from the inaccessibility of inner fibers but also due to the promotion of lignin adhesion.

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

    SciTech Connect

    Daumer-Haas, C.; Schuffenhauer, S.; Walther, J.U.; Portsmann, T.; Korenberg, J.R.; Schipper, R.D.

    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.

  13. Anatomy of a Photodissociation Region: High angular resolution images of molecular emission in the Orion Bar

    NASA Technical Reports Server (NTRS)

    Tauber, Jan A.; Tielens, A. G. G. M.; Meixner, Margaret; Foldsmith, Paul F.

    1994-01-01

    We present observations of the molecular component of the Orion Bar, a prototypical Photodissociation Region (PDR) illuminated by the Trapezium cluster. The high angular resolution (6 sec-10 sec) that we have achieved by combining single-dish and interferometric observations has allowed us to examine in detail the spatial and kinematic morphology of this region and to estimate the physical characteristics of the molecular gas it contains. Our observations indicate that this PDR can be essentially described as a homogeneously distributed slab of moderately dense material (approximately 5 x 10(exp 4)/cu cm), in which are embedded a small number of dense (greater than 10(exp 6)/cu cm) clumps. The latter play little or no role in determining the thickness and kinetic temperature structure of this PDR. This observational picture is largely supported by PDR model calculations for this region, which we describe in detail in this work. We also find our model predictions of the intensities of a variety of atomic and molecular lines to be in good general agreement with a number of previous observations.

  14. Radiation-magnetohydrodynamic simulations of H II regions and their associated PDRs in turbulent molecular clouds

    NASA Astrophysics Data System (ADS)

    Arthur, S. J.; Henney, W. J.; Mellema, G.; de Colle, F.; Vázquez-Semadeni, E.

    2011-06-01

    We present the results of radiation-magnetohydrodynamic simulations of the formation and expansion of H II regions and their surrounding photodissociation regions (PDRs) in turbulent, magnetized, molecular clouds on scales of up to 4 pc. We include the effects of ionizing and non-ionizing ultraviolet radiation and X-rays from population synthesis models of young star clusters. For all our simulations we find that the H II region expansion reduces the disordered component of the magnetic field, imposing a large-scale order on the field around its border, with the field in the neutral gas tending to lie along the ionization front, while the field in the ionized gas tends to be perpendicular to the front. The highest pressure-compressed neutral and molecular gas is driven towards approximate equipartition between thermal, magnetic and turbulent energy densities, whereas lower pressure neutral/molecular gas bifurcates into, on the one hand, quiescent, magnetically dominated regions and, on the other hand, turbulent, demagnetized regions. The ionized gas shows approximate equipartition between thermal and turbulent energy densities, but with magnetic energy densities that are 1-3 orders of magnitude lower. A high velocity dispersion (˜8 km s-1) is maintained in the ionized gas throughout our simulations, despite the mean expansion velocity being significantly lower. The magnetic field does not significantly brake the large-scale H II region expansion on the length and time-scales accessible to our simulations, but it does tend to suppress the smallest scale fragmentation and radiation-driven implosion of neutral/molecular gas that forms globules and pillars at the edge of the H II region. However, the relative luminosity of ionizing and non-ionizing radiation has a much larger influence than the presence or absence of the magnetic field. When the star cluster radiation field is relatively soft (as in the case of a lower mass cluster, containing an earliest spectral

  15. Gravity Binding and Pressure Bounding of HII Regions and Molecular Clouds in Interacting Galaxies

    NASA Astrophysics Data System (ADS)

    Beckman, John Etienne; Zaragoz-Cardiel, Javier; Font, Joan; Amram, Philippe; Camps-Fariña, Artemi

    2015-08-01

    We have observed a sample of 12 interacting galaxies using the Fabry-Perot interferometer GHαFaS (Galaxy Hα Fabry-Perot system) on the 4.2m William Herschel Telescope (WHT) at the Observatorio del Roque de los Muchachos, La Palma, deriving maps in Hα surface brightness, velocity and velocity dispersion. We extracted the physical parameters (Hα luminosities, velocity dispersions, and effective radii) of 1300 HII regions for the full sample with techniques for which velocity tagging is an essential step. We found two populations of HII regions, with a break at a gas mass of 106.5 solar masses. The mean density of the regions falls with radius for smaller masses, but rises with radius for larger masses. This is because in the lower mass range the HII regions are pressure bounded while in the upper range they are gravitationally bound. This analysis is underscored by using the turbulent velocity dispersion to show that the virial parameter for the regions shows values consistent with gravitational equilibrium in the upper range only. We were able to use ALMA observations of the molecular clouds in one of our objects, the Antennae galaxies, showing that for clouds with masses above 106.5 solar masses their densities increase with mass. The mass functions of the molecular clouds and HII regions in the Antennae show bimodal distributions, with the break at 106.5 solar masses clearly in evidence. We draw two conclusions of interest. Firstly the classical Larson scaling relation between surface density and mass does not operate in the upper mass range, implying higher star formation efficiency there. Secondly the similarity in the mass functions and density radius relations for the GMC’s and HII regions suggests that, at least in the upper mass range, the former remain gravitationally bound even after massive star formation has occurred.

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

    SciTech Connect

    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.

  17. A molecular face-on view of the Galactic Centre region

    NASA Astrophysics Data System (ADS)

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Handa, Toshihiro; Cohen, R. J.

    2004-04-01

    We present a method to derive positions of molecular clouds along the lines of sight from a quantitative comparison between 2.6-mm CO emission lines and 18-cm OH absorption lines, and apply it to the central kiloparsecs of the Milky Way. With some simple but justifiable assumptions, we derive a face-on distribution of the CO brightness and corresponding radial velocity in the Galactic Centre without any help of kinematical models. The derived face-on distribution of the gas is elongated and inclined so that the Galactic-eastern (positive longitude) side is closer to us. The gas distribution is dominated by a bar-like central condensation, whose apparent size is 500 × 200 pc. A ridge feature is seen to stretch from one end of the central condensation, though its elongated morphology might be artificial. The velocity field shows clear signs of non-circular motion in the central condensation. The `expanding molecular ring' feature corresponds to the peripheral region surrounding the central condensation, with the Galactic-eastern end being closer to us. These characteristics agree with a picture in which the kinematics of the gas in the central kiloparsec of the Galaxy is under the strong influence of a barred potential. The face-on distribution of the in situ pressure of the molecular gas is derived from the CO multiline analysis. The derived pressure is found to be highest in the central 100 pc. In this region, the gas is accumulating and is forming stars.

  18. The molecular gas content of the nuclear region of M33

    NASA Astrophysics Data System (ADS)

    Wilson, Christine D.; Scoville, Nick

    1989-12-01

    The nearby Sc galaxy M33 has been mapped at half-beamwidth spacing out to a 3.5 arcmin radius in the CO J = 1-0 line using the NRAO 12 m telescope. The map reveals seven large-scale features with sizes of 200-400 pc, and in several cases they are associated with spiral arms. The masses of these structures are insufficient to gravitationally or tidally bind them given their measured sizes and velocity dispersions, and distances from the center of M33. The total mass of molecular hydrogen in the region mapped is 3.4 x 10 to the 7th solar, roughly twice the mass in atomic hydrogen. Within a radius of 800 pc, no evidence is seen for an exponential decrease in the azimuthally averaged molecular hydrogen column density. The rotation curve obtained from the molecular gas agrees well with previous observations, yielding a disk mass of 5 x 10 to the 8th solar, out to a radius of 800 pc and a molecular gas mass total mass ratio of 4 percent.

  19. Statistical properties of dense molecular clouds in the Galactic center region

    NASA Astrophysics Data System (ADS)

    Miyazaki, A.; Tsuboi, M.

    We report physical properties of molecular clouds from the Galactic center r egion survey in CS J = 1-0 with the Nobeyama 45-m telescope (Tsuboi, Handa, an d Ukita, 1996). We identified over 70 molecular cloud cores in the region. We determined the statistical properties such as size-line width and LTE mass -virial theorem mass relations for the clouds. The size-line width relation is obscure in this survey data because of narrow in the radius range of the observed clouds. But the line width of the Galactic center cloud is about fi ve times larger than that of the disk clouds (Solomon et al.1987). Virial th eorem masses of the Galactic center clouds are 1-2 order of magnitude larger than the LTE masses. These are consistent with the results for larger size c louds around the Galactic center from CO J = 2-1 (Oka 1996).

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

    SciTech Connect

    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 role 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 role 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 via

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

    SciTech Connect

    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.

  2. Far Infrared Line Profiles from Photodissociation Regions and Warm Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Boreiko, R. T.; Betz, A. L.

    1998-01-01

    This report summarizes the work done under NASA Grant NAG2-1056 awarded to the University of Colorado. The aim of the project was to analyze data obtained over the past several years with the University of Colorado far-infrared heterodyne spectrometer aboard the Kuiper Airborne Observatory. Of particular interest were observations of CO and ionized carbon (C II) in photodissociation regions (PDRS) at the interface between UV-ionized H II regions and the neutral molecular clouds supporting star formation. These data, obtained with a heterodyne spectrometer having a resolution of 3.2 MHz, which is equivalent to a velocity resolution of 0.2 km s(exp -1) at 60 microns and 1.0 km s(exp -1) at 300 microns, were analyzed to obtain physical parameters such as density and temperature in the observed PDR.

  3. Mitochondrial DNA control region of three mackerels, genus Rastrelliger: structure, molecular diversity and phylogenetic relationship.

    PubMed

    Jondeung, Amnuay; Karinthanyakit, Wirangrong

    2016-07-01

    The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era. PMID:26119119

  4. An infrared study of the NGC 1977 H II region/molecular cloud interface

    NASA Technical Reports Server (NTRS)

    Makinen, P.; Harvey, P. M.; Wilking, B. A.; Evans, N. J., II

    1985-01-01

    The results of an infrared study of the H II region NGC 1977 and the adjacent dense molecular cloud are reported. Extensive far-infrared maps with 45 arcsec resolution allow the spatial structure of the dust temperature and optical depth variations across the ionization front to be delineated. Analysis of the dust energetics indicates that the only significant energy source is the B1 V star HD 37018 which ionizes the H II region. This result, together with a favorable geometry, provides a good opportunity to determine the ratio of ultraviolet absorption efficiency to far-infrared emission efficiency, 790 + 460 or - 180. Analysis of the gas energetics indicates that collisions with warm dust grains can explain the observed gas temperatures.

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

    NASA Astrophysics Data System (ADS)

    Kim, Jeong-Gyu; Kim, Woong-Tae; Ostriker, Eve C.

    2016-03-01

    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 semianalytic 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 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 semianalytic 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 ɛmin required for cloud disruption as a function of the cloud's total mass and mean surface density. Within the adopted spherical geometry, we find that typical giant molecular clouds in normal disk galaxies have ɛmin ≲ 10%, with comparable gas and radiation pressure effects on shell expansion. Massive cluster-forming clumps require a significantly higher efficiency of ɛmin ≳ 50% for disruption, produced mainly by radiation-driven expansion. The disruption time is typically of the order of a free-fall timescale, suggesting that the cloud disruption occurs rapidly once a sufficiently luminous H II region is formed. We also discuss limitations of the spherical idealization.

  6. Molecular Characterization of HIV-1 Subtype C gp-120 Regions Potentially Involved in Virus Adaptive Mechanisms

    PubMed Central

    Cenci, Alessandra; D'Avenio, Giuseppe; Tavoschi, Lara; Chiappi, Michele; Becattini, Simone; Narino, Maria del Pilar; Picconi, Orietta; Bernasconi, Daniela; Fanales-Belasio, Emanuele; Vardas, Eftyhia; Sukati, Hosea; Presti, Alessandra Lo; Ciccozzi, Massimo; Monini, Paolo; Ensoli, Barbara; Grigioni, Mauro; Buttò, Stefano

    2014-01-01

    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. PMID:24788065

  7. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

    PubMed Central

    Araya, Carlos L.; Cenik, Can; Reuter, Jason A.; Kiss, Gert; Pande, Vijay S.; Snyder, Michael P.; Greenleaf, William J.

    2015-01-01

    Cancer sequencing studies have primarily identified cancer-driver genes by the accumulation of protein-altering mutations. An improved method would be annotation-independent, sensitive to unknown distributions of functions within proteins, and inclusive of non-coding drivers. We employed density-based clustering methods in 21 tumor types to detect variably-sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and non-coding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs reveal spatial clustering of mutations at molecular domains and interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated among tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally-agnostic driver identification. PMID:26691984

  8. Formation pumping of molecular hydrogen in the Messier 17 photodissociation region

    NASA Astrophysics Data System (ADS)

    Burton, M. G.; Londish, D.; Brand, P. W. J. L.

    2002-07-01

    We have imaged the emission from the near-infrared v=1-0 S(1), 1-0 S(7), 2-1 S(1) and 6-4 O(3) lines of molecular hydrogen in the Northern and South Western Bars of M17, together with the hydrogen Brγ and Br10 lines. This includes the first emission-line image ever to be obtained of a line from the highly excited v=6 level of molecular hydrogen. In both Bars, the H2 emission is generally distributed in clumps along filamentary features. The 1-0 S(1) and 2-1 S(1) images have similar morphologies. Together with their relative line ratios, this supports a fluorescent origin for their emission, within a photodissociation region. The SW-Bar contains a clumpy medium, but in the N-Bar the density is roughly constant. The 1-0 S(7) line image is also similar to the 1-0 S(1) image, but the 6-4 O(3) image is significantly different from it. Since the emission wavelengths of these two lines are similar (1.748 to 1.733μm), this cannot be due to differential extinction between the v=6 and the v=1 lines. We attribute the difference to the pumping of newly formed H2 into the v=6, or to a nearby, level. However, this also requires a time-dependent photodissociation region (where molecule formation does not balance dissociation), rather than it to be in steady state, and/or for the formation spectrum to vary with position in the source. If this interpretation of formation pumping of molecular hydrogen is correct, it is the first clear signature from this process to be seen.

  9. Molecular evidence of synaptic pathology in the CA1 region in schizophrenia

    PubMed Central

    Matosin, Natalie; Fernandez-Enright, Francesca; Lum, Jeremy S; Engel, Martin; Andrews, Jessica L; Gassen, Nils C; Wagner, Klaus V; Schmidt, Mathias V; Newell, Kelly A

    2016-01-01

    Alterations of postsynaptic density (PSD)95-complex proteins in schizophrenia ostensibly induce deficits in synaptic plasticity, the molecular process underlying cognitive functions. Although some PSD95-complex proteins have been previously examined in the hippocampus in schizophrenia, the status of other equally important molecules is unclear. This is especially true in the cornu ammonis (CA)1 hippocampal subfield, a region that is critically involved in the pathophysiology of the illness. We thus performed a quantitative immunoblot experiment to examine PSD95 and several of its associated proteins in the CA1 region, using post mortem brain samples derived from schizophrenia subjects with age-, sex-, and post mortem interval-matched controls (n=20/group). Our results indicate a substantial reduction in PSD95 protein expression (−61.8%). Further analysis showed additional alterations to the scaffold protein Homer1 (Homer1a: +42.9%, Homer1b/c: −24.6%), with a twofold reduction in the ratio of Homer1b/c:Homer1a isoforms (P=0.011). Metabotropic glutamate receptor 1 (mGluR1) protein levels were significantly reduced (−32.7%), and Preso, a protein that supports interactions between Homer1 or PSD95 with mGluR1, was elevated (+83.3%). Significant reduction in synaptophysin (−27.8%) was also detected, which is a validated marker of synaptic density. These findings support the presence of extensive molecular abnormalities to PSD95 and several of its associated proteins in the CA1 region in schizophrenia, offering a small but significant step toward understanding how proteins in the PSD are altered in the schizophrenia brain, and their relevance to overall hippocampal and cognitive dysfunction in the illness. PMID:27430010

  10. Molecular Epidemiological Characterization and Health Burden of Thalassemias in the Chaoshan Region, People's Republic of China.

    PubMed

    Zheng, Xiangbin; Lin, Min; Yang, Hui; Pan, Mei-Chen; Cai, Ying-Mu; Wu, Jiao-Ren; Lin, Fen; Zhan, Xiao-Fen; Luo, Zhao-Yun; Yang, Hui-Tian; Yang, Li-Ye

    2016-01-01

    Thalassemia is one of the most prevalent inherited disease in southern China. However, there have been only a few epidemiological studies of thalassemia in the Chaoshan region of Guangdong Province, People's Republic of China (PRC). A total of 6231 unrelated subjects in two main geographical cities of the Chaoshan region was analyzed for thalassemia. Seven hundred and thirty-six cases of suspected thalassemia carriers with microcytosis [mean corpuscular volume (MCV) <82.0 fL] were found by complete blood cell (CBC) count, and were tested by reverse dot-blot gene chip to reveal a total of 331 mutant chromosomes, including 278 α-thalassemia (α-thal) alleles and 53 β-thalassemia (β-thal) alleles. The most common α-thal mutations were the Southeast Asian (- -(SEA)), followed by the -α(3.7) (rightward) and -α(4.2) (leftward) deletions. The two most common β-thal mutations were HBB: c.316-197C>T and HBB: c.126_129delCTTT, accounting for 69.81% of the β-thal defects in the studied individuals. In addition, a rare mutation, Cap +1 (A>C) (HBB: c.-50A>C) was described for the first time in the Chaoshan region. Our results gave a heterozygote frequency of 5.31% for common α- and β-thal in the Chaoshan region, and also indicated a higher prevalence of thalassemia with a heterozygote frequency of 6.29% in Chaozhou, followed by Shantou (3.37%). This study provided a detailed prevalence and molecular characterization of thalassemia in the Chaoshan region, and will be valuable for developing a strategy for prevention of thalassemia and reducing excessive health care costs in this area. PMID:26865073

  11. MOLECULAR CLUMPS AND INFRARED CLUSTERS IN THE S247, S252, AND BFS52 REGIONS

    SciTech Connect

    Shimoikura, Tomomi; Dobashi, Kazuhito; Saito, Hiro; Nakamura, Fumitaka; Matsumoto, Tomoaki; Nishimura, Atsushi; Kimura, Kimihiro; Onishi, Toshikazu; Ogawa, Hideo

    2013-05-01

    We present results of the observations carried out toward the S247, S252, and BFS52 H II regions with various molecular lines using the 1.85 m radio telescope and the 45 m telescope at Nobeyama Radio Observatory. There are at least 11 young infrared clusters (IR clusters) within the observed region. We found that there are two velocity components in {sup 12}CO (J = 2-1), and also that their spatial distributions show an anti-correlation. The IR clusters are located at their interfaces, suggesting that two distinct clouds with different velocities are colliding with each other, which may have induced the cluster formation. Based on {sup 13}CO (J = 1-0) and C{sup 18}O (J = 1-0) observations, we identified 16 clumps in and around the three H II regions. Eleven of the clumps are associated with the IR clusters and the other five clumps are not associated with any known young stellar objects. We investigated variations in the velocity dispersions of the 16 clumps as a function of the distance from the center of the clusters or the clumps. Clumps with clusters tend to have velocity dispersions that increase with distance from the cluster center, while clumps without clusters show a flat velocity dispersion over the clump extents. A {sup 12}CO outflow has been found in some of the clumps with IR clusters but not in the other clumps, supporting a strong relation of these clumps to the broader velocity dispersion region. We also estimated a mean star formation efficiency of {approx}30% for the clumps with IR clusters in the three H II regions.

  12. Brain regions and molecular pathways responding to food reward type and value in honey bees.

    PubMed

    McNeill, M S; Kapheim, K M; Brockmann, A; McGill, T A W; Robinson, G E

    2016-03-01

    The ability of honey bees to evaluate differences in food type and value is crucial for colony success, but these assessments are made by individuals who bring food to the hive, eating little, if any, of it themselves. We tested the hypothesis that responses to food type (pollen or nectar) and value involve different subsets of brain regions, and genes responsive to food. mRNA in situ hybridization of c-jun revealed that brain regions responsive to differences in food type were mostly different from regions responsive to differences in food value, except those dorsal and lateral to the mushroom body calyces, which responded to all three. Transcriptomic profiles of the mushroom bodies generated by RNA sequencing gave the following results: (1) responses to differences in food type or value included a subset of molecular pathways involved in the response to food reward; (2) genes responsive to food reward, food type and food value were enriched for (the Gene Ontology categories) mitochondrial and endoplasmic reticulum activity; (3) genes responsive to only food and food type were enriched for regulation of transcription and translation; and (4) genes responsive to only food and food value were enriched for regulation of neuronal signaling. These results reveal how activities necessary for colony survival are channeled through the reward system of individual honey bees. PMID:26566901

  13. Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

    PubMed Central

    Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K. P.; Woo, Patrick C. Y.

    2015-01-01

    Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study. PMID:26506340

  14. Studies of Molecular Lasers, Atmospheric Molecules and Imaging in the Millimeter/submillimeter Spectral Region.

    NASA Astrophysics Data System (ADS)

    Crownover, Richard L.

    The millimeter/submillimeter portion of the electromagnetic spectrum is able to address fundamental questions in astronomy, cosmology, atmospheric science, molecular physics, quantum electronics, plasma physics, and other fields. Also, this spectral region has transmission characteristics which make it desirable for communications within the atmosphere and potentially for imaging. In order to demonstrate that detector technology in this region is sufficiently mature to permit the construction of reliable quasi-optical devices using off the shelf components, we have generated passive images using a broadband detector cooled to 0.35 K with a commercially produced ^3He refrigerator. We have shown the possibility of an extremely simple, highly sensitive, passive imaging system which operates in an attractive spectral region and is capable of upscaling to provide practical spatial resolution and real time operation over useful ranges. International public concern about acid rain, ozone depletion, and urban smog has spurred intense study of atmospheric chemistry. Spectra of two minor atmospheric constituents (HNO_3, ^ {16}O^{18}O) have been studied in the laboratory to assist with remote monitoring of atmospheric dynamics, modelling of atmospheric chemistry, and selection of communication frequencies which have some immunity to atmospheric perturbations. The nitric acid observations have allowed us to determine effective rotational constants for the first five vibrational states (nu_0, nu_9 , nu_7, nu _6, nu_8) and assign transitions in the perturbed nu_5 state. In addition, the concentration of ^{16}O^{18 }O in interstellar molecular clouds has been identified as a key discriminator between competing models of stellar formation; the measurements presented here will assist astronomers attempting to determine the abundance of this species in molecular clouds and proto-stars. We have recorded and analyzed the spectra of two important lasing species (^{12} CH_3F, ^{12 }CH_2

  15. Molecular Cores in Different Evolutionary Stages near Luminous IRAS Sources and UC HII Regions

    NASA Astrophysics Data System (ADS)

    Zhu, Lei; Wu, Yue-Fang

    2007-06-01

    We report the results of 12CO and 13CO J=1 0 observations of eight candidates of Ultra-Compact (UC) HII regions with the Purple Mountain Observatory (PMO) Qinghai 13.7 -m telescope, which resulted in revealing 11 molecular cores. Their masses range from 130 to 1.7×104 Modot, with different spatial scales (1~ 6 pc). Also presented are the relevant HCO+ J=1 0 maps, which enabled us to investigate more detailed structures of these cores. Further comparisons show that four of the cores deviated from the centers of infrared (MIR) emission of Midcourse Space Experiment (MSX), while others correspond either to bright MIR sources or diffuse MIR background. This indicates various evolutionary phases of the cores, including quite early ones for those without MIR sources.

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

    PubMed

    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. PMID:26166496

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

    PubMed

    Zhang, Jiapu; Wang, Feng

    2014-01-01

    Prion diseases which are serious neurodegenerative diseases that affect humans and animals occur in various of species. Unlike many other neurodegenerative diseases affected by amyloid, prion diseases can be highly infectious. Prion diseases occur in many species. In humans, prion diseases include the fatal human neurodegenerative diseases such as Creutzfeldt-Jakob Disease (CJD), Fatal Familial Insomnia (FFI), Gerstmann-Strussler-Scheinker syndrome (GSS) and Kuru etc. In animals, prion diseases are related to the bovine spongiform encephalopathy (BSE or 'mad-cow' disease) in cattle, the chronic wasting disease (CWD) found in deer and elk, and scrapie seen in sheep and goats, etc. More seriously, the fact that transmission of the prion diseases across the species barrier to other species such as humans has caused a major public health concern worldwide. For example, the BSE in Europe, the CWD in North America, and variant CJDs (vCJDs) in young people of UK. Fortunately, it is discovered that the hydrophobic region of prion proteins (PrP) controls the formation of diseased prions (PrP(Sc)), which provide some clues in control of such diseases. This article provides a detailed survey of recent studies with respect to the PrP hydrophobic region of human PrP(110-136) using molecular dynamics studies. PMID:25373387

  18. Far Infrared Line Profiles from Photodissociation Regions and Warm Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Boreiko, R. T.; Betz, A. L.

    1998-01-01

    This report summarizes the work done under NASA Grant NAG2-1056 awarded to the University of Colorado. The aim of the project was to analyze data obtained over the past several years with the University of Colorado far-infrared heterodyne spectrometer (Betz & Boreiko 1993) aboard the Kuiper Airborne Observatory. Of particular interest were observations of CO and ionized carbon (C II) in photodissociation regions (PDRs) at the interface between UV-ionized H II regions and the neutral molecular clouds supporting star formation. These data, obtained with a heterodyne spectrometer having a resolution of 3.2 MHz, which is equivalent to a velocity resolution of 0.2 km/s at 60 microns and 1.0 km/s at 300 microns, were analyzed to obtain physical parameters such as density and temperature in the observed PDR. The publication resulting from the work reported here is appended. No inventions were made nor was any federally owned property acquired as a result of the activities under this grant.

  19. Far Infrared Line Profiles from Photodissociation Regions and Warm Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Boreiko, R. T.; Betz, A. L.

    1998-01-01

    This report summarizes the work done under NASA Grant NAG2-1056 awarded to the University of Colorado. The aim of the project was to analyze data obtained over the past several years with the University of Colorado far-infrared heterodyne spectrometer (Betz Boreiko 1993) aboard the Kuiper Airborne Observatory. Of particular interest were observations of CO and ionized carbon (C II) in photodissociation regions (PDRS) at the interface between UV-ionized H II regions and the neutral molecular clouds supporting star formation. These data, obtained with a heterodyne spectrometer having a resolution of 3.2 MHz, which is equivalent to a velocity resolution of 0.2 km/s at 60 microns and 1.0 km/s at 300 microns, were analyzed to obtain physical parameters such as density and temperature in the observed PDR. The publication resulting from the work reported here is appended. No inventions were made nor was any federally owned property acquired as a result of the activities under this grant.

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Hα emission-line stars in molecular clouds. II. The M 42 region

    NASA Astrophysics Data System (ADS)

    Pettersson, Bertil; Armond, Tina; Reipurth, Bo

    2014-10-01

    We present a deep survey of Hα emission-line stars in the M 42 region using wide-field objective prism films. A total of 1699 Hα emission-line stars were identified, of which 1025 were previously unknown, within an area of 5.̊5 × 5.̊5 centred on the Trapezium Cluster. We present Hα strength estimates, positions, and JHKs photometry extracted from 2MASS, and comparisons to previous surveys. The spatial distribution of the bulk of the stars follows the molecular cloud as seen in CO and these stars are likely to belong to the very young population of stars associated with the Orion Nebula Cluster. Additionally, there is a scattered population of Hα emission-line stars distributed all over the region surveyed, which may consist partly of foreground stars associated with the young NGC 1980 cluster, as well as some foreground and background dMe or Be stars. The present catalogue adds a large number of candidate low-mass young stars belonging to the Orion population, selected independently of their infrared excess or X-ray emission. Full Table 2 is only available in electronic form at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/570/A30

  2. Diversity and distribution of avian haematozoan parasites in the western Indian Ocean region: a molecular survey.

    PubMed

    Ishtiaq, Farah; Beadell, Jon S; Warren, Ben H; Fleischer, Robert C

    2012-02-01

    The genetic diversity of haematozoan parasites in island avifauna has only recently begun to be explored, despite the potential insight that these data can provide into the history of association between hosts and parasites and the possible threat posed to island endemics. We used mitochondrial DNA sequencing to characterize the diversity of 2 genera of vector-mediated parasites (Plasmodium and Haemoproteus) in avian blood samples from the western Indian Ocean region and explored their relationship with parasites from continental Africa. We detected infections in 68 out of 150 (45·3%) individuals and cytochrome b sequences identified 9 genetically distinct lineages of Plasmodium spp. and 7 lineages of Haemoproteus spp. We found considerable heterogeneity in parasite lineage composition across islands, although limited sampling may, in part, be responsible for perceived differences. Two lineages of Plasmodium spp. and 2 lineages of Haemoproteus spp. were shared by hosts in the Indian Ocean and also on mainland Africa, suggesting that these lineages may have arrived relatively recently. Polyphyly of island parasites indicated that these parasites were unlikely to constitute an endemic radiation and instead probably represent multiple colonization events. This study represents the first molecular survey of vector-mediated parasites in the western Indian Ocean, and has uncovered a diversity of parasites. Full understanding of parasite community composition and possible threats to endemic avian hosts will require comprehensive surveys across the avifauna of this region. PMID:22075855

  3. Communication: Phase diagram of C36 by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    NASA Astrophysics Data System (ADS)

    Abramo, M. C.; Caccamo, C.; Costa, D.; Munaò, G.

    2014-09-01

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. We first show that free energies obtained via thermodynamic integrations along isotherms displaying "van der Waals loops," are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C36, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400-1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C36 fullerite and of its liquid state, at variance with what previously experienced for C60.

  4. Molecular cytogenetic analysis of Xq critical regions in premature ovarian failure

    PubMed Central

    2013-01-01

    Background One of the frequent reasons for unsuccessful conception is premature ovarian failure/primary ovarian insufficiency (POF/POI) that is defined as the loss of functional follicles below the age of 40 years. Among the genetic causes the most common one involves the X chromosome, as in Turner syndrome, partial X deletion and X-autosome translocations. Here we report a case of a 27-year-old female patient referred to genetic counselling because of premature ovarian failure. The aim of this case study to perform molecular genetic and cytogenetic analyses in order to identify the exact genetic background of the pathogenic phenotype. Results For premature ovarian failure disease diagnostics we performed the Fragile mental retardation 1 gene analysis using Southern blot technique and Repeat Primed PCR in order to identify the relationship between the Fragile mental retardation 1 gene premutation status and the premature ovarion failure disease. At this early onset, the premature ovarian failure affected patient we detected one normal allele of Fragile mental retardation 1 gene and we couldn’t verify the methylated allele, therefore we performed the cytogenetic analyses using G-banding and fluorescent in situ hybridization methods and a high resolution molecular cytogenetic method, the array comparative genomic hybridization technique. For this patient applying the G-banding, we identified a large deletion on the X chromosome at the critical region (ChrX q21.31-q28) which is associated with the premature ovarian failure phenotype. In order to detect the exact breakpoints, we used a special cytogenetic array ISCA plus CGH array and we verified a 67.355 Mb size loss at the critical region which include total 795 genes. Conclusions We conclude for this case study that the karyotyping is definitely helpful in the evaluation of premature ovarian failure patients, to identify the non submicroscopic chromosomal rearrangement, and using the array CGH technique we can

  5. STRUCTURAL VARIATION OF MOLECULAR GAS IN THE SAGITTARIUS ARM AND INTERARM REGIONS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Sugimoto, Masahiro; Koda, Jin; Handa, Toshihiro

    2012-06-20

    We have carried out survey observations toward the Galactic plane at l Almost-Equal-To 38 Degree-Sign in the {sup 12}CO and {sup 13}CO J = 1-0 lines using the Nobeyama Radio Observatory 45 m telescope. A wide area (0.{sup 0}8 Multiplication-Sign 0.{sup 0}8) was mapped with high spatial resolution (17''). The line of sight samples the gas in both the Sagittarius arm and the interarm regions. The present observations reveal how the structure and physical conditions vary across a spiral arm. We classify the molecular gas in the line of sight into two distinct components based on its appearance: the bright and compact B component and the fainter and diffuse (i.e., more extended) D component. The B component is predominantly seen at the spiral arm velocities, while the D component dominates at the interarm velocities and is also found at the spiral arm velocities. We introduce the brightness distribution function and the brightness distribution index (BDI, which indicates the dominance of the B component) in order to quantify the map's appearance. The radial velocities of BDI peaks coincide with those of high {sup 12}CO J = 3-2/{sup 12}CO J = 1-0 intensity ratio (i.e., warm gas) and H II regions, and tend to be offset from the line brightness peaks at lower velocities (i.e., presumably downstream side of the arm). Our observations reveal that the gas structure at small scales changes across a spiral arm: bright and spatially confined structures develop in a spiral arm, leading to star formation at the downstream side, while extended emission dominates in the interarm region.

  6. Molecular analysis of the glpFKX regions of Escherichia coli and Shigella flexneri.

    PubMed Central

    Truniger, V; Boos, W; Sweet, G

    1992-01-01

    We have identified a new gene, glpX, belonging to the glp regulon of Escherichia coli, located directly downstream of the glpK gene. The transcription of glpX is inducible with glycerol and sn-glycerol-3-phosphate and is constitutive in a glpR mutant. glpX is the third gene in the glpFKX operon. The function of GlpX remains unknown. GlpX has an apparent molecular weight of 40,000 on sodium dodecyl sulfate-polyacrylamide gels. In addition to determining the E. coli glpX sequence, we also sequenced the corresponding glpFKX region originating from Shigella flexneri, which after transfer into E. coli was instrumental in elucidating the function of glpF in glycerol transport (D. P. Richey and E. C. C. Lin, J. Bacteriol. 112:784-790, 1972). Sequencing of the glpFKX region of this hybrid strain revealed an amber mutation instead of the tryptophan 215 codon in glpF. The most striking difference between the E. coli and S. flexneri DNA was found directly behind glpK, where two repetitive (REP) sequences were present in S. flexneri, but not in the E. coli sequence. The presence or absence of these REP sequences had no effect on transport or on growth on glycerol. Not including the REP sequence-containing region, only 1.1% of a total of 2,167 bp sequenced was different in the two sequences. Comparison of the sequence with those in the EMBL data library revealed a 99% identity between the last third of glpX and the first part of a gene called mvrA. We show that the cloned mvrA gene (M. Morimyo, J. Bacteriol. 170:2136-2142, 1988) originated from the 88-min region of the Escherichia coli chromosome and not, as reported, from the 7-min region and that the gene product identified as MvrA is in fact encoded by a gene distal to glpX. Images PMID:1400248

  7. Molecular Epidemiology of Enterovirus 71 Infection in the Central Region of Taiwan from 2002 to 2012

    PubMed Central

    Lin, Yu-Ting; Huang, Szu-Wei; Liu, Hsin-Fu; Wang, John; Chen, Yi-Ming Arthur

    2013-01-01

    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. PMID:24391812

  8. Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities

    PubMed Central

    Chen, Chun-Chun; Winkler, Candace M.; Pfenning, Andreas R.; Jarvis, Erich D.

    2013-01-01

    In our companion study (Jarvis et al., 2013) we used quantitative brain molecular profiling to discover that distinct subdivisions in the avian pallium above and below the ventricle and the associated mesopallium lamina have similar molecular profiles, leading to a hypothesis that they may form as continuous subdivisions around the lateral ventricle. To explore this hypothesis, here we profiled the expression of 16 genes at 8 developmental stages. The genes included those that define brain subdivisions in the adult and some that are also involved in brain development. We found that phyletic hierarchical cluster and linear regression network analyses of gene expression profiles implicated single and mix ancestry of these brain regions at early embryonic stages. Most gene expression-defined pallial subdivisions began as one ventral or dorsal domain that later formed specific folds around the lateral ventricle. Subsequently a clear ventricle boundary formed, partitioning them into dorsal and ventral pallial subdivisions surrounding the mesopallium lamina. These subdivisions each included two parts of the mesopallium, the nidopallium and hyperpallium, and the arcopallium and hippocampus, respectively. Each subdivision expression profile had a different temporal order of appearance, similar in timing to the order of analogous cell types of the mammalian cortex. Further, like the mammalian pallium, expression in the ventral pallial subdivisions became distinct during pre-hatch development, whereas the dorsal portions did so during post-hatch development. These findings support the continuum hypothesis of avian brain subdivision development around the ventricle and influence hypotheses on homologies of the avian pallium with other vertebrates. PMID:23818174

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

    We have carried out a high spectral resolution (λ/Δλ ~ 6800-9700) line survey towards the Orion Kleinmann-Low (KL) cluster from 44 to 188 μm. The observations were taken with the Long Wavelength Spectrometer (LWS) in Fabry-Pérot 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 photodissociation region (PDR) or shocked gas and [O III] and [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 (FIR) 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. Analysis of the [OI] and [CII] fine structure lines indicates that although a shock model can reproduce the observed [OI] surface brightness levels, it falls short of the observed [CII] level by more than a factor of 30. A PDR model can reproduce the [OI] 63.2 μm and [CII] surface brightness levels within 35 per cent, although overpredicting the LWS [OI] 145.5 μm-emission by a factor of 2.7. The 70 water lines and 22 OH lines detected by the survey appear with mainly P Cygni profiles at the shortest survey wavelengths and with mainly pure emission profiles at the longest survey wavelengths. The emission and absorption velocity peaks of the water and OH lines indicate that they are associated with gas expanding in the outflow from the KL cluster. The estimated column densities are (2-5) × 1014 cm-2 for H2O and (2.5-5.1) × 1016 cm-2 for OH. The 26 detected CO lines confirm the presence of three distinct components, with temperature and column density combinations ranging from 660 K, 6 × 1017

  10. Molecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region

    PubMed Central

    Ieda, Shinsuke; Moriyama, Masafumi; 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. PMID:24979710

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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 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 Sgr 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.

  12. Molecular mapping of genomic regions underlying barley yellow dwarf tolerance in cultivated oat (Avena sativa L.).

    PubMed

    Zhu, S; Kolb, F L; Kaeppler, H F

    2003-05-01

    Barley yellow dwarf (BYD) is one of the most important viral diseases in small grains, including oat (Avena sativa L.). Breeding for BYD tolerance is an effective and efficient means to control the disease. Characterization of major sources of tolerance, and identification of marker and the trait associations, will directly benefit breeding for BYD tolerance. Genomic regions underlying BYD tolerance were mapped and characterized in an oat population consisting of 152 recombinant inbred lines from the cross of 'Ogle' (tolerant)/MAM17-5 (sensitive). Tolerance was evaluated in replicated field trials across 2 years under artificial inoculation with viruliferous aphids harboring BYD virus isolate PAV-IL. Composite interval mapping was used for quantitative trait loci (QTLs) analysis with a framework map consisting of 272 molecular markers. Four QTLs, BYDq1, BYDq2, BYDq3 and BYDq4, for BYD tolerance were identified on linkage groups OM1, 5, 7 and 24, respectively. All but BYDq2 were consistently detected across both years. Significant epistasis was found between some QTLs. The final model including the epistatic effect explained 50.3 to 58.2% of the total phenotypic variation for BYD tolerance. Some QTLs for BYD tolerance were closely linked to QTLs for plant height and days to heading. Potential problems with QTL mapping for BYD tolerance have been discussed. The identified association of markers and tolerance should be useful to pyramid favorable alleles for BYD tolerance into individual oat lines. PMID:12748782

  13. Excitation of the molecular gas in the nuclear region of M 82

    NASA Astrophysics Data System (ADS)

    Loenen, A. F.; van der Werf, P. P.; 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.

    2010-10-01

    We present high-resolution HIFI spectroscopy of the nucleus of the archetypical starburst galaxy M 82. Six 12CO lines, 2 13CO lines and 4 fine-structure lines have been 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 = 103.5 cm-3) clouds, with column densities of NH = 1021.5 cm-2 and a relatively low UV radiation field (G0 = 102). The remaining gas is predominantly found in clouds with higher densities (n = 105 cm-3) and radiation fields (G0 = 102.75), but somewhat lower column densities (NH = 1021.2 cm-2). The highest J CO lines are dominated by a small (1% relative surface filling) component, with an even higher density (n = 106 cm-3) and UV field (G0 = 103.25). These results show the strength of multi-component modelling for interpretating the integrated properties of galaxies.

  14. A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics.

    PubMed

    Yerle, M; Echard, G; Robic, A; Mairal, A; Dubut-Fontana, C; Riquet, J; Pinton, P; Milan, D; Lahbib-Mansais, Y; Gellin, J

    1996-01-01

    A panel of 27 pig x rodent somatic cell hybrids was produced and characterized cytogenetically. The first step of this study consisted of hybridizing a SINE probe to GTG-banded metaphases of each hybrid clone in order to count and identify the normal pig chromosomes and to detect rearranged ones. The second step consisted of using the DNA of each clone as a probe after pIRS-PCR (porcine interspersed repetitive sequence-polymerase chain reaction) amplification to highly enrich it in pig sequences. These probes, hybridized to normal pig metaphase chromosomes, enabled the identification of the complete porcine complement in the hybrid lines. Whole chromosomes and fragments were characterized quickly and precisely, and results were compared. In addition to this cytogenetic characterization, molecular verification was also carried out by using primers specific to six microsatellites and to one gene previously mapped to pig chromosomes. The results obtained allow us to conclude that we have produced a panel that is informative for all porcine chromosomes. This panel constitutes a highly efficient tool to establish not only assignments of genes and markers but also regional localizations on pig chromosomes. PMID:8697807

  15. Surveillance of Carbapenem-Resistant Klebsiella pneumoniae: Tracking Molecular Epidemiology and Outcomes through a Regional Network

    PubMed Central

    Perez, Federico; Rudin, Susan D.; Cober, Eric; Hanrahan, Jennifer; Ziegler, Julie; Webber, Raymond; Fox, Jacqueline; Mason, Pamela; Richter, Sandra S.; Cline, Marianne; Hall, Geraldine S.; Kaye, Keith S.; Jacobs, Michael R.; Kalayjian, Robert C.; Salata, Robert A.; Segre, Julia A.; Conlan, Sean; Evans, Scott; Fowler, Vance G.

    2014-01-01

    Carbapenem resistance in Gram-negative bacteria is on the rise in the United States. A regional network was established to study microbiological and genetic determinants of clinical outcomes in hospitalized patients with carbapenem-resistant (CR) Klebsiella pneumoniae in a prospective, multicenter, observational study. To this end, predefined clinical characteristics and outcomes were recorded and K. pneumoniae isolates were analyzed for strain typing and resistance mechanism determination. In a 14-month period, 251 patients were included. While most of the patients were admitted from long-term care settings, 28% of them were admitted from home. Hospitalizations were prolonged and complicated. Nonsusceptibility to colistin and tigecycline occurred in isolates from 7 and 45% of the patients, respectively. Most of the CR K. pneumoniae isolates belonged to repetitive extragenic palindromic PCR (rep-PCR) types A and B (both sequence type 258) and carried either blaKPC-2 (48%) or blaKPC-3 (51%). One isolate tested positive for blaNDM-1, a sentinel discovery in this region. Important differences between strain types were noted; rep-PCR type B strains were associated with blaKPC-3 (odds ratio [OR], 294; 95% confidence interval [CI], 58 to 2,552; P < 0.001), gentamicin nonsusceptibility (OR, 24; 95% CI, 8.39 to 79.38; P < 0.001), amikacin susceptibility (OR, 11.0; 95% CI, 3.21 to 42.42; P < 0.001), tigecycline nonsusceptibility (OR, 5.34; 95% CI, 1.30 to 36.41; P = 0.018), a shorter length of stay (OR, 0.98; 95% CI, 0.95 to 1.00; P = 0.043), and admission from a skilled-nursing facility (OR, 3.09; 95% CI, 1.26 to 8.08; P = 0.013). Our analysis shows that (i) CR K. pneumoniae is seen primarily in the elderly long-term care population and that (ii) regional monitoring of CR K. pneumoniae reveals insights into molecular characteristics. This work highlights the crucial role of ongoing surveillance of carbapenem resistance determinants. PMID:24798270

  16. Molecular fingerprinting reflects different histotypes and brain region in low grade gliomas

    PubMed Central

    2013-01-01

    (MAPK) pathway in LGGs, but still point to an active involvement of TGF-beta signaling pathway in the PA development and pick out some hitherto unreported genes worthy of further investigation for the mixed glial-neuronal tumours. Conclusions The identification of a brain region-specific gene signature suggests that LGGs, with similar pathological features but located at different sites, may be distinguishable on the basis of cancer genetics. Molecular fingerprinting seems to be able to better sub-classify such morphologically heterogeneous tumours and it is remarkable that mixed glial-neuronal tumours are strikingly separated from PAs. PMID:23947815

  17. Diagnostics of the molecular component of photon-dominated regions with mechanical heating

    NASA Astrophysics Data System (ADS)

    Kazandjian, M. V.; Meijerink, R.; Pelupessy, I.; Israel, F. P.; Spaans, M.

    2012-06-01

    Context. Multitransition CO observations of galaxy centers have revealed that significant fractions of the dense circumnuclear gas have high kinetic temperatures, which are hard to explain by pure photon excitation, but may be caused by dissipation of turbulent energy. Aims: We aim to determine to what extent mechanical heating should be taken into account while modeling PDRs. To this end, the effect of dissipated turbulence on the thermal and chemical properties of PDRs is explored. Methods: Clouds are modeled as 1D semi-infinite slabs whose thermal and chemical equilibrium is solved for using the Leiden PDR-XDR code, where mechanical heating is added as a constant term throughout the cloud. An extensive parameter space in hydrogen gas density, FUV radiation field and mechanical heating rate is considered, covering almost all possible cases for the ISM relevant to the conditions that are encountered in galaxies. Effects of mechanical heating on the temperature profiles, column densities of CO and H2O and column density ratios of HNC, HCN and HCO+ are discussed. Results: In a steady-state treatment, mechanical heating seems to play an important role in determining the kinetic temperature of the gas in molecular clouds. Particularly in high-energy environments such as starburst galaxies and galaxy centers, model gas temperatures are underestimated by at least a factor of two if mechanical heating is ignored. The models also show that CO, HCN and H2O column densities increase as a function of mechanical heating. The HNC/HCN integrated column density ratio shows a decrease by a factor of at least two in high density regions with n ~ 105 cm-3, whereas that of HCN/HCO+ shows a strong dependence on mechanical heating for this same density range, with boosts of up to three orders of magnitude. Conclusions: The effects of mechanical heating cannot be ignored in studies of the molecular gas excitation whenever the ratio of the star formation rate to the gas density (SFR/n3

  18. Molecular Astrophysics from Space: the Physical and Chemical Effects of Star Formation and the Destruction of Planetary Systems around Evolved Stars

    NASA Technical Reports Server (NTRS)

    Neufeld, David

    2005-01-01

    The research conducted during the reporting period is grouped into three sections: 1) Warm molecular gas in the interstellar medium (ISM); 2) Absorption line studies of "cold" molecular clouds; 3) Vaporization of comets around the AGB star IRC+10216.

  19. A Genetic and Molecular Analysis of the 46c Chromosomal Region Surrounding the Fmrfamide Neuropeptide Gene in Drosophila Melanogaster

    PubMed Central

    O'Brien, M. A.; Roberts, M. S.; Taghert, P. H.

    1994-01-01

    We have analyzed the FMRFamide neuropeptide gene region of Drosophila melanogaster. This gene maps to the 46C region of chromosome 2R; this interval previously was not well characterized. For this genetic and molecular analysis, we have used X-ray mutagenesis, EMS mutagenesis, and the recently reported local P element transposition method. We identified four overlapping deletions, two of which have proximal breakpoints that define a 50-60-kb region surrounding the FMRFamide gene in 46C. To this small region, we mapped three lethal complementation groups; 10 additional lethal complementation groups were mapped to more distal regions of 46CD. One of these groups corresponds to even-skipped, the other 12 are previously unidentified. Using various lines of evidence we excluded the possibility that FMRFamide corresponds to any of the three lethal complementation groups mapping to its immediate 50-60-kb vicinity. The positions of two of the three lethal complementation groups were identified with P elements using a local transposition scheme. The third lethal complementation group was excluded as being FMRFamide mutants by sequence analysis and by immunocytochemistry with proFMRFamide precursor-specific antibodies. This analysis has (1) provided a genetic map of the 46CD chromosomal region and a detailed molecular map of a portion of the 46C region and (2) provided additional evidence of the utility of local transposition for targeting nearby genes. PMID:8056304

  20. Molecular analysis of Gaucher disease: screening of patients in the Montreal/Quebec region.

    PubMed

    Choy, F Y; Woo, M; Der Kaloustian, V M

    1991-12-15

    Gaucher disease, the most prevalent lysosomal storage disease, is an autosomal recessive sphingolipidosis resulting from deficient glucocerebrosidase activity. Genomic DNA of the structural gene of glucocerebrosidase from normal individuals and fifteen unrelated patients with the three clinical forms of Gaucher disease from the Montreal/Quebec region were amplified by the polymerase chain reaction technique. Allele-specific oligonucleotide dot blot hybridization and restriction fragment length polymorphism were used to screen for five of the mutations [mutations 120, 370, 415, 444 (Nci), and 463] in exons 5, 9, and 10 of glucocerebrosidase gene. It was noted that all of the patients had at least one of the known mutant alleles. However, 9 patients (9/15 = 60%) had an unknown allele. Mutation 370 in exon 9 was present in the heteroallelic form in eight out of the nine patients with type 1 Gaucher disease, but was present in none of the six patients with type 2 or type 3 Gaucher disease. The Nci mutation in exon 10 was present in the heteroallelic form in three patients with type 1 Gaucher disease and in either the heteroallelic or homoallelic form in all of the six patients with type 2 or type 3 Gaucher disease. The 415/Nci mutations were found in a mildly affected 29-year-old patient with type 1 Gaucher disease, as well as in an infant with the type 2 form. These findings demonstrate the clinical and molecular genetic heterogeneities of Gaucher disease, the presence of unknown Gaucher allele(s) in most (60%) of the patients surveyed, and the occasional inexplicable lack of phenotype-genotype correlation among some patients.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1776640

  1. Pathology of Camel Tuberculosis and Molecular Characterization of Its Causative Agents in Pastoral Regions of Ethiopia

    PubMed Central

    Mamo, Gezahegne; Bayleyegn, Gizachew; Sisay Tessema, Tesfaye; Legesse, Mengistu; Medhin, Girmay; Bjune, Gunnar; Abebe, Fekadu; Ameni, Gobena

    2011-01-01

    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 (χ2 = 4.789; P = 0.029). The tropism of TB lesions was significantly different among the lymph nodes (χ2 = 22.697; P = 0.002) and lung lobes (χ2 = 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. PMID:21283668

  2. Analysis of the properties of the molecular-cluster xenon mixture in the mesoscopic phase transition region

    NASA Astrophysics Data System (ADS)

    Kurlapov, L. I.; Kassymov, A. B.

    2016-04-01

    We report on the results of calculation of the concentrations of cluster subcomponents in a molecular-cluster xenon mixture at temperatures and pressures at which the gas experiences a mesoscopic phase transition. The existence of such a transition follows from singularities of the temperature dependence of viscosity, from the behavior of the cluster thermodiffusion coefficient, and from the features of the distributions of cluster subcomponents in the centrifuge. The mesoscopic phase transition is manifested in the intermediate position of the molecular-cluster mixture between the gas and the liquid judging from its properties in the transition region.

  3. THE HIGH-VELOCITY MOLECULAR OUTFLOWS IN MASSIVE CLUSTER-FORMING REGION G10.6-0.4

    SciTech Connect

    Liu Hauyu Baobab; Ho, Paul T. P.; Zhang Qizhou E-mail: pho@asiaa.sinica.edu.t

    2010-12-20

    We report the arcsecond resolution Submillimeter Array observations of the {sup 12}CO (2-1) transition in the massive cluster-forming region G10.6-0.4. In these observations, the high-velocity {sup 12}CO emission is resolved into individual outflow systems, which have a typical size scale of a few arcseconds. These molecular outflows are energetic and are interacting with the ambient molecular gas. By inspecting the shock signatures traced by CH{sub 3}OH, SiO, and HCN emissions, we suggest that abundant star formation activities are distributed over the entire 0.5 pc scale dense molecular envelope. The star formation efficiency over one global free-fall timescale (of the 0.5 pc molecular envelope, {approx}10{sup 5} years) is about a few percent. The total energy feedback of these high-velocity outflows is higher than 10{sup 47} erg, which is comparable to the total kinetic energy in the rotational motion of the dense molecular envelope. From order-of-magnitude estimations, we suggest that the energy injected from the protostellar outflows is capable of balancing the turbulent energy dissipation. No high-velocity bipolar molecular outflow associated with the central OB cluster is directly detected, which can be due to the photoionization.

  4. CN emission in Orion. The high density interface between the H II region and the molecular cloud

    NASA Astrophysics Data System (ADS)

    Rodriguez-Franco, A.; Martin-Pintado, J.; Fuente, A.

    1998-01-01

    We present high angular-resolution (12''-26'') large-scale mapping (19'x22') of the Orion A molecular complex in the N=1->0 and N=2->1 rotational transitions of the CN radical. The CN emission is not only confined to the molecular ridge and the optical bar, but it reveals filamentary emission toward the north and southwest of the Trapezium cluster and surrounding M43. The morphology and the kinematics of the CN emission supports the idea that the CN filaments represent the interfaces between the molecular cloud and the major ionization fronts of M42 and M43. The CN lines have been used to estimate the physical conditions of the molecular gas which confines the ionized material in M42 and M43. Surprisingly, the largest line intensity ratios between the N=1->0 and the N=2->1 lines are not observed toward the molecular ridge or the ionization fronts, but towards the Trapezium cluster and in the direction of the ionized gas in M43. Model calculations for the CN excitation implies H_2 densities of ~ 10(5) cm(-3) toward the ridge and ionization fronts and >6*E(6) cm(-3) toward the region surrounding the Trapezium stars. This suggests that for the first time we have detected the confining material behind M42. We estimate that the CN emission arises from a thin ( ~ 1.2*E(15) cm), dense (>6*E(6) cm(-3) ) layer which might have been compressed by the expansion of the HII region. The morphology of the CN emission, dominated by the ionization fronts of the HII regions, indicates that this molecule is an excellent tracer of regions affected by UV radiation. The comparison between the HC_3N and the CN abundance shows dramatic changes (more than 4 orders of magnitude) between the different features observed in OMC1. The [HC_3N]/[CN] abundance ratio varies from values of ~ 10(-3) for the ionization fronts surrounding the HII regions, to 100 for the hot core in Orion. Our data shows that the [HC_3N]/[CN] abundance ratio is an excellent tracer of photon dominated regions (PDRs) and

  5. Morphological and molecular characterization of Sarcocystis miescheriana from pigs in the central region of China.

    PubMed

    Yan, Wenchao; Qian, Weifeng; Li, Xiaojun; Wang, Tianqi; Ding, Ke; Huang, Tengfei

    2013-03-01

    Sarcocystosis is an important food-borne parasitosis in humans and various animals. Sarcocystis miescheriana and Sarcocystis suihominis are pathogenic to pigs; S. suihominis is also distinctly pathogenic to humans. Intermediate and final hosts can harbor more than one Sarcocystis species, so the exact identification for Sarcocystis infection in various hosts is essential to control sarcocystosis in humans and important economic animals including pigs. In this study, four isolates of sarcocysts from slaughtered pigs (SmJY1-SmJY4) in the central region of China, in Henan province, were collected and examined by transmission electron microscopy and 18S rRNA sequence analysis to identify the Sarcocystis species in pigs in China. The results showed that cysts in the diaphragm muscles have a thick cyst wall with a number of palisade-like protrusions up to 4.38 μm in length. Inside these protrusions, there were 13-16 fibrils per protrusion. Bradyzoites in cysts showed typical characteristics of Apicomplexa including a conoid, many micronemes, dense bodies, one big nucleus, and a number of amylopectin granules. These ultrastructural results suggest that characteristics of tissue cysts of the isolates SmJY1-SmJY4 were similar to those of S. miescheriana. The sequence similarities of SmJY1-SmJY4 with S. miescheriana were 99-99.5 %, and the sequence similarities of SmJY1-SmJY4 with S. suihominis were much lower. Results of the ultrastructural observation in combination with molecular characterization based on the 18S rRNA sequence represent the first demonstration of S. miescheriana in pigs in China. In addition, results of the histological examination showed that the cysts of S. miescheriana had two types of cyst wall, a palisade-like thick wall and another smoothly thin wall, and could cause obvious atrophy, degeneration, and necrosis of muscle fibers in the diaphragm of naturally infected pigs. These findings will provide an important reference for the examination of

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    More than 450 air samples that were collected in the upper troposphere - lower stratosphere (UTLS) region around the tropopause (TP) 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 (m(H2)) and H2 isotopic composition (deuterium content, δD). More than 120 of the analysed samples consisted of air from the lowermost stratosphere (LMS). These show that m(H2) does not vary appreciably with O3-derived height above the thermal TP, whereas δD does increase with height. The isotope enrichment is caused by competing 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 (CH4) and nitrous oxide (N2O), as a result of the relatively long lifetimes of these three species. The correlations are described by δ D [‰]=-0.35 · m(CH4)[ppb]+768 and δD [‰]=-1.90 · m(N2O)[ppb]+745. These correlations are similar to previously published results and likely hold globally. 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 m(H2), but δD is up to 15‰ lower in the July, August and September monsoon samples. This δD lowering is correlated with m(CH4) increase. The significant correlation with m(CH4) and the absence of a perceptible m(H2) increase that accompanies the δD lowering 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 m(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 collected close to airports

  8. Near-Infrared spectroscopy of shocked molecular hydrogen in star formation regions

    NASA Astrophysics Data System (ADS)

    Fernandes, Amadeu J. L.

    1993-11-01

    The work presented in this thesis is devoted to the study of the physics of shock waves in dense molecular cloud environments that are typical of star forming regions. The structure of these shock waves are analysed in terms of the two basic models: J-shock and C-shock. We have investigated the H2 emission properties from Herbig-Haro 7 and the DR 21 bipolar outflow by measuring several spectral lines arising in the K band. These H2 lines cover a wide range in energy of the upper level (6000-25000 K) and enables a detailed study of the temperature distribution of the gas. The calculated column density ratios have been compared to J and C-shock models for different shock geometries. We have shown that current oblique J- and C-shock models fail to explain the observed H2 column density ratios. J-shock models fail to provide sufficient hot gas from behind the shock front and are not able to explain the large line intensities observed in the high-vibrational H2 lines. The line emission from the 6 positions observed within the HH 7 bow are shown to be consistent with a paraboloidal bow shock geometry, which however necessitates of an extra source of excitation of the high energy levels to explain the H2 line ratios. We present a study of the effects of the UV radiation field associated with the bow shock structure and show that a shock-induced Far-UV radiation field with a strength of G0 = 102 - 103, can account for the observed H2 line ratios. We suggest that shocks are responsible for the low-lying level excitation of the H2 molecule while Lyα resonance pumping is responsible for the high-excitation line emission. Measurements of several infrared emission lines of H2 in the K window from the DR 21 bipolar outflow, show different excitation conditions for the East and West lobes of H2 emission. The higher H2 line ratios measured for the East lobe is indicative of enhanced excitation for the high-excitation levels of the H2 molecule, which can be caused by either shock

  9. Molecular characterization of a region of DNA associated with mutations at the agouti locus in the mouse.

    PubMed Central

    Bultman, S J; Russell, L B; Gutierrez-Espeleta, G A; Woychik, R P

    1991-01-01

    Molecular characterization of a radiation-induced agouti (a)-locus mutation has resulted in the isolation of a segment of DNA that maps at or near the a locus on chromosome 2 in the mouse. This region of DNA is deleted in several radiation- or chemical-induced homozygous-lethal a-locus mutations and is associated with specific DNA structural alterations in two viable a-locus mutations. We propose that DNA probes from this region of chromosome 2 will be useful for ultimately characterizing the individual gene or genes associated with a-locus function. Images PMID:1896452

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

    NASA Astrophysics Data System (ADS)

    Tremblin, P.; Anderson, L. D.; Didelon, P.; Raga, A. C.; Minier, V.; Ntormousi, E.; Pettitt, A.; Pinto, C.; Samal, M. R.; Schneider, N.; Zavagno, A.

    2014-08-01

    Aims: This work aims to improve 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. Methods: Using analytical solutions, one-dimensional (1D), and three-dimensional (3D) simulations, we constrained the expansion of the ionized bubble depending on the turbulence 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 us to date a large sample of OB associations that we obtained from the H ii Region Discovery Survey (HRDS). Results: 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 built a grid of 1D models of the expansion of H ii regions in a profile based on Larson's laws. We take the 3D turbulence into account with an effective 1D temperature profile. The ages estimated by the isochrones of this grid agree well with literature values of well known regions such as Rosette, RCW 36, RCW 79, and M 16. We thus propose that this method can be used to find ages of young OB associations through the Galaxy and also in nearby extra-galactic sources.

  11. Facioscapulohumeral dystrophy: a distinct regional myopathy with a novel molecular pathogenesis. FSH Consortium.

    PubMed

    Tawil, R; Figlewicz, D A; Griggs, R C; Weiffenbach, B

    1998-03-01

    Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common inherited diseases of muscle. Until recently, FSHD had received little attention because of its relatively benign course and the perception that it represented a syndrome rather than a distinct myopathy. Research interest into this disease was reignited with the demonstration of linkage of FSHD to chromosome 4q35 in 1990. Clinical and molecular genetic research in FSHD has since helped define it as a distinct clinical entity, outlined its natural history, and defined the primary molecular defect associated with the condition. FSHD is now known to be associated with large deletions of variable size on chromosome 4q35. These deletions, however, do not appear to disrupt a transcribed gene but are thought to interfere with the expression of a gene or genes located proximal to the deletions. These observations complicate the search for the FSHD gene but also imply the presence of a potentially novel molecular pathogenesis. PMID:9506542

  12. Transient magnetic tunneling mediated by a molecular bridge in the junction region

    NASA Astrophysics Data System (ADS)

    Kalvová, A.; Špička, V.; Velický, B.

    2014-07-01

    This paper extends our recent theoretical study of transient currents in molecular bridge junctions [1] to magnetic tunneling. Presently, we calculate the excess magnetic tunneling through the molecular bridge shunting the junction. The system is represented by two ferromagnetic electrodes bridged by a molecular size island with one electronic level and a local Hubbard type correlation. The island is linked with the electrodes by tunneling junctions whose coupling strength is assumed to undergo rapid changes affecting the connectivity of the system. We employ the non-equilibrium Green's functions. The numerical solution is obtained solving the real-time Dyson equation in the integro-differential form self-consistently. The switching events controlling the junctions give rise to transient changes of magnetisation of the island. They strongly depend on the static galvanic bias between the electrodes, mutual alignment of their magnetisation and on the time scale of the switching.

  13. The Sarcomeric M-Region: A Molecular Command Center for Diverse Cellular Processes

    PubMed Central

    Hu, Li-Yen R.; Ackermann, Maegen A.; Kontrogianni-Konstantopoulos, Aikaterini

    2015-01-01

    The sarcomeric M-region anchors thick filaments and withstands the mechanical stress of contractions by deformation, thus enabling distribution of physiological forces along the length of thick filaments. While the role of the M-region in supporting myofibrillar structure and contractility is well established, its role in mediating additional cellular processes has only recently started to emerge. As such, M-region is the hub of key protein players contributing to cytoskeletal remodeling, signal transduction, mechanosensing, metabolism, and proteasomal degradation. Mutations in genes encoding M-region related proteins lead to development of severe and lethal cardiac and skeletal myopathies affecting mankind. Herein, we describe the main cellular processes taking place at the M-region, other than thick filament assembly, and discuss human myopathies associated with mutant or truncated M-region proteins. PMID:25961035

  14. RNA sequencing reveals region-specific molecular mechanisms associated with epileptogenesis in a model of classical hippocampal sclerosis

    PubMed Central

    Vieira, A. S.; de Matos, A. H.; do Canto, A. M.; Rocha, C. S.; Carvalho, B. S.; Pascoal, V. D. B.; Norwood, B.; Bauer, S.; Rosenow, F.; Gilioli, R.; Cendes, F.; Lopes-Cendes, I.

    2016-01-01

    We report here the first complete transcriptome analysis of the dorsal (dDG) and ventral dentate gyrus (vDG) of a rat epilepsy model presenting a hippocampal lesion with a strict resemblance to classical hippocampal sclerosis (HS). We collected the dDG and vDG by laser microdissection 15 days after electrical stimulation and performed high-throughput RNA-sequencing. There were many differentially regulated genes, some of which were specific to either of the two sub-regions in stimulated animals. Gene ontology analysis indicated an enrichment of inflammation-related processes in both sub-regions and of axonal guidance and calcium signaling processes exclusively in the vDG. There was also a differential regulation of genes encoding molecules involved in synaptic function, neural electrical activity and neuropeptides in stimulated rats. The data presented here suggests, in the time point analyzed, a remarkable interaction among several molecular components which takes place in the damaged hippocampi. Furthermore, even though similar mechanisms may function in different regions of the DG, the molecular components involved seem to be region specific. PMID:26935982

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

    PubMed Central

    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

    2016-01-01

    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. PMID:27025950

  16. Russian populations of Puccinia triticina in distant regions are not differentiated for virulence and molecular genotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to determine whether genetically distinct groups of Puccinia triticina are present in four regions of Russia. Collections of P. triticina were obtained from the Central, North Caucasus, Volga, and West Siberia regions of Russia from 2006 to 2010. Ninety-nine single ur...

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

    NASA Astrophysics Data System (ADS)

    Paron, S.; Ortega, M. E.; Dubner, G.; Yuan, Jing-Hua; Petriella, A.; Giacani, E.; Li, Jin Zeng; 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.

  18. Source regions for recruitment of Calanus finmarchicus to Georges Bank: evidence from molecular population genetic analysis of mtDNA

    NASA Astrophysics Data System (ADS)

    Bucklin, Ann; Kocher, Thomas D.

    Molecular population genetic analysis has provided evidence that the copepod, Calanus finmarchicus, of the Labrador Current, Gulf of St Lawrence, Scotian Shelf, Gulf of Maine, and Georges Bank constitute a single, interbreeding population. The DNA sequence of a 350 base pair portion of the mitochondrial large subunit (16S) ribosomal RNA (rRNA) gene was determined for a total of 72 individuals collected in 1992, and 110 individuals collected in 1993 from these regions. There was significant heterogeneity in haplotype frequencies among the samples collected in 1992, but this heterogeneity did not resolve into regional patterns. The only regional differences seen were between pooled samples of the western N. Atlantic and those of the Norwegian Sea. There were no significant differences in haplotype frequencies among the samples collected in 1993, and fewer haplotypes were observed in these samples. Intraspecific molecular variation was typical of other marine species: there were 29 haplotypes among the 182 individuals sequenced. The frequency distribution of the haplotypes was highly skewed: 128 individuals shared one haplotype and 19 individuals were unique. There were 24 variable sites among the 350 bases sequenced; estimated nucleotide diversity was 0.0042. The genetic character of C. finmarchicus populations in the western N. Atlantic was stable over time in that three of the haplotypes (including the most abundant) occurred in both 1992 and 1993. However, haplotype frequencies differed significantly between the two years. The lack of regional structure in the 1992 samples and the genetic homogeneity of samples collected in 1993 across the domain from the Labrador Current to the Gulf of St Lawrence to Georges Bank and the Gulf of Maine indicated that there is significant gene flow across this region. The persistent genetic pattern suggests that the Gulf of St Lawrence may be an important source region for recruitment of C. finmarchicus to Georges Bank

  19. Spatially resolved physical conditions of molecular gas: a zoom-in from circumnuclear region of M83 to Carina nebula.

    NASA Astrophysics Data System (ADS)

    Wu, Ronin; Madden, Suzanne; Galliano, Frédéric; Wilson, Christine; Onaka, Takashi; Nakamura, Tomohiko

    2015-08-01

    Since the launch of the Herschel Space Observatory, our understanding about the photo-dissociation regions (PDR) has taken a step forward. In the bandwidth of the Fourier Transform Spectrometer (FTS) of the Spectral and Photometric Imaging REceiver (SPIRE) on board Herschel, ten CO rotational transitions, including J=4-3 to J=13-12, and three fine structure lines, including [CI] 609, [CI] 370, and [NII] 250 micron, are covered. This presentation focuses on the physical conditions of molecular gas probed by the Herschel SPIRE/FTS.Based on the spatially resolved physical parameters derived from the CO spectral line energy distribution (SLED) map and the comparisons with the dust properties and star-formation tracers, I will first present our findings at the circumnuclear region of M83, and then zoom in toward the young open cluster, Trumpler 14, in Carina nebula. I will discuss (1) the potential of using [NII] 250 and [CI] 370 micron as star-formation tracers; (2) the reliability of tracing molecular gas with CO; (3) the excitation mechanisms of warm CO; (4) the possibility of studying stellar feedback by tracing the thermal pressure of intersetllar molecular gas.

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

    PubMed Central

    Feng, Shangguo; Jiang, Yan; Wang, Shang; Jiang, Mengying; Chen, Zhe; Ying, Qicai; Wang, Huizhong

    2015-01-01

    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. PMID:26378526

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

    PubMed

    Feng, Shangguo; Jiang, Yan; Wang, Shang; Jiang, Mengying; Chen, Zhe; Ying, Qicai; Wang, Huizhong

    2015-01-01

    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. PMID:26378526

  2. Modeling Star-Forming Regions using a 3D Molecular Transport Code

    NASA Astrophysics Data System (ADS)

    Loughnane, R. M.; Redman, M. P.; Keto, E. R.

    2012-07-01

    This paper presents the 3-dimensional non-LTE radiative transfer code, MOLLIE (MOLelcular LIne Explorer), for solving molecular and atomic excitation and radiation transfer in a molecular gas and predicting emergent spectra. The code implementation makes use of the Accelerated Lambda Iteration (ALI) method of Rybicki & Hummer (1991) to solve the radiative transfer equation along rays passing through a spherical model cloud. When convergence between level populations, the radiation field, and the point separation has been obtained, the grid is ray-traced to produce images that can be readily compared to observations. The optimization technique, Fast Simulated Annealing (FSA), adopted by MOLLIE to increase the probability of arriving at a satisfactory output in a timely fashion, is briefly considered.

  3. Modeling radiative transfer in molecular clouds. 1: HCO(+) in the star-forming region W49A North

    NASA Technical Reports Server (NTRS)

    Dickel, Helene R.; Auer, Lawrence H.

    1994-01-01

    A new general multilevel, non-Local Thermodynamic Equilibrium (LTE) radiative transfer code, valid for any velocity field, is applied to HCO(+) observations of W49A North. Three classes of collapse models are considered: free-fall collapse (v proportional to 1/sq. root of r), rho proportional to r(exp -3/2) throughout the molecular cloud, successfully reproduces the features of the observations and gives the best fit to the J = 1-0 and J = 3-2 profiles both toward the prominent H II component G of W49A North and off the center. In addition to a slow radial fall-off of density, the theoretical modeling implies the following for the molecular cloud: the large line widths result from motions occurring within the inner 1 pc, and there are probably one or more fragments with peculiar velocities within this same region.

  4. Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region.

    PubMed

    Shazib, Shahed Uddin Ahmed; Vďačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

    2016-09-01

    Morphological and molecular delimitation of Spirostomum species is currently under debate. We addressed species boundaries within the genus Spirostomum, using the ITS1-5.8S-ITS2 region and the secondary structure of the ITS2 molecule, and 18S and 28S (D1D2) sequences additionally. The Spirostomum ITS region is among the shortest within the ciliates hitherto studied. The Spirostomum ITS2 molecule matches the "ring model", but exhibits only two helices radiating from a common loop. According to comparative analyses, they very likely correspond to helices II and III of other eukaryotes. Our phylogenetic analyses of the ITS region revealed a complex genealogical structure within the genus Spirostomum. However, boundaries among Spirostomum species could not be unambiguously determined either by phylogenetic trees, networks or sequence divergence cutoffs, because ITS2 sequences transcended species boundaries of the following morphospecies: S. ambiguum, S. minus, S. subtilis and S. teres. According to molecular diversity analysis, this is very likely caused by polymorphism in S. minus and S. teres, and by the lack of variability in S. ambiguum and S. subtilis. No compensatory base changes (CBCs) were detected in helices of the ITS2 molecule between different Spirostomum species, documenting that CBC analysis per se is not able to effectively discriminate Spirostomum species. PMID:27261253

  5. Molecular flux measurements in the back flow region of a nozzle plume

    NASA Technical Reports Server (NTRS)

    Chirivella, J. E.

    1973-01-01

    A series of tests were conducted to measure the mass flux in the far field of a nozzle plume in a high vacuum with emphasis on the back flow region. The measurements presented provided fairly accurate data for off-axis angles as large as 140 deg (i.e., in the back flow region). This region, since it is well behind the exit plane, is of paticular interest to those concerned with instrument contamination. Usually sensitive spacecraft surfaces are located in the region affected by the back flow. Parameters such as expansion ratio, throat diameter, nozzle lip shape, and plenum (chamber) pressure were varied, carbon dioxide and nitrogen gases were flowed and mass flux measurements were taken using quartz crystal microbalances in as many as nine different locations relative to the tests nozzle. Several conclusions with respect to the effect of nozzle and gas parameters on the amount of back flow mass flux are offered, and it was demonstrated that gaseous mass fluxes, which are not predictable by present theories, are encountered in the region behind the nozzle exit plane. This knowledge is significant if materials incompatible with the gaseous exhaust products are used in this region.

  6. Intragenomic Variation in the Internal Transcribed Spacer 1 Region of Dientamoeba fragilis as a Molecular Epidemiological Marker▿

    PubMed Central

    Bart, Aldert; van der Heijden, Harold M.; Greve, Sophie; Speijer, Dave; Landman, Wil J.; van Gool, Tom

    2008-01-01

    Dientamoeba fragilis is a parasite that has been recognized to be a causative agent of gastrointestinal symptoms. Because in most studies only some infected persons experience symptoms, it is possible that D. fragilis is a heterogeneous species with variants that display similar morphologies but different pathogenicities. The search for genetic variation in D. fragilis was based on the small-subunit rRNA gene, which was not found to be useful for molecular epidemiology. In this report, we describe the isolation and characterization of additional rRNA gene cluster sequences, the internal transcribed spacer 1 (ITS-1)-5.8S rRNA gene-ITS-2 region. For comparative purposes, we also isolated the ITS-1-5.8S rRNA gene-ITS-2 region of Histomonas meleagridis, a protozoan parasite of birds and a close relative of D. fragilis. This region was found to be highly variable, and 11 different alleles of the ITS-1 sequence could be identified. Variation in the ITS-1 region was found to be intragenomic, with up to four different alleles in a single isolate. So-called C profiles were produced from the ITS-1 repertoire of single isolates,. Analysis of the C profiles of isolates from nonrelated patients identified several clearly distinguishable strains of D. fragilis. Within families, it was shown that members can be infected with the same or different strains of D. fragilis. In conclusion, the ITS-1 region can serve as a molecular epidemiological tool for the subtyping of D. fragilis directly from feces. This may serve as a means of studying the transmission, geographical distribution, and relationships between strains and the pathogenicity of this parasite. PMID:18650356

  7. Modeling Far-UV Fluorescent Emission Features of Warm Molecular Hydrogen in the Inner Regions of Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Hoadley, Keri; France, Kevin

    2015-01-01

    Probing the surviving molecular gas within the inner regions of protoplanetary disks (PPDs) around T Tauri stars (1 - 10 Myr) provides insight into the conditions in which planet formation and migration occurs while the gas disk is still present. We model observed far ultraviolet (FUV) molecular hydrogen (H₂) fluorescent emission lines that originate within the inner regions (< 10 AU) of 9 well-studied Classic T Tauri stars, using the Hubble Space Telescope Cosmic Origins Spectrograph (COS), to explore the physical structure of the molecular disk at different PPD dust evolutionary stages. We created a 2D radiative transfer model that estimates the density and temperature distributions of warm, inner radial H₂ (T > 1500 K) with a set of 6 free parameters and produces a data cube of expected emission line profiles that describe the physical structure of the inner molecular disk atmosphere. By comparing the modeled emission lines with COS H₂ fluorescence emission features, we estimate the physical structure of the molecular disk atmosphere for each target with the set of free parameters that best replicate the observed lines. First results suggest that, for all dust evolutionary stages of disks considered, ground-state H₂ populations are described by a roughly constant temperature T(H₂) = 2500 +/- 1000 K. Possible evolution of the density structure of the H₂ atmosphere between intact and depleting dust disks may be distinguishable, but large errors in the inferred best-fit parameter sets prevent us from making this conclusion. Further improvements to the modeling framework and statistical comparison in determining the best-fit model-to-data parameter sets are ongoing, beginning with improvements to the radiative transfer model and use of up-to-date HI Lyman α absorption optical depths (see McJunkin in posters) to better estimate disk structural parameters. Once improvements are implemented, we will investigate the possible presence of a molecular wind

  8. Regional vulnerability in Huntington's disease: fMRI-guided molecular analysis in patients and a mouse model of disease.

    PubMed

    Lewandowski, Nicole M; Bordelon, Yvette; Brickman, Adam M; Angulo, Sergio; Khan, Usman; Muraskin, Jordan; Griffith, Erica Y; Wasserman, Paula; Menalled, Liliana; Vonsattel, Jean Paul; Marder, Karen; Small, Scott A; Moreno, Herman

    2013-04-01

    Although the huntingtin gene is expressed in brain throughout life, phenotypically Huntington's disease (HD) begins only in midlife and affects specific brain regions. Here, to investigate regional vulnerability in the disease, we used functional magnetic resonance imaging (fMRI) to translationally link studies in patients with a mouse model of disease. Using fMRI, we mapped cerebral blood volume (CBV) in three groups: HD patients, symptom-free carriers of the huntingtin genetic mutation, and age-matched controls. In contrast to a region in the anterior caudate, in which dysfunction was linked to genotype independent of phenotype, a region in the posterior body of the caudate was differentially associated with disease phenotype. Guided by these observations, we harvested regions from the anterior and posterior body of the caudate in postmortem control and HD human brain tissue. Gene-expression profiling identified two molecules whose expression levels were most strongly correlated with regional vulnerability - protein phosphatase 1 regulatory subunit 7 (PPP1R7) and Wnt inhibitory factor-1 (WIF-1). To verify and potentially extend these findings, we turned to the YAC128 (C57BL/6J) HD transgenic mice. By fMRI we longitudinally mapped CBV in transgenic and wildtype (WT) mice, and over time, abnormally low fMRI signal emerged selectively in the dorsal striatum. A relatively unaffected brain region, primary somatosensory cortex (S1), was used as a control. Both dorsal striatum and S1 were harvested from transgenic and WT mice and molecular analysis confirmed that PPP1R7 deficiency was strongly correlated with the phenotype. Together, converging findings in human HD patients and this HD mouse model suggest a functional pattern of caudate vulnerability and that variation in expression levels of herein identified molecules correlate with this pattern of vulnerability. PMID:23220414

  9. Molecular Analysis of Vancomycin-Resistant Enterococci Isolated from Regional Hospitals in Trinidad and Tobago

    PubMed Central

    Akpaka, Patrick E.; Kissoon, Shivnarine; Jayaratne, Padman

    2016-01-01

    Geographic spread of vancomycin-resistant enterococci (VRE) clones in cities, countries, or even continents has been identified by molecular techniques. This study aimed at characterizing virulent genes and determining genetic relatedness of 45 VRE isolates from Trinidad and Tobago using molecular tools, including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE), and Random Amplification Polymorphic DNA (RAPD). The majority (84%) of the isolates were Enterococcus faecium possessing vanA gene while the rest (16%) were Enterococcus faecalis possessing vanB. The esp gene was found in all 45 VRE isolates while hyl genes were found only in E. faecium species. The E. faecium species expressed five distinct PFGE patterns. The predominant clones with similar or common patterns belonged to clones one and three, and each had 11 (29%) of the VRE isolates. Plasmid content was identified in representative isolates from each clonal group. By contrast, the E. faecalis species had one PFGE pattern suggesting the presence of an occult and limited clonal spread. The emergence of VRE in the country seems to be related to intra/interhospital dissemination of an epidemic clone carrying the vanA element. Therefore, infection control measures will be warranted to prevent any potential outbreak and spread of VRE in the country. PMID:27299153

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Three-dimensional molecular line transfer: a simulated star-forming region

    NASA Astrophysics Data System (ADS)

    Rundle, David; Harries, Tim J.; Acreman, David M.; Bate, Matthew R.

    2010-09-01

    We present the first non-local thermodynamic equilibrium (non-LTE), comoving frame molecular line calculations of a star-forming cluster simulated using smoothed particle hydrodynamics (SPH), from which we derive high-resolution synthetic observations. We have resampled a particle representation on to an adaptive mesh and self-consistently solved the equations of statistical equilibrium in the comoving frame, using TORUS, a three-dimensional adaptive mesh refined radiative transfer code. We verified the applicability of the code to the conditions of the SPH simulation by testing its output against other codes. We find that the level populations obtained for optically thick and thin scenarios closely match the ensemble average of the other codes. We have used the code to obtain non-LTE level populations of multiple molecular species throughout the cluster and have created three-dimensional velocity-resolved spatial maps of the emergent intensity. Line profiles of cores traced by N2H+ (1-0) are compared to probes of low-density gas, 13CO (1-0) and C18O (1-0), surrounding the cores along the line of sight. The relative differences of the line centre velocities are shown to be small compared to the velocity dispersion, matching recent observations. We conclude that one cannot reject competitive accretion as a viable theory of star formation based on observed velocity profiles.

  12. Molecular Analysis of Vancomycin-Resistant Enterococci Isolated from Regional Hospitals in Trinidad and Tobago.

    PubMed

    Akpaka, Patrick E; Kissoon, Shivnarine; Jayaratne, Padman

    2016-01-01

    Geographic spread of vancomycin-resistant enterococci (VRE) clones in cities, countries, or even continents has been identified by molecular techniques. This study aimed at characterizing virulent genes and determining genetic relatedness of 45 VRE isolates from Trinidad and Tobago using molecular tools, including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE), and Random Amplification Polymorphic DNA (RAPD). The majority (84%) of the isolates were Enterococcus faecium possessing vanA gene while the rest (16%) were Enterococcus faecalis possessing vanB. The esp gene was found in all 45 VRE isolates while hyl genes were found only in E. faecium species. The E. faecium species expressed five distinct PFGE patterns. The predominant clones with similar or common patterns belonged to clones one and three, and each had 11 (29%) of the VRE isolates. Plasmid content was identified in representative isolates from each clonal group. By contrast, the E. faecalis species had one PFGE pattern suggesting the presence of an occult and limited clonal spread. The emergence of VRE in the country seems to be related to intra/interhospital dissemination of an epidemic clone carrying the vanA element. Therefore, infection control measures will be warranted to prevent any potential outbreak and spread of VRE in the country. PMID:27299153

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

    SciTech Connect

    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.

  14. Molecular genetics of a three-gene cluster in the Amy region of Drosophila.

    PubMed

    Doane, W W; Thompson, D B; Norman, R A; Hawley, S A

    1990-01-01

    Analysis of amylase RNA levels in the anterior and posterior midgut regions of flies from the Amy1,6 mapA and c Amy2,3 mapC strains of D. melanogaster, reared on yeast and on yeast supplemented with glucose, indicates that the trans-acting map gene controls the abundance of amylase RNA tissue-specifically, i.e., in the adult posterior midgut. This is consistent with the view that its role in controlling Amy expression is that of a transcription factor. Dietary glucose represses Amy expression in the anterior and posterior midgut regions of adults, reducing the abundance of amylase RNA, which suggests that it also controls Amy transcriptional activity. However, the mechanism for glucose repression appears to act systemically in the midgut, in a manner that is independent of the effects of map on Amy expression. A new glucose repressible TU was identified that is located just proximal to the Amy locus in region 54A of polytene chromosome 2R. It is transcribed in the direction opposite to that of the proximal Amy gene and encodes an RNA about 1500 bases long. Its RNA is expressed in both larvae and adults of the above strains of D. melanogaster, but the nature of the product it encodes is unknown. We speculate that all three genes in the cluster at 54A, namely the two Amy gene copies and the new glucose repressible TU, are coordinately controlled by the same mechanism that regulates Amy gene expression in response to dietary glucose. Somatic transformation experiments suggest that 5' cis-regulatory mechanisms required for the correct spatial expression of the proximal and distal Amylase genes from a Canton-S strain of D. melanogaster, Amy-p1 and Amy-d3, are located within 450 bp and 463 bp of their respective translation start sites. These regions also contain sequences responsive to dietary glucose repression, which is mediated at the DNA level of exogenous Amy genes in somatically transformed larvae reared on a yeast + glucose diet. A positive activator is located

  15. Molecular circumscription of the hornworts (Anthocerotophyta) based on the chloroplast DNA trnL-trnF region.

    PubMed

    Stech, Michael; Quandt, Dietmar; Frey, Wolfgang

    2003-10-01

    In phylogenetic trees generated from partial trnL(UAA) intron sequences, the hornworts (represented by nine species from the genera Anthoceros, Dendroceros, Megaceros, Notothylas and Phaeoceros) are resolved as a monophyletic group and are separated from the clades of mosses, liverworts and tracheophytes. A secondary structure of the trnL(UAA) intron of Anthoceros agrestis is presented, displaying the arrangement of the stem-loop regions P1-P9. Compensatory base-pair changes (coevolutionary sites) are detected in regions P4/5 and P9 within the hornwort sequences. The original homology of the most variable region, P8, cannot be detected anymore due to the extremely fast divergent evolution of this segment in the major land plant groups. Similarly, a high sequence divergence occurs in the trnL-trnF intergenic spacer. Apart from synapomorphic substitutions in the trnL(UAA) intron, the hornworts are characterised by a large P6 region consisting of many repetitive elements. The molecular data therefore support the hornworts as representing an independent land plant lineage (Anthocerotophyta). Although relationships between hornworts and the other land plant groups remain unresolved in the trnL(UAA) intron trees, it is rather unlikely that bryophytes are monophyletic in their traditional circumscription, i.e. comprising hornworts, mosses and liverworts. PMID:12955570

  16. Water masers associated with compact molecular clouds and ultracompact H II regions - The extended sample

    NASA Astrophysics Data System (ADS)

    Cesaroni, R.; Comoretto, G.; Felli, M.; Palla, F.; Brand, J.; Caselli, P.

    We present the results of a survey of water maser emission at 22.2 GHz towards a selected sample of IRAS-PSC sources which are believed to be associated with very young massive stars. The sample consists of 591 sources. The observations have been carried out using the Medicina 32-m radiotelescope, operated by the Istituto di Radioastronomia - C.N.R., Bologna. Whereas previous searches for maser emission have been directed towards known H II regions, the aim of the present survey is to identify new sources in an even earlier evolutionary phase, corresponding to the development of an ultracompact H II region. It is shown that our sample contains a significant number of sources that could be considered good candidates of massive protostellar cores still in the main accretion phase.

  17. Gonadoblastoma: Molecular definition of the susceptibility region on the Y chromosome and role of TSPY

    SciTech Connect

    Tsuchiya, K.; Sultana, R.; Donlan, M.

    1994-09-01

    Gonadoblastomas are gonadal neoplasms that arise almost exclusively in the dysgenetic gonads of 46,XY sex-reversed females. The frequency of gonadoblastoma in patients who have dysgenetic gonads and a Y chromosome is at least 30%. In contrast 45,X Turner females who also have dysgenetic gonads do not develop this tumor. The high frequency of gonadoblastoma in sex-reversed females compared to Turner females has led to the hypothesis that there is a gene on the Y chromosome that is involved in the development of the tumor. This gene has been called the gonadoblastoma locus on the Y chromosome, or GBY. Deletion mapping of sex-reversed females with gonadoblastoma and partial Y chromosomes has previously localized the GBY gene to a region near the centromere. Using sequence-tagged sites, we have further sublocalized GBY in a patient with gonadoblastoma and a minute Y-derived marker chromosome. This region includes parts of intervals 3 and 4 of the Y chromosome. Based on the overlapping YAC contig map of the Y chromosome, this critical region is approximately 3 Mb. Using sex-reversed females with different deletions of Yp we have also localized the testis-specific protein, Y-encoded (TSPY) gene to interval 3D, which is within the gonadoblastoma critical region. TSPY consists of a repetitive gene family that is part of the DYZ5 locus. Expression of this gene has previously been shown to be limited to the testis. We have found expression of TSPY by RT-PCR in gonadoblastomas from two different individuals. In one of these patients, expression was observed in a unilateral gonadoblastoma, but not in the contralateral streak gonad. These findings suggest that TSPY may play a role in the development of gonadoblastomas.

  18. Molecular characterization of hepatitis C virus core region in moroccan intravenous drug users.

    PubMed

    Trimbitas, Roxana-Delia; Fayssel, Naouar; Serghini, Fatima-Zahra; Wakrim, Lahcen; Khyatti, Meriem; Essalhi, Mohammed; Bellefquih, Abdelkrim Meziane; Benani, Abdelouaheb

    2016-08-01

    Intravenous drug users (IDUs) represent a highly-infected reservoir for Hepatitis C virus (HCV) worldwide, harboring some of the most elevated prevalences and majority of the epidemic in developed nations. Studies aimed at sequencing regions of the viral genome uncovered amino acid mutations, some of which have been implicated in resistance to standard of care pegylated interferon/Ribavirin double therapy. Using the nested PCR method on the Core region of HCV strains in Moroccan IDUs living in the Tangier region this study sought to identify genotype-specific amino acid mutations, followed by Phylogenetic methods in order to compare them with international strains so as to identify sequences of highest homology. Genotyping was confirmed and recombination events excluded by line-probe assay. Italy was found most homologous for genotypes 1a and 3a, Iran for genotype 1a and Egypt for genotype 4a. Amino Acid Mutation analysis revealed the following novel genotype 3a-specific mutations: N16I, L36V, T49A, P71S, T75S, and T110N. The outcome of this work describes the HCV genetic heterogeneity in high-risk intravenous drug users, and it gives clues to the global migratory flow of genotypes as they cross geographical boundaries between various IDU populations and identifies "signature" amino acid mutations traceable to HCV genotype 3a. Identification of key amino acid positions in the HCV Core region with higher rates of mutations paves the way for eventual clinical trials seeking to establish a link between these recurrent mutations and response to standard of care Interferon and Ribavirin antiviral therapy. J. Med. Virol. 88:1376-1383, 2016. © 2016 Wiley Periodicals, Inc. PMID:26754854

  19. Molecular cloning and characterization of the promoter region of the porcine apolipoprotein E gene.

    PubMed

    Xia, Jihan; Hu, Bingjun; Mu, Yulian; Xin, Leilei; Yang, Shulin; Li, Kui

    2014-05-01

    Apolipoprotein E (APOE), a component of lipoproteins plays an important role in the transport and metabolism of cholesterol, and is associated with hyperlipoproteinemia and Alzheimer's disease. In order to further understand the characterization of APOE gene, the promoter of APOE gene of Landrace pigs was analyzed in the present study. The genomic structure and amino acid sequence in pigs were analyzed and found to share high similarity in those of human but low similarity in promoter region. Real-time PCR revealed the APOE gene expression pattern of pigs in diverse tissues. The highest expression level was observed in liver, relatively low expression in other tissues, especially in stomach and muscle. Furthermore, the promoter expressing in Hepa 1-6 was significantly better at driving luciferase expression compared with C2C12 cell. After analysis of porcine APOE gene promoter regions, potential transcription factor binding sites were predicted and two GC signals, a TATA box were indicated. Results of promoter activity analysis indicated that one of potential regulatory elements was located in the region -669 to -259, which was essential for a high expression of the APOE gene. Promoter mutation and deletion analysis further suggested that the C/EBPA binding site within the APOE promoter was responsible for the regulation of APOE transcription. Electrophoretic mobility shift assays also showed the binding site of the transcription factor C/EBPA. This study advances our knowledge of the promoter of the porcine APOE gene. PMID:24464129

  20. Molecular definition of the smallest region of deletion overlap in the Wolf-Hirschhorn syndrome

    SciTech Connect

    Gandelman, K.Y.; Gibson, L.; Meyn, M.S.; Yang-Feng, T.L. )

    1992-09-01

    Wolf-Hirschhorn syndrome (WHS), associated with a deletion of chromosome 4p, is characterized by mental and growth retardation and typical dysmorphism. A girl with clinical features of WHS was found to carry a subtle deletion of chromosome 4p. Initially suggested by high-resolution chromosome analysis, her deletion was confirmed by fluorescence in situ hybridization (FISH) with cosmid probes, E13, and Y2, of D4S113. To delineate this 4p deletion, the authors performed a series of FISH and pulsed-field gel electrophoresis analysis by using probes from 4p16.3. A deletion of [approximately]2.5 Mb with the breakpoint at [approximately]80 kb distal to D4S43 was defined in this patient and appears to be the smallest WHS deletion so far identified. To further refine the WHS critical region, they have studied three unrelated patients with presumptive 4p deletions, two resulting from unbalanced segregations of parental chromosomal translocations and one resulting from an apparently de novo unbalanced translocation. Larger deletions were identified in two patients with WHS. One patient who did not clinically present with WHS had a smaller deletion that thus eliminates the distal 100-300 kb from the telomere as being part of the WHS region. This study has localized the WHS region to [approximately]2 MB between D4S43 and D4S142. 37 refs., 4 figs., 1 tab.

  1. Molecular detection and characterization of Theileria infection in cattle and yaks from Tibet Plateau Region, China.

    PubMed

    Qin, Gege; Li, Youquan; Liu, Junlong; Liu, Zhijie; Yang, Jifei; Zhang, Lin; Liu, Guangyuan; Guan, Guiquan; Luo, Jianxun; Yin, Hong

    2016-07-01

    Theileriosis continues to threaten the livestock industry worldwide, but comprehensive epidemiological surveys for this disease have not been conducted in the Tibet Plateau Region, China. In this study, we screened 154 cattle blood samples from the Tibet Plateau Region (Lhasa, Lhoka, and Tianzhu), China, for detection of Theileria pathogens by polymerase chain reaction (PCR) with species-specific primers. The results revealed that the prevalence was 6.9 % (2/29) for Theileria orientalis and 27.6 % (8/29) for Theileria sinensis in Lhasa, 0 % (0/30) for T. orientalis and 26.7 % (8/30) for T. sinensis in Lhoka, and 0 % (0/95) for T. orientalis and 30.5 % (29/95) for T. sinensis in Tianzhu. Interestingly, Theileria luwenshuni, which was a previously reported pathogenic Theileria sp. in sheep and goats, was detected in blood samples from cattle and yaks for the first time, with a prevalence of 10 % (3/30) in Lhoka and 1.1 % (1/95) in Tianzhu. No other Theileria sp. was detected in these samples. T. sinensis and T. orientalis infections were detected in cattle and yaks, and T. luwenshuni was discovered for the first time in cattle and yaks in the Tibet Plateau Region, China. PMID:27000088

  2. Molecular epidemiology and viral load of HCV in different regions of Punjab, Pakistan

    PubMed Central

    2014-01-01

    Background Hepatitis C virus (HCV) is highly infectious pathogen which is responsible for causing Hepatitis around 200 million individuals worldwide. In Pakistan, 4.7% of HCV prevalence has been reported and HCV genotype 3a has been found to be the major source of infection in Pakistan but still there is lack of information on distribution of HCV genotypes and viral load in various geographical regions of Pakistan. Therefore, current study was designed to determine distribution of HCV genotypes as well viral load in different areas of Punjab province of Pakistan. Findings A total of 995 serum samples were taken from those individuals in which antibodies against HCV were detected through ELISA, from different regions of Punjab i.e. Lahore 317(31.85%), Faisalabad 70(7.03%), Gujranwala 129(12.96%), Gujrat 106(10.65%), Sialkot 94(9.44%), Sargodha 60(6.03%), Mandibaha-ud-din 135(13.56%), Jhang 86(8.64%). Qualitative PCR was performed to determine viral load and genotyping was performed using Nested PCR. Chi-square test was used to determine the age and sex-wise prevalence of HCV. Out of 995 samples, 888 samples were found positive for HCV RNA. In all regions, genotype 3a showed highest prevalence (82.81%) followed by genotype 1 (3.41%), mixed genotypes (2.41%), genotype 2 (0.50%), genotype 5 (0.1%) and unclassified genotypes (10.75%). Viral load in 29.5% patients infected with genotype 3a was less than 600,000 IU/mL, while it was between 600,000-800,000 IU/mL in 27.9% patients and 25.22% patients had more than 800,000 IU/mL viral load. Conclusion HCV genotype 3a is the most prevalent genotype in various regions of Punjab. Viral load of HCV patients in these different regions of Punjab are reported for the first time. Moreover, based upon these results the Patients having viral load below 800,000 IU/mL would be expected to show better response of anti-HCV therapy. PMID:24512668

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

    NASA Astrophysics Data System (ADS)

    Smith, Rachel L.; Blake, Geoffrey; Boogert, Adwin; Pontoppidan, Klaus Martin; Lockwood, Alexandra C.

    2015-08-01

    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

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

    PubMed

    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. PMID:26994789

  5. Molecular characterization of a human matrix attachment region that improves transgene expression in CHO cells.

    PubMed

    Sun, Qiu-Li; Zhao, Chun-Peng; Chen, Shao-Nan; Wang, Li; Wang, Tian-Yun

    2016-05-15

    Chinese hamster ovary (CHO) cells offer many advantages for recombinant gene expression, including proper folding and post-translational modification of the recombinant protein. However, due to positional effects resulting from the neighboring chromatin, transgenes are often expressed at low levels in these cells. While previous studies demonstrated that matrix attachment regions (MARs) can be utilized to increase transgene expression by buffering transgene silencing, the mechanism by which this occurs is poorly understood. We therefore performed a deletion analysis of the human β-globin MAR sequence to characterize the regions that are necessary to enhance transgene expression in CHO cells. Our results indicate that of the six β-globin MAR fragments tested (MAR-1-6; nucleotides 1-540, 420-1020, 900-1500, 1380-1980, 1860-2460, and 2340-2999, respectively), MAR-2, followed by MAR-3, was the most effective region for promoting stable and elevated transgene expression. Meanwhile, bioinformatic analyses demonstrated that these fragments encode a MAR-like motif and several transcription factor binding sites, including special AT-rich binding protein 1 (SATB1), CCAAT-enhancer-binding proteins (C/EBP), CCCTC-binding factor (CTCF), and Glutathione (GSH) binding motifs, indicating that these elements may contribute to the MAR-mediated enhancement of transgene expression. In addition, we found that truncated MAR derivatives yield more stable transgene expression levels than transgenes lacking the MAR. We concluded that the MAR-mediated transcriptional activation of transgenes requires a specific AT-rich sequence, as well as specific transcription factor-binding motifs. PMID:26869318

  6. Molecular epidemiology of Mycobacterium tuberculosis strains isolated from different regions of Italy and Pakistan.

    PubMed Central

    Sechi, L A; Zanetti, S; Delogu, G; Montinaro, B; Sanna, A; Fadda, G

    1996-01-01

    The use of the (GTG)5 oligonucleotide, a repetitive marker in the Mycobacterium tuberculosis chromosome, as a primer in association with an IS6110 outlooking primer has been successfully applied to a PCR-based fingerprinting method. This method classified 62 strains of M. tuberculosis, isolated from human immunodeficiency virus-seropositive and -seronegative patients in different regions of Italy and Pakistan, as having 53 different patterns. The results were compared with traditional IS6110 fingerprinting, by which 47 distinct patterns were observed. PMID:8784602

  7. Molecular analysis of 16S-23S spacer regions of Acetobacter species.

    PubMed

    Kretová, M; Grones, J

    2005-01-01

    16S-23S rDNA internal transcribed spacer regions (ITS) similarities were determined in 8 Acetobacter and 1 Gluconacetobacter strains. ITS-PCR amplification of the 16S-23S spacers showed 2 products of similar size in 7 strains; only 1 product of similar size was found in the 2 remaining strains. Analysis of the PCR products using restriction endonucleases HaeIII, HpaII and AluI revealed 3 different restriction groups of A. pasteurianus for AluI and HaeIII, and 4 restriction groups for HpaII. ITS nucleotide sequences of all studied strains exhibited a 52-98% similarity. PMID:16408846

  8. Molecular hydrogen line ratios in four regions of shock-excited gas

    NASA Technical Reports Server (NTRS)

    Burton, M. G.; Brand, P. W. J. L.; Geballe, T. R.; Webster, A. S.

    1989-01-01

    Five emission lines of molecular hydrogen, with wavelengths in the ranges of 2.10-2.25 and 3.80-3.85 microns, have been observed in four objects of different type in which the line emission is believed to be excited by shocks. The relative intensities of the lines 1 - 0 S(1):1 - 0 S(O):2 - 1 S(1) are approximately 10.5:2.5:1.0 in all four objects. The 0 - 0 S(13):1 - 0 O(7) line ratio, however, varies from 1.05 in OMC-1 to about 2.3 in the Herbig-Haro object HH 7. The excitation temperature derived from the S(13) and O(7) lines is higher than that derived from the 1 - 0 and 2 - 1 S(1) lines in all four objects, so the shocked gas in these objects cannot be characterized by a single temperature. The constancy of the (1-0)/(2-1) S(1) line ratio between sources suggests that the post-shock gas is 'thermalized' in each source. The S(13)/O(7) ratio is particularly sensitive to the density and temperature conditions in the gas.

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

    PubMed

    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. PMID:26174574

  10. Molecular Probe Dynamics Reveals Suppression of Ice-Like Regions in Strongly Confined Supercooled Water

    PubMed Central

    Banerjee, Debamalya; Bhat, Shrivalli N.; Bhat, Subray V.; Leporini, Dino

    2012-01-01

    The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice [Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448–11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed. PMID:23049747

  11. Molecular analysis of mitochondrial hypervariable region 1 in 394 Japanese individuals.

    PubMed

    Kato, Hideaki; Maeno, Yoshitaka; Ohira, Hiroshi; Yamada, Yoshihiro; Nagao, Masataka

    2009-04-01

    Mitochondrial DNA (mtDNA) is a powerful tool for forensic casework when the resource is highly putrefied or very limited. It is important that mtDNA sequence databases continue to be generated and published, to extend mtDNA typing capability to additional populations and to increase the size of existing databases. The aim of this study was to analyze hypervariable region 1 (HV1) of mtDNA and establish a new database of mtDNA in Japanese population. Three hundred and ninety-four unrelated Japanese individuals were investigated. They were classified into 193 haplotypes based on HV1 sequence. Nucleotide substitutions were clustered in several positions and were 79% at 16,223, 50% at 16,362, and 29% at 16,189. Transition accounts for 81% of all the mutations and especially transition from cytosine to thymine (33%) was the most frequent substitution. 16,223-16,362 was observed in 34 individuals, following 16,129-16,223-16,362 in 29 individuals, and haplotype 16,223-16,278-16,362 in 14 individuals. Genetic diversity and random match probability in this population were estimated to 0.987% and 1.95%, respectively. In conclusion, HV1 of mitochondria sequence has a high discrimination power, but in addition to HV1, analysis of other region such as HV2 and HV3 are required in certain cases. PMID:19254861

  12. Cytogenetic and molecular delineation of the smallest commonly deleted region of chromosome 5 in malignant myeloid diseases.

    PubMed Central

    Le Beau, M M; Espinosa, R; Neuman, W L; Stock, W; Roulston, D; Larson, R A; Keinanen, M; Westbrook, C A

    1993-01-01

    Loss of a whole chromosome 5 or a deletion of its long arm (5q) is a recurring abnormality in malignant myeloid neoplasms. To determine the location of genes on 5q that may be involved in leukemogenesis, we examined the deleted chromosome 5 homologs in a series of 135 patients with malignant myeloid diseases. By comparing the breakpoints, we identified a small segment of 5q, consisting of band 5q31, that was deleted in each patient. This segment has been termed the critical region. Distal 5q contains a number of genes encoding growth factors, hormone receptors, and proteins involved in signal transduction or transcriptional regulation. These include several genes that are good candidates for a tumor-suppressor gene, as well as the genes encoding five hematopoietic growth factors (CSF2, IL3, IL4, IL5, and IL9). By using fluorescence in situ hybridization, we have refined the localization of these genes to 5q31.1 and have determined the order of these genes and of other markers within 5q31. By hybridizing probes to metaphase cells with overlapping deletions involving 5q31, we have narrowed the critical region to a small segment of 5q31 containing the EGR1 gene. The five hematopoietic growth factor genes and seven other genes are excluded from this region. The EGR1 gene was not deleted in nine other patients with acute myeloid leukemia who did not have abnormalities of chromosome 5. By physical mapping, the minimum size of the critical region was estimated to be 2.8 megabases. This cytogenetic map of 5q31, together with the molecular characterization of the critical region, will facilitate the identification of a putative tumor-suppressor gene in this band. PMID:8516290

  13. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region.

    PubMed

    Dong, Lingli; Huo, Naxin; Wang, Yi; Deal, Karin; Luo, Ming-Cheng; Wang, Daowen; Anderson, Olin D; Gu, Yong Qiang

    2012-12-01

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A(u)A(u)) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A(m)A(m)), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A(u) genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A(u) genome. The difference in the compared region between A(u) and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A(u) than to A(m). The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A(u) sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat. PMID:23052831

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

    EPA Science Inventory

    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 ...

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

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  16. A molecular phylogeny of aquatic gastropods provides a new perspective on biogeographic history of the Snake River Region.

    PubMed

    Hershler, Robert; Liu, Hsiu-Ping

    2004-09-01

    Mitochondrial DNA sequences of aquatic gastropods of the subgenus Pyrgulopsis (Natricola) were analyzed to test a commonly accepted hypothesis concerning the early history of the Snake River in the northwestern US. Distributions of Natricola and other regional biota were previously used to infer that the Snake River flowed to the Pacific through southeastern Oregon and northern California during the Neogene prior to its capture by the Columbia River in the late Pliocene (2 Ma). A molecular phylogeny based on partial sequences of COI and NDI (1149 bp) indicates that the Natricola clade is restricted to the modern Snake-Columbia River Basin and the Oregon Lakes region whereas northern California populations previously assigned to this subgenus belong to other lineages. The Natricola clade is not deeply subdivided into Oregon Lakes and Snake River Basin units consistent with late Pliocene fragmentation of the hypothesized paleodrainage, but instead is shallowly structured and contains multiple transitions among these two geographic areas. The strongly supported sister relationship between Natricola and a species from northwest Nevada (P. imperialis) is consistent with a recent proposal that the ancestral Snake River did not flow through southeast Oregon but instead flowed south to the Humboldt River. Within the context of this hypothesis, the multiple transitions between the Snake River Basin and the Oregon Lakes region that occurred within Natricola may be attributed to a late Pleistocene connection between these areas that was unrelated to the early course of the Snake River. PMID:15288067

  17. Molecular characterization and sequence analysis of the 2B region of Aichivirus C strains in Japan and Thailand.

    PubMed

    Okitsu, Shoko; Khamrin, Pattara; Thongprachum, Aksara; Kalesaran, Angela F C; Takanashi, Sayaka; Shimizu, Hiroyuki; Maneekarn, Niwat; Mizuguchi, Masashi; Hayakawa, Satoshi; Ushijima, Hiroshi

    2014-08-01

    Aichivirus C is the third species in the genus Kobuvirus, family Picornaviridae, and the virus is circulating in pigs worldwide. Aichivirus A in humans and Aichivirus B in cows have been shown to associate with diarrheal diseases, however, the pathogenesis of Aichivirus C has not been demonstrated clearly. In this study, the full genome nucleotide sequence of the Thai strain, CMP06/2007/THA collected from stool sample of a diarrheal piglet was analyzed and identified as a variant type with a 90-nt deletion in the 2B-coding region. In addition, molecular characterization of nucleotide sequences of the 2B-coding region of Aichivirus C strains from six diarrheal and six healthy piglets in Thailand, and four strains from healthy pigs in Japan revealed that all of the strains in this study were variant types. These findings indicate that variant strains of Aichivirus C are circulating in Asian countries such as China, Thailand and Japan, and deletion of tandem repeat of 2B-region is unlikely to associate with the pathogenesis of the virus. PMID:24837671

  18. Molecular and phenotypic data support the recognition of the Wakatobi Flowerpecker (Dicaeum kuehni) from the unique and understudied Sulawesi region.

    PubMed

    Kelly, Seán B A; Kelly, David J; Cooper, Natalie; Bahrun, Andi; Analuddin, Kangkuso; Marples, Nicola M

    2014-01-01

    Accurate estimates of species richness are essential to macroecological and macroevolutionary research, as well as to the effective management and conservation of biodiversity. The resolution of taxonomic relationships is therefore of vital importance. While molecular methods have revolutionised taxonomy, contemporary species delimitation requires an integrative, multi-disciplinary approach. Despite boasting a remarkably high level of endemism, the avifauna of the Sulawesi region of Indonesia remains poorly studied. Previous studies of avian diversity in Sulawesi have focussed predominantly on phenotypic characteristics, thus potentially overlooking any genetically distinct lineages. Grey-sided Flowerpecker Dicaeum celebicum populations from the Wakatobi archipelago were originally described as a separate species from those on nearby mainland Sulawesi. However, for reasons that remain unknown, the Wakatobi populations were reclassified as a subspecies of the mainland form. Combining estimates of genetic divergence with phylogenetic and morphological analyses, we reassessed the status of Wakatobi populations. Our results describe the Wakatobi populations as a separate species to those on mainland Sulawesi; reproductively isolated, genetically and morphologically distinct. We therefore recommend the reclassification of these populations to their original status of Dicaeum kuehni and propose the vernacular name 'Wakatobi Flowerpecker'. In consideration of our findings and the lack of integrative ornithological research within the Sulawesi region, we believe species richness and avian endemism within the region are underestimated. PMID:24896822

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region.

    PubMed Central

    Walker, D C; McCloskey, D A; Simard, L R; McInnes, R R

    1990-01-01

    Argininosuccinic acid lyase (ASAL) deficiency is a clinically heterogeneous autosomal recessive urea cycle disorder. We previously established by complementation analysis that 28 ASAL-deficient patients have heterogeneous mutations in a single gene. To prove that the ASAL structural gene is the affected locus, we sequenced polymerase chain reaction-amplified ASAL cDNA of a representative mutant from the single complementation group. Fibroblast strain 944 (approximately 1% of residual ASAL activity), from a late-onset patient who was the product of a consanguineous mating, had only a single base-pair change in the coding region, a C-283----T transition at a CpG dinucleotide in exon 3. This substitution converts Arg-95 to Cys (R95C), occurs in a stretch of 13 residues that is identical in yeast and human ASAL, and was present in both of the patient's alleles but not in 14 other mutant or 10 normal alleles. Expression in COS cells demonstrated that the R95C mutation produces normal amounts of ASAL mRNA but little protein and less than 1% ASAL activity. We observed that amplified cDNA from mutant 944 and normal cells (liver, keratinocytes, lymphoblasts, and fibroblasts) contained, in addition to the expected 5' 513-base-pair band, a prominent 318-base-pair ASAL band formed by the splicing of exon 2 from the transcript. The short transcript maintains the ASAL reading frame but removes Lys-51, a residue that may be essential for catalysis, since it binds the argininosuccinate substrate. We conclude (i) that the identification of the R95C mutation in strain 944 demonstrates that virtually all ASAL deficiency results from defects in the ASAL structural gene and (ii) that minor alternative splicing of the coding region occurs at the ASAL locus. Images PMID:2263616

  1. Molecular analysis of human argininosuccinate lyase: Mutant characterization and alternative splicing of the coding region

    SciTech Connect

    Walker, D.C. ); McCloskey, D.A.; Simard, L.R.; McInnes, R.R. )

    1990-12-01

    Argininosuccinic acid lyase (ASAL) deficiency is a clinically heterogeneous autosomal recessive urea cycle disorder. The authors previously established by complementation analysis that 29 ASAL-deficient patients have heterogeneous mutations in a single gene. To prove that the ASAL structural gene is the affected locus, they sequenced polymerase chain reaction-amplified ASAL cDNA of a representative mutant from the single complementation group. Fibroblast strain 944 from a late-onset patient who was the product of a consanguineous mating, had only a single base-pair change in the coding region, a C-283{r arrow} T transition at a CpG dinucleotide in exon 3. This substitution converts Arg-95 to Cys (R95C), occurs in a stretch of 13 residues that is identical in yeast and human ASAL, and was present in both of the patient's alleles but not in 14 other mutant or 10 normal alleles. They observed that amplified cDNA from mutant 944 and normal cells (liver, keratinocytes, lymphoblasts, and fibroblasts) contained, in addition to the expected 5{prime} 513-base-pair band, a prominent 318-base-pair ASAL band formed by the splicing of exon 2 from the transcript. The short transcript maintains the ASAL reading frame but removes Lys-51, a residue that may be essential for catalysis, since it binds the argininosuccinate substrate. They conclude (i) that the identification of the R95C mutation in strain 944 demonstrates that virtually all ASAL deficiency results from defects in the ASAL structural gene and (ii) that minor alternative splicing of the coding region occurs at the ASAL locus.

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

    PubMed

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

    2016-01-01

    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

  3. Molecular detection of Leishmania spp. isolated from cutaneous lesions of patients referred to Herat regional hospital, Afghanistan.

    PubMed

    Mosawi, S H; Dalimi, A

    2016-12-01

    Cutaneous leishmaniasis is one of the main public health problems in Afghanistan, particularly in Herat. To identify Leishmania spp., molecular techniques were applied to samples from 64 cutaneous leishmaniasis patients referred to Herat regional hospital during 2013. Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the ribosomal RNA gene internal transcribed spacer-1 (ITS1) was used. Most of the patients demonstrated dry type single lesions on the head. The results of direct microscopy detection using Giemsastained skin scrapings were compared with that of ITS PCR-RFLP for the diagnosis of cutaneous leishmaniasis. Light microscopy examination showed 37/64 positive cases (58%). PCR revealed 50 positive cases (78%), from which ITS PCR-RFLP identified 48 cases (96%) as L. tropica and 2 cases (4%) as L. major. Cutaneous leishmaniasis in Herat appears to be endemic and of the clinically dry type, caused mainly by L. tropica and occasionally by L. major. PMID:26996360

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

    PubMed

    Al-Saleh, Mohammed A; Amer, Mahmoud A

    2013-12-01

    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. PMID:25288969

  5. Molecular cloning of the mouse CCK gene: expression in different brain regions and during cortical development.

    PubMed Central

    Vitale, M; Vashishtha, A; Linzer, E; Powell, D J; Friedman, J M

    1991-01-01

    In this paper we describe experiments that address specific issues concerning the regulation of the mouse cholecystokinin gene in brain and intestine. The mouse cholecystokinin gene was cloned and sequenced. Extensive homology among the mouse, man and rat genes was noted particularly in the three exons and the regions upstream of the RNA start site. RNAse protection assays for each of the three exons were used to demonstrate that CCK is expressed in only a subset of tissues and that the same cap site and splice choices are used in brain, intestine as well as in cerebellum, cortex, midbrain, hypothalamus and hippocampus. CCK RNA was also noted to be detectable in kidney. Thus the same gene using the same promoter is expressed in subsets of cells that differ in their biochemical, morphologic and functional characteristics. The level of expression of CCK was also monitored during mouse cortical development and the appearance of CCK RNA was compared to glutamate decarboxylase (GAD), enkephalin and somatostatin. It was noted that each of these cortical markers was first expressed at different times during cortical development. The appearance of CCK RNA during intestinal development was also measured and found to precede appearance in cortex by several days. Images PMID:2011497

  6. Molecular basis for mid-region amyloid-β capture by leading Alzheimer's disease immunotherapies

    PubMed Central

    Crespi, Gabriela A. N.; Hermans, Stefan J.; Parker, Michael W.; Miles, Luke A.

    2015-01-01

    Solanezumab (Eli Lilly) and crenezumab (Genentech) are the leading clinical antibodies targeting Amyloid-β (Aβ) to be tested in multiple Phase III clinical trials for the prevention of Alzheimer's disease in at-risk individuals. Aβ capture by these clinical antibodies is explained here with the first reported mid-region Aβ-anti-Aβ complex crystal structure. Solanezumab accommodates a large Aβ epitope (960 Å2 buried interface over residues 16 to 26) that forms extensive contacts and hydrogen bonds to the antibody, largely via main-chain Aβ atoms and a deeply buried Phe19-Phe20 dipeptide core. The conformation of Aβ captured is an intermediate between observed sheet and helical forms with intramolecular hydrogen bonds stabilising residues 20–26 in a helical conformation. Remarkably, Aβ-binding residues are almost perfectly conserved in crenezumab. The structure explains the observed shared cross reactivity of solanezumab and crenezumab with proteins abundant in plasma that exhibit this Phe-Phe dipeptide. PMID:25880481

  7. Molecular basis for mid-region amyloid-β capture by leading Alzheimer's disease immunotherapies.

    PubMed

    Crespi, Gabriela A N; Hermans, Stefan J; Parker, Michael W; Miles, Luke A

    2015-01-01

    Solanezumab (Eli Lilly) and crenezumab (Genentech) are the leading clinical antibodies targeting Amyloid-β (Aβ) to be tested in multiple Phase III clinical trials for the prevention of Alzheimer's disease in at-risk individuals. Aβ capture by these clinical antibodies is explained here with the first reported mid-region Aβ-anti-Aβ complex crystal structure. Solanezumab accommodates a large Aβ epitope (960 Å(2) buried interface over residues 16 to 26) that forms extensive contacts and hydrogen bonds to the antibody, largely via main-chain Aβ atoms and a deeply buried Phe19-Phe20 dipeptide core. The conformation of Aβ captured is an intermediate between observed sheet and helical forms with intramolecular hydrogen bonds stabilising residues 20-26 in a helical conformation. Remarkably, Aβ-binding residues are almost perfectly conserved in crenezumab. The structure explains the observed shared cross reactivity of solanezumab and crenezumab with proteins abundant in plasma that exhibit this Phe-Phe dipeptide. PMID:25880481

  8. First Molecular Identification and Genetic Characterization of Theileria lestoquardi in Sheep of the Maghreb Region.

    PubMed

    Rjeibi, M R; Darghouth, M A; Rekik, M; Amor, B; Sassi, L; Gharbi, M

    2016-06-01

    Theileria lestoquardi is the most prominent Theileria species in small ruminants that causes malignant theileriosis of sheep in Africa and Asia. In the present survey, blood samples and ticks were collected in Kebili (southern Tunisia) from 166 Queue Fine de l'Ouest sheep. Giemsa-stained blood smears, immunofluorescent antibody test (IFAT) and PCR were performed. The DNA was extracted from blood and analysed by PCR targeting 18S rRNA gene of Theileria spp. and then sequenced. A total number of 140 ticks were collected from a total number of 166 sheep during the four seasons. The ticks belonged to two genera and 4 species; the most frequent tick was Hyalomma excavatum 84.3% (118/140) and then Rhipicephalus spp. 15.7% (22/140). Only two animals had positive Giemsa-stained blood smears, and they were also positive by IFAT. The amplicons had 99.3 and 99.6% homology with the BLAST published T. lestoquardi amplicons. To our knowledge, this is the first report of T. lestoquardi in small ruminants within the Maghreb region. PMID:25208526

  9. Cellular and molecular determinants targeting the Caenorhabditis elegans PHR protein RPM-1 to perisynaptic regions.

    PubMed

    Abrams, Benjamin; Grill, Brock; Huang, Xun; Jin, Yishi

    2008-03-01

    Caenorhabditis elegans RPM-1 is a member of a conserved protein family, the PHR proteins, that includes human Pam, mouse Phr1, zebrafish Esrom, and Drosophila Highwire. PHR proteins play important roles in the development of the nervous system. In particular, mutations in rpm-1 cause a disruption of synaptic architecture, affecting the distribution of synaptic vesicles and the number of presynaptic densities. Using antibodies against RPM-1, we determined the localization of the endogenous RPM-1 protein in wild-type and in several mutants that affect synaptic development. Our analyses show that, in mature neurons, RPM-1 resides in a distinct region that is close to, but does not overlap with, the synaptic exo- and endocytosis domains. The localization of RPM-1 occurs independently of several proteins that function in the transport or assembly of synapse components, and its abundance is partially dependent on its binding partner the F-box protein FSN-1. RPM-1 has been shown to target the MAPKKK DLK-1 for degradation. We show that activated DLK-1 may be preferentially targeted for degradation. Furthermore, using transgene analysis, we identified a critical role of the conserved PHR domain of RPM-1 in its subcellular localization. PMID:18224716

  10. Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

    PubMed Central

    Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

    2011-01-01

    Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and

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

    PubMed

    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. PMID:25027738

  12. Communication: Phase diagram of C{sub 36} by atomistic molecular dynamics and thermodynamic integration through coexistence regions

    SciTech Connect

    Abramo, M. C.; Caccamo, C. Costa, D.; Munaò, G.

    2014-09-07

    We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C{sub 36}. We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C{sub 36}, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C{sub 36} fullerite and of its liquid state, at variance with what previously experienced for C{sub 60}.

  13. Two Novel Y-Type High Molecular Weight Glutenin Genes in Chinese Wheat Landraces of the Yangtze-River Region

    PubMed Central

    Zhang, Yujuan; Islam, Shahidul; Sun, Dongfa; Ma, Wujun

    2015-01-01

    High molecular weight glutenin subunits (HMW-GSs) are key determinants for the end-use quality of wheat. Chinese wheat landraces are an important resource for exploring novel HMW-GS genes to improve the wheat baking quality. Two novel Glu-1Dy HMW-GSs (designated as 1Dy12.6 and 1Dy12.7) were identified and cloned from two Chinese wheat landraces Huazhong830 and Luosimai. The 1Dy12.6 and 1Dy12.7 subunits were deposited as the NCBInr Acc. No KR262518, and KR262519, respectively. The full open reading frames (ORFs) of 1Dy12.6 and 1Dy12.7 were 2022 bp and 1977 bp, encoding for proteins of 673 and 658 amino acid residues, respectively. Each contains four typical primary regions of HMW-GSs (a signal peptide, N- and C-terminal regions, and a central repetitive region). Their deduced molecular masses (70,165 Da and 68,400 Da) were strikingly consistent with those identified by MALDI-TOF-MS (69,985Da and 68,407 Da). The 1Dy12.6 is the largest 1Dy glutenin subunits cloned in common wheat up to date, containing longer repetitive central domains than other 1Dy encoded proteins. In comparison with the most similar active 1Dy alleles previously reported, the newly discovered alleles contained a total of 20 SNPs and 3 indels. The secondary structure prediction indicated that 1Dy12.6 and 1Dy12.7 have similar proportion of α-helix, β-turn, and β-bend to those of 1Dy10 (X12929). The phylogenetic analysis illustrated that the x- and y-type subunits of glutenins were well separated, but both 1Dy12.6 and 1Dy12.7 were clustered with the other Glu-1Dy alleles. Our results revealed that the 1Dy12.6 and 1Dy12.7 subunit have potential to strengthen gluten polymer interactions, and are valuable genetic resources for wheat quality improvement. PMID:26540300

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

    PubMed Central

    Dixon, Brent; Dion, Réjean; Levesque, Benoît; Cantin, Philippe; Cédilotte, Lyne; Ndao, Momar; Proulx, Jean-François; Yansouni, Cedric P.

    2016-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions/Significance 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

  15. A study of dynamical processes in the Orion KL region using ALMA—probing molecular outflow and inflow

    SciTech Connect

    Wu, Yuefang; Liu, Tie; Qin, Sheng-Li

    2014-08-20

    This work reports high spatial resolution observations toward the Orion KL region with high critical density lines of CH{sub 3}CN (12{sub 4}-11{sub 4}) and CH{sub 3}OH (8{sub –1,8}-7{sub 0,7}), as well as a continuum at ∼1.3 mm band. The observations were made using the Atacama Large Millimeter/Submillimeter Array with a spatial resolution of ∼1.''5 and sensitivity of about 0.07 K and ∼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 east and south of the region that are 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{sub 2} jets, the young stellar objects, and molecular gas suggest that BN is the explosive center. The burst time was estimated to be ≤1300 yr. At the same time, signatures of gravitational collapse toward Source I and the hot core were detected with material infall velocities of 1.5 km s{sup –1} and ∼0.6 km s{sup –1}, corresponding to mass accretion rates of 1.2 × 10{sup –3} M {sub ☉}/yr and 8.0 × 10{sup –5} M {sub ☉}/yr, respectively. These observations may support the belief that high-mass stars form via the accretion model, similar to their low-mass counterparts.

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

    PubMed

    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. PMID:25260692

  17. Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in diarrhoeic patients in the Qikiqtani Region, Nunavut, Canada

    PubMed Central

    Iqbal, Asma; Goldfarb, David M.; Slinger, Robert; Dixon, Brent R.

    2015-01-01

    Background Although the prevalences of infection with the protozoan parasites Cryptosporidium spp. and Giardia duodenalis in humans appear to be relatively high in the Canadian North, their transmission patterns are poorly understood. Objective To determine the detection rate and the molecular characteristics of Cryptosporidium spp. and Giardia duodenalis in diarrhoeic patients in the Qikiqtani (Baffin Island) Region of Nunavut, Canada, in order to better understand the burden of illness and the potential mechanisms of transmission. Study design/methods Diarrhoeal stool specimens (n=108) submitted to the Qikiqtani General Hospital for clinical testing were also tested for the presence of Cryptosporidium spp. and Giardia duodenalis using epifluorescence microscopy and polymerase chain reaction (PCR). DNA sequencing and restriction fragment length polymorphism (RFLP) analyses were performed on PCR-positive specimens to determine the species, genotypes and sub-genotypes of the parasites. Results Cryptosporidium was detected in 15.7% of the diarrhoeic patients, while Giardia was detected in 4.6%. DNA sequencing of a fragment of the small subunit rRNA gene indicated that all of the Cryptosporidium amplicons had a 100% homology to C. parvum, and a gp60 assay showed that all aligned with C. parvum sub-genotype IIa. Microsatellite analysis revealed 3 cases of sub-genotype IIaA15G2R1, 2 of IIaA15G1R and 1 case each of sub-genotypes IIaA16G1R1 and IIaA15R1. For Giardia, results based on the amplification of both the 16S rRNA gene and the gdh gene were generally in agreement, and both DNA sequencing and RFLP demonstrated the presence of the G. duodenalis Assemblage B genotype. Conclusions Both C. parvum and G. duodenalis Assemblage B were present in human diarrhoeal stool specimens from Nunavut, which was suggestive of zoonotic transmission, although human-to-human transmission cannot be ruled out. To fully understand the public health significance of the different

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

    PubMed

    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. PMID:26061287

  19. Molecular and phylogenetic analysis of the porcine kobuvirus VP1 region using infected pigs from Sichuan Province, China

    PubMed Central

    2013-01-01

    Background Porcine kobuvirus (PKoV) is a member of the Kobuvirus genus within the Picornaviridae family. PKoV is distributed worldwide with high prevalence in clinically healthy pigs and those with diarrhea. Methods Fecal and intestinal samples (n = 163) from pig farms in Sichuan Province, China were obtained to determine the presence of PKoV using reverse transcription polymerase chain reaction assays. Specific primers were used for the amplification of the gene encoding the PKoV VP1 protein sequence. Sequence and phylogenetic analyses were conducted to clarify evolutionary relationships with other PKoV strains. Results Approximately 53% (87/163) of pigs tested positive for PKoV. PKoV was widespread in asymptomatic pigs and those with diarrhea. A high prevalence of PKoV was observed in pigs younger than 4 weeks and in pigs with diarrhea. Phylogenetic analysis of 36 PKoV VP1 protein sequences showed that Sichuan PKoV strains formed four distinct clusters. Two pigs with diarrhea were found to be co-infected with multiple PKoV strains. Sequence and phylogenetic analyses revealed diversity within the same host and between different hosts. Significant recombination breakpoints were observed between the CHN/SC/31-A1 and CHN/SC/31-A3 strains in the VP1 region, which were isolated from the same sample. Conclusion PKoV was endemic in Sichuan Province regardless of whether pigs were healthy or suffering from diarrhea. Based on our statistical analyses, we suggest that PKoV was the likely causative agent of high-mortality diarrhea in China from 2010. For the first time, we provide evidence for the co-existence of multiple PKoV strains in one pig, and possible recombination events in the VP1 region. Our findings provide further insights into the molecular properties of PKoV, along with its epidemiology. PMID:24025093

  20. Molecular epidemiology of rabies from Maranhão and surrounding states in the northeastern region of Brazil.

    PubMed

    Sato, G; Kobayashi, Y; Shoji, Y; Sato, T; Itou, T; Ito, F H; Santos, H P; Brito, C J C; Sakai, T

    2006-11-01

    Although many outbreaks of rabies have been reported in northern Brazil, few epidemiological studies of these outbreaks have been undertaken. In this study, molecular epidemiological analyses were performed using 41 rabies virus samples isolated in the Maranhão (MA), Pará (PA), and Tocantins (TO) states of northeastern Brazil. A 599-bp region of the glycoprotein (G) gene was first amplified from each sample by RT-PCR, then sequenced and subjected to phylogenetic analysis. A phylogenetic tree divided the 41 isolates into two clades: Clade I was associated with terrestrial carnivores and Clade II was associated with vampire bats. The Clade I isolates were further sub-divided into two groups. The first group was closer to carnivore isolates that predominate in central Brazil, whereas the second group more closely resembled wild fox isolates from the northeastern coastal state of Paraíba (PB). MA isolates of Clade II formed an entirely separate group. These results demonstrate that bat- and dog-transmitted rabies occur in northwestern Brazil. PMID:16773238

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

    PubMed

    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. PMID:24502561

  2. Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among clades in the homeobox region.

    PubMed

    Segatto, Ana Lúcia A; Thompson, Claudia E; Freitas, Loreta B

    2016-07-01

    Gene families have been shown to play important roles in plant evolution and are associated with diversification and speciation. Genes of WUSCHEL-related homeobox family of transcription factors have important functions in plant development and are correlated with the appearance of evolutionary novelties. There are several published studies related to this family, but little is known about the relationships among the main clades in the phylogeny and the molecular evolution of the family. In this study, we obtained a well-resolved Bayesian phylogenetic tree establishing the relationships among the main clades and determining the position of Selaginella moellendorffii WOX genes. Moreover, a correlation was identified between the number of genes in the genomes and the events of whole-genome duplications. The intron-exon structure is more consistent across the modern clade, which appeared more recently in the WOX evolutionary history, and coincides with the development of higher complexity in plant species. No positive selection was detected among sites through the branches in the tree. However, with regard to the main clades, functional divergence among certain amino acids in the homeodomain region was found. Relaxed purifying selection could be the main driving force in the evolution of these genes and in agreement with some genes have been demonstrated to be functionally redundant. PMID:27150824

  3. Far-infrared molecular lines from low- to high-mass star forming regions observed with Herschel

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

    Aims: Our aim is to study the response of the gas-to-energetic processes associated with high-mass star formation and compare it with previously published studies on low- and intermediate-mass young stellar objects (YSOs) using the same methods. The quantified far-IR line emission and absorption of CO, H2O, OH, and [O i] reveals the excitation and the relative contribution of different atomic and molecular species to the gas cooling budget. Methods: Herschel/PACS spectra covering 55-190 μm are analyzed for ten high-mass star forming regions of luminosities Lbol ~ 104-106 L⊙ and various evolutionary stages on spatial scales of ~104 AU. Radiative transfer models are used to determine the contribution of the quiescent envelope to the far-IR CO emission. Results: The close environments of high-mass protostars show strong far-IR emission from molecules, atoms, and ions. Water is detected in all 10 objects even up to high excitation lines, often in absorption at the shorter wavelengths and in emission at the longer wavelengths. CO transitions from J = 14 - 13 up to typically 29 - 28 (Eu/kB ~ 580-2400 K) show a single temperature component with a rotational temperature of Trot ~ 300 K. Typical H2O excitation temperatures are Trot ~250 K, while OH has Trot ~ 80 K. Far-IR line cooling is dominated by CO (~75%) and, to a smaller extent, by [O i] (~20%), which becomes more important for the most evolved sources. H2O is less important as a coolant for high-mass sources because many lines are in absorption. Conclusions: Emission from the quiescent envelope is responsible for ~45-85% of the total CO luminosity in high-mass sources compared with only ~10% for low-mass YSOs. The highest- J lines (Jup ≥ 20) originate most likely in shocks, based on the strong correlation of CO and H2O with physical parameters (Lbol, Menv) of the sources from low- to high-mass YSOs. The excitation of warm CO described by Trot ~ 300 K is very similar for all mass regimes, whereas H2O

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

    PubMed

    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

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

    PubMed Central

    Kultanov, Berikbay Z.; Dosmagambetova, Raushan S.; Ivasenko, Svetlana A.; Tatina, Yelena S.; Kelmyalene, Assel A.; Assenova, Lyazzat H.

    2016-01-01

    BACKGROUND: Extreme environmental situation in the Aral crisis has caused a massive chemical pollution of the territory for decades with high doses of pesticides, herbicides. Discharge of industrial waste into the rivers that feed the Aral Sea has lead to the development of various pathological processes in the human body, as well as disruption of reproductive function in young men. AIM: To evaluate the performance of molecular cellular changes in the sperm of men under the influence of dust and salt aerosols in Aral Sea region. MATERIAL AND METHODS: Clinical and laboratory studies were conducted in men 5 settlements (Aralsk-city, v. Aiteke-Bi, v. Zhalagash, v. Zhusaly, v. Shieli). We have studied male ejaculate obtained after 4-5 days of abstinence, and placed it in a warm tube with a glass stopper. On the investigation proceeded ejaculate within 20-30 minutes after its preparation, during which time he was subjected to liquefaction. Isolation and quantification of ASF, RNA, DNA, and determining the fraction of histones in sperm was performed by the method of Markusheva and Savina. RESULTS: It was found that the value of ASF in the semen of men living in the zone of ecological disaster higher compared with the values of parameters in men living in the area of environmental crisis, and this trend is observed in all age groups. The study of circulating extracellular DNA and RNA in the sperm of men registered their decline with a corresponding increase of acid precursors that can be attributed to the degradation of nucleic acids under the influence of negative factors in the complex area of ecological trouble. Also, according to a study in men residing in the areas of environmental catastrophe at the age of 18-29 years, found an increased content of the H1 histone H2A lower total fraction, H3, H4 - and a sharp increase in histone H2B content - histones. CONCLUSIONS: Men living in environmentally disadvantaged areas of Kyzylorda region under the influence of dust and

  6. Susceptibility to thyroid autoimmune disease: molecular analysis of HLA-D region genes identifies new markers for goitrous Hashimoto's thyroiditis.

    PubMed

    Badenhoop, K; Schwarz, G; Walfish, P G; Drummond, V; Usadel, K H; Bottazzo, G F

    1990-11-01

    Hashimoto's thyroiditis has been shown to be associated with the HLA-specificities DR4 and DR5. Since former association studies yielded variable results, we used novel molecular typing methods to assess predisposing immunogenetic factors. Gene analysis of the HLA-DR-DQ and tumor necrosis factor region was performed in a group of Hashimoto's thyroiditis patients and randomly chosen controls using standards and nomenclature of the 10th International Histocompatibility Workshop. Genomic DNA of patients and controls was analyzed using a cDNA probe of the DQB1 gene. The resulting restriction fragment patterns allowed the determination of newly defined DQw-types 1-9. We find the strongest relative risk conferred by DQw7 (RR = 4.7), that is observed in 36 of 64 patients (56%) and only 21 of 98 controls (21%) (P corr less than 0.002). Comparison of DNA sequence variation in the DQB1 gene, that is found predominantly in Hashimoto's thyroiditis patients, indicates that codons 45 and 57 are critical features in DQw7 which distinguish it from other DQw specificities. The adjacent DQA1 genes also display a significant association with Hashimoto's thyroiditis (DQA1*0201/*0301 heterozygotes were found in 37% of patients and 15% controls, P less than 0.03). No significant association could be found with polymorphisms of the tumor necrosis factor gene. These results provide a new basis for the concept of genetic susceptibility in Hashimoto's thyroiditis and will help to elucidate the underlying autoimmune mechanisms that lead to disease at the functional level. PMID:1977755

  7. The effect of various atomic partial charge schemes to elucidate consensus activity-correlating molecular regions: a test case of diverse QSAR models.

    PubMed

    Kumar, Sivakumar Prasanth; Jha, Prakash C; Jasrai, Yogesh T; Pandya, Himanshu A

    2016-03-01

    The estimation of atomic partial charges of the small molecules to calculate molecular interaction fields (MIFs) is an important process in field-based quantitative structure-activity relationship (QSAR). Several studies showed the influence of partial charge schemes that drastically affects the prediction accuracy of the QSAR model and focused on the selection of appropriate charge models that provide highest cross-validated correlation coefficient ([Formula: see text] or q(2)) to explain the variation in chemical structures against biological endpoints. This study shift this focus in a direction to understand the molecular regions deemed to explain SAR in various charge models and recognize a consensus picture of activity-correlating molecular regions. We selected eleven diverse dataset and developed MIF-based QSAR models using various charge schemes including Gasteiger-Marsili, Del Re, Merck Molecular Force Field, Hückel, Gasteiger-Hückel, and Pullman. The generalized resultant QSAR models were then compared with Open3DQSAR model to interpret the MIF descriptors decisively. We suggest the regions of activity contribution or optimization can be effectively determined by studying various charge-based models to understand SAR precisely. PMID:25997097

  8. The molecular, temporal and region-specific requirements of the beta isoform of Calcium/Calmodulin-dependent protein kinase type 2 (CAMK2B) in mouse locomotion.

    PubMed

    Kool, Martijn J; van de Bree, Jolet E; Bodde, Hanna E; Elgersma, Ype; van Woerden, Geeske M

    2016-01-01

    Genetic approaches using temporal and brain region-specific restricted gene deletions have provided a wealth of insight in the brain regions and temporal aspects underlying spatial and associative learning. However, for locomotion such extensive studies are still scarce. Previous studies demonstrated that Camk2b(-/-) mice, which lack the β isoform of Calcium/Calmodulin-dependent protein kinase 2 (CAMK2B), show very severe locomotion deficits. However, where these locomotion deficits originate is unknown. Here we made use of novel Camk2b mutants (Camk2b(f/f) and Camk2b(T287A)), to explore the molecular, temporal and brain region-specific requirements of CAMK2B for locomotion. At the molecular level we found that normal locomotion requires Calcium/Calmodulin mediated activation of CAMK2B, but CAMK2B autonomous activity is largely dispensable. At a systems level, we found that global deletion of Camk2b in the adult mouse causes only mild locomotion deficits, suggesting that the severe locomotion deficits of Camk2b(-/-) mice are largely of developmental origin. However, early onset deletion of Camk2b in cerebellum, striatum or forebrain did not recapitulate the locomotion deficits, suggesting that these deficits cannot be attributed to a single brain area. Taken together, these results provide the first insights into the molecular, temporal and region-specific role of CAMK2B in locomotion. PMID:27244486

  9. The molecular, temporal and region-specific requirements of the beta isoform of Calcium/Calmodulin-dependent protein kinase type 2 (CAMK2B) in mouse locomotion

    PubMed Central

    Kool, Martijn J.; van de Bree, Jolet E.; Bodde, Hanna E.; Elgersma, Ype; van Woerden, Geeske M.

    2016-01-01

    Genetic approaches using temporal and brain region-specific restricted gene deletions have provided a wealth of insight in the brain regions and temporal aspects underlying spatial and associative learning. However, for locomotion such extensive studies are still scarce. Previous studies demonstrated that Camk2b–/– mice, which lack the β isoform of Calcium/Calmodulin-dependent protein kinase 2 (CAMK2B), show very severe locomotion deficits. However, where these locomotion deficits originate is unknown. Here we made use of novel Camk2b mutants (Camk2bf/f and Camk2bT287A), to explore the molecular, temporal and brain region-specific requirements of CAMK2B for locomotion. At the molecular level we found that normal locomotion requires Calcium/Calmodulin mediated activation of CAMK2B, but CAMK2B autonomous activity is largely dispensable. At a systems level, we found that global deletion of Camk2b in the adult mouse causes only mild locomotion deficits, suggesting that the severe locomotion deficits of Camk2b–/– mice are largely of developmental origin. However, early onset deletion of Camk2b in cerebellum, striatum or forebrain did not recapitulate the locomotion deficits, suggesting that these deficits cannot be attributed to a single brain area. Taken together, these results provide the first insights into the molecular, temporal and region-specific role of CAMK2B in locomotion. PMID:27244486

  10. Prevalence and molecular basis of glucose-6-phosphate dehydrogenase deficiency in Afghan populations: implications for treatment policy in the region

    PubMed Central

    2013-01-01

    Background Glucose-6-phosphate dehydrogenase deficiency (G6PD), an x-linked inherited enzymopathy, is a barrier to malaria control because primaquine cannot be readily applied for radical cure in individuals with the condition. In endemic areas, including in Afghanistan, the G6PD status of vivax patients is not routinely determined so the drug is rarely, if ever, prescribed even though it is included as a recommended treatment in local, regional and global guidelines. This study assessed the prevalence and genotype of G6PD deficiency in Afghan populations and examined the need for routine G6PD testing as a malaria treatment and control tool. Methods A cross-sectional household survey was conducted using random sampling in five Afghan cities to determine the prevalence of G6PD deficiency in Afghan ethnic groups. Filter-paper blood spots were analysed for phenotypic G6PD deficiency using a fluorescent spot test. Molecular analysis was conducted to identify the genetic basis of the disorder. Results Overall, 45/1,436 (3.1%) people were G6PD deficient, 36/728 (5.0%) amongst males and 9/708 (1.3%) amongst females. Amongst males the prevalence was highest in the Pashtun ethnic group (10%, 26/260) while in Tajik males it was 8/250 (3.2%); in Hazara males it was 1/77 (1.3%) and in Uzbek males is was 0/125. Genetic testing in those with deficiency showed that all were of the Mediterranean type (Med-) characterized by a C-T change at codon 563 of the G6PD gene. Conclusion Prevalence of G6PD deficiency in Afghanistan varies considerably by ethnic group and is predominantly of the Mediterranean type. G6PD deficient individuals are susceptible to potentially severe and life-threatening haemolysis after standard primaquine treatment. If the aim of increasing access to radical treatment of vivax is to be successful reliable G6PD testing needs to be made routinely available within the health system. PMID:23834949

  11. Abundant molecular gas and inefficient SF in intra-cluster regions of a ram pressure stripped tail

    NASA Astrophysics Data System (ADS)

    Jáchym, P.; Sun, M.; Combes, F.; Cortese, L.; Kenney, J. D. P.

    2015-02-01

    For the first time in any ram pressure stripped galaxy, we detect large amounts of cold molecular gas in the X-ray bright, and star forming tail of ESO 137-001 in the Norma cluster. We find very low star formation efficiency in the stripped gas, similar to values found in the outer spiral disks where however molecular gas is mostly undetected. The results were recently published in Jáchym et al. (2014).

  12. [Nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana and its molecular evolution analyses].

    PubMed

    Hao, Gang-Ping; Wu, Zhong-Yi; Cao, Ming-Qing; Pelletier, Georges; Brunel, Dominique; Huang, Cong-Lin; Yang, Qing

    2004-12-01

    Intraspecific nucleotide polymorphism in the drought induced transcription factor CBF4 region of Arabidopsis thaliana was analyzed with 17 core accessions growing in different ecoclimate. High density of single nucleotide polymorphism (SNP) and insertion/deletion (Indel) were found, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. Nucleotide polymorphism in non-coding region was three times higher than that in coding region. In coding region of CBF4, SNP frequency is one SNP per 96.4 bp, one nonsynonymous mutation was detected from 25 av, 203 av and 244 av accessions, which is the 205th site amino acid variation: gly <--> val caused by the 1034th site (corresponding to 19,696 site nucleotide of GenBank No. AB015478 as 1) nucleotide variation: G <--> T. Statistical result of nucleotide diversity showed that linkage disequilibrium (LD) existed in large-scale region of CBF4 and recombination event was also detected in 5' non-coding region. Identical to the results of other genes of Arabidopsis, different regions of the gene were seemingly under different selective pressures. Balancing selection resulted in high nucleotide diversity in 3' non-coding region, and the neutral mutation hypothesis can explain the DNA polymorphism in coding region, whereas, nature positive selection in the population affected nucleotide variation in 5' non-coding region of gene. PMID:15633649

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

    PubMed Central

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

    2014-01-01

    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. PMID:24571598

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

    PubMed

    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. PMID:24571598

  15. Molecular and functional characterization of the promoter region of the mouse LDH/C gene: enhancer-assisted, Sp1-mediated transcriptional activation.

    PubMed Central

    Yang, J; Thomas, K

    1997-01-01

    Molecular and functional studies of the LDH/C 5' upstream promoter elements were undertaken to elucidate the molecular mechanisms involved in temporal activation of LDH/C gene expression in differentiating germ cells. Ligation mediated-PCR (LM-PCR) gene walking techniques were exploited to isolate a 2.1 kb fragment of the mouse LDH/C 5' promoter region. DNA sequence analysis of this isolated genomic fragment indicated that the mouse LDH/C promoter contained TATA and CCAT boxes as well as a GC-box (Sp1-binding site) situated upstream from the transcription start site. PCR-based in vivo DNase I footprinting analysis of a 600 bp fragment of the proximal LDH/C promoter region (-524/+38) in isolated mouse pachytene spermatocytes identified a single footprint over the GC-box motif. Three DNase I hypersensitive sites were also detectable in vivo, in a region containing (CT)n(GA)n repeats upstream from the CCAT box domain. Functional characterization of the promoter region was carried out in a rat C6 glioma cell line and an SV40 transformed germ cell line (GC-1 spg) using wild-type and mutated LDH/C promoter CAT reporter constructs. These studies provide experimental evidence suggesting that transcriptional activation of the LDH/C promoter is regulated by enhancer-mediated coactivation of the Sp1 proteins bound to the GC-box motif footprinted in vivo in pachytene spermatocytes. PMID:9153323

  16. Abundant Molecular Gas and Inefficient Star Formation in Intracluster Regions: Ram Pressure Stripped Tail of the Norma Galaxy ESO137-001

    NASA Astrophysics Data System (ADS)

    Jáchym, Pavel; Combes, Françoise; Cortese, Luca; Sun, Ming; Kenney, Jeffrey D. P.

    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 12CO(2-1) emission corresponding to more than 109 M ⊙ of H2 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 × 108 M ⊙ of H2 found in the most distant region is similar to molecular masses of tidal dwarf galaxies, though the standard Galactic CO-to-H2 factor could overestimate the H2 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 (τdep > 1010 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 H2 in the ESO 137-001 tail suggests that some stripped gas may survive ram pressure stripping in the molecular phase. Based on observations made with ESO telescopes at La Silla Paranal Observatory under program ID 088.B-0934.

  17. Using Molecular Models To Show Steric Clash in Peptides: An Illustration of Two Disallowed Regions in the Ramachandran Diagram

    ERIC Educational Resources Information Center

    Halkides, Christopher J.

    2013-01-01

    In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…

  18. Molecularly targeted radiosensitization chances towards gene aberration-due organ confined/regionally advanced prostate cancer radioresistance

    PubMed Central

    ALBERTI, C.

    2015-01-01

    Considering that the prostate cancer radioresistance occurs in a significant percentage – as 20–40% of prostate cancer (PCa) patients undergone external beam radiation therapy developing, within ten years, recurrent and more aggressive tumor – the resort to customized radiosensitizer measures, focusly targeting PCa radioresistance-linked individual molecular aberrations, can increase the successful outcomes of PCa radiotherapy. PMID:26188759

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

    SciTech Connect

    Leana-Cox, J. ); Jenkins, L. ); Palmer, C.G.; Plattner, R. ); Sheppard, L. ); Flejter, W.L. ); Zackowski, J. ); Tsien, F. ); Schwartz, S. )

    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.

  20. Iras-Selected Galactic Star-Forming Regions - Part One - New 6/16-5/23 Water Maser Detections in Molecular Cores North of DEC +15DEG

    NASA Astrophysics Data System (ADS)

    Palumbo, G. G. C.; Scappini, F.; Pareschi, G.; Codella, C.; Caselli, P.; Attolini, M. R.

    1994-01-01

    The results are presented of a survey, performed with the Medicina 32-m parabolic reflector, of a sample of IRAS-selected sources associated with molecular clouds for water masers at 22 GHz (616 → 523). The final aim is to study the occurrence of maser emission from star-forming regions in the very early stages of evolution. The whole sample consists of 1409 IRAS sources selected by applying Emerson's colour criteria. In the present paper, results are given for sources with declinations greater than +15°, belonging to two subsamples that satisfy more restrictive colour criteria which should identify ultracompact H II regions (subsample A, 288 sources) and H II regions (subsample B, 133 sources). The main result of the present study is that 59 IRAS sources in the samples are water maser emitters, 11 of which are new detections from the present survey.

  1. A prospective epidemiological study of new incident GISTs during two consecutive years in Rhône Alpes region: incidence and molecular distribution of GIST in a European region

    PubMed Central

    Cassier, P A; Ducimetière, F; Lurkin, A; Ranchère-Vince, D; Scoazec, J-Y; Bringuier, P-P; Decouvelaere, A-V; Méeus, P; Cellier, D; Blay, J-Y; Ray-Coquard, I

    2010-01-01

    Background: Preliminary data indicate that the molecular epidemiology of localised gastrointestinal stromal tumour (GIST) may be different from that of advanced GIST. We sought to investigate the molecular epidemiology of sarcomas, including GIST, in the Rhone-Alpes region in France. Patients and methods: A prospective and exhaustive study in the Rhone-Alpes Region in France to assess the precise incidence of primary sarcomas with systematic centralised pathological review and molecular analysis was conducted for 2 consecutive years. Results: Among 760 patients with a confirmed diagnosis of sarcoma, 131 (17%) had a GIST. The majority of patients had gastric primaries (61%). Mutational analysis could be performed in 106 tumour samples (74%), and 71 (67%) had exon 11 mutations. PDGFRA mutations were found in 16% of cases, which is twice as high as previously reported for advanced GIST. Conclusion: Data indicate that PDGFRA mutations in localised GIST may be twice as high as what was previously reported in patients with advanced disease. This finding may have important consequences for patients offered adjuvant imatinib, although most of these tumours are in the low-risk group. PMID:20588273

  2. Conjugated-protein mimics with molecularly imprinted reconstructible and transformable regions that are assembled using space-filling prosthetic groups.

    PubMed

    Takeuchi, Toshifumi; Mori, Takuya; Kuwahara, Atsushi; Ohta, Takeo; Oshita, Azusa; Sunayama, Hirobumi; Kitayama, Yukiya; Ooya, Tooru

    2014-11-17

    Conjugated-protein mimics were obtained using a new molecular imprinting strategy combined with post-imprinting modifications. An antibiotic was employed as a model template molecule, and a polymerizable template molecule was designed, which was composed of the antibiotic and two different prosthetic groups attached through a disulfide bond and Schiff base formation. After co-polymerization with a cross-linker, the template molecule was removed together with the prosthetic groups, yielding the apo-type scaffold. Through conjugation of the two different prosthetic groups at pre-determined positions within the apo-type scaffold, the apo cavity was transformed into a functionalized holo cavity, which enables the on/off switching of the molecular recognition ability, signal transduction activity for binding events, and photoresponsive activity. PMID:25257234

  3. Molecular and genetic analysis of the transferred DNA regions of the root-inducing plasmid of Agrobacterium rhizogenes.

    PubMed Central

    White, F F; Taylor, B H; Huffman, G A; Gordon, M P; Nester, E W

    1985-01-01

    The T-DNA regions of the root-inducing (Ri) plasmid pRiA4b of Agrobacterium rhizogenes were characterized. Two regions, designated TL-DNA and TR-DNA, were found to be integrated and stably maintained in the plant genome. The TL-DNA spanned a 15- to 20-kilobase region of pRiA4b and was separated from the TR-DNA region by at least 15 kilobases of nonintegrated plasmid DNA. The TR-DNA region also spanned a 15- to 20-kilobase region of pRiA4b and included a region of homology to the tms morphogenic loci of the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens. Eighteen deletions and 95 transposon insertions were generated in the T-DNA regions and tested for alterations in virulence. Insertions into four loci in the TL-DNA affected the morphology of root formation of Kalanchoë diagremontiana leaves and stems, but had no visible effects on other host plants. Insertions into two loci (tms-1 and tms-2) in the TR-DNA eliminated virulence symptoms on all plants tested, with the exception of K. diagremontiana stems, where sparse root formation occurred. Complementation experiments with Ri and Ti plasmid T-DNA mutations indicate that the tms genes of the two plasmids serve similar functions and suggest a functional relationship between one or more genes of the TL-DNA and the cytokinin synthesis locus tmr of the Ti plasmid. Images PMID:4044524

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

    PubMed

    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. PMID:27192892

  5. THE DISCOVERY OF THE YOUNGEST MOLECULAR OUTFLOW ASSOCIATED WITH AN INTERMEDIATE-MASS PROTOSTELLAR CORE, MMS-6/OMC-3

    SciTech Connect

    Takahashi, Satoko; Ho, Paul T. P.

    2012-01-20

    We present subarcsecond resolution HCN (4-3) and CO (3-2) observations made with the Submillimeter Array, toward an extremely young intermediate-mass protostellar core, MMS 6-main, located in the Orion Molecular Cloud 3 region (OMC-3). We have successfully imaged a compact molecular outflow lobe ( Almost-Equal-To 1000 AU) associated with MMS 6-main, which is also the smallest molecular outflow ever found in the intermediate-mass protostellar cores. The dynamical timescale of this outflow is estimated to be {<=}100 yr. The line width dramatically increases downstream at the end of the molecular outflow ({Delta}v {approx} 25 km s{sup -1}) and clearly shows the bow-shock-type velocity structure. The estimated outflow mass ( Almost-Equal-To 10{sup -4} M{sub Sun }) and outflow size are approximately two to four orders and one to three orders of magnitude smaller, respectively, while the outflow force ( Almost-Equal-To 10{sup -4} M{sub Sun} km s{sup -1} yr{sup -1}) is similar, compared to the other molecular outflows studied in OMC-2/3. These results show that MMS 6-main is a protostellar core at the earliest evolutionary stage, most likely shortly after the second core formation.

  6. Clinical characteristics and molecular genetic analysis of 22 patients with neonatal diabetes from the South-Eastern region of Turkey: predominance of non-KATP channel mutations

    PubMed Central

    Demirbilek, Huseyin; Arya, Ved Bhushan; Ozbek, Mehmet Nuri; Houghton, Jayne A L; Baran, Riza Taner; Akar, Melek; Tekes, Selahattin; Tuzun, Heybet; Mackay, Deborah J; Flanagan, Sarah E; Hattersley, Andrew T; Ellard, Sian; Hussain, Khalid

    2015-01-01

    Background Neonatal diabetes mellitus (NDM) is a rare form of monogenic diabetes and usually presents in the first 6 months of life. We aimed to describe the clinical characteristics and molecular genetics of a large Turkish cohort of NDM patients from a single centre and estimate an annual incidence rate of NDM in South-Eastern Anatolian region of Turkey. Design and methods NDM patients presenting to Diyarbakir Children State Hospital between 2010 and 2013, and patients under follow-up with presumed type 1 diabetes mellitus, with onset before 6 months of age were recruited. Molecular genetic analysis was performed. Results Twenty-two patients (59% males) were diagnosed with NDM (TNDM-5; PNDM-17). Molecular genetic analysis identified a mutation in 20 (95%) patients who had undergone a mutation analysis. In transient neonatal diabetes (TNDM) patients, the genetic cause included chromosome 6q24 abnormalities (n=3), ABCC8 (n=1) and homozygous INS (n=1). In permanent neonatal diabetes (PNDM) patients, homozygous GCK (n=6), EIF2AK3 (n=3), PTF1A (n=3), and INS (n=1) and heterozygous KCNJ11 (n=2) mutations were identified. Pancreatic exocrine dysfunction was observed in patients with mutations in the distal PTF1A enhancer. Both patients with a KCNJ11 mutation responded to oral sulphonylurea. A variable phenotype was associated with the homozygous c.-331C>A INS mutation, which was identified in both a PNDM and TNDM patient. The annual incidence of PNDM in South-East Anatolian region of Turkey was one in 48 000 live births. Conclusions Homozygous mutations in GCK, EIF2AK3 and the distal enhancer region of PTF1A were the commonest causes of NDM in our cohort. The high rate of detection of a mutation likely reflects the contribution of new genetic techniques (targeted next-generation sequencing) and increased consanguinity within our cohort. PMID:25755231

  7. Transient stability of the helical pattern of region F19-L22 of the N-terminal domain of p53: a molecular dynamics simulation study.

    PubMed

    Espinoza-Fonseca, L Michel; Trujillo-Ferrara, José G

    2006-04-28

    Two molecular dynamics simulations of the region E17-N29 of p53 (p53(17-29)) at different temperatures were performed for a total time of 0.2 micros, to study the conformational landscape of this region. Previous studies have suggested that this region displays different structural motifs, such as helix of a double beta-turn, and that its secondary structure might be transiently stable. Interestingly, in this study it was found that the region F19-L25, and particularly its fragment F19-L22, display a stable, transient helical pattern at sub-microsecond periods. The region F19-L22, which contains one of the most important residues needed for the interaction of p53 with MDM2, seems to be formed and stabilized by the existence of one hydrophobic and one aromatic cluster. The main function of these clusters is to help their surrounding area to desolvate, to allow the hydrogen bond network, therefore favoring the formation of a stable helix. This preliminary study would be useful for a better understanding of the structure and function of the N-terminal domain of p53 and its implications for the control of different types of cancer. PMID:16530164

  8. A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoter.

    PubMed

    Lehmeyer, Mona; Hanko, Erik K R; Roling, Lena; Gonzalez, Lilian; Wehrs, Maren; Hehl, Reinhard

    2016-06-01

    The high gene density in Arabidopsis thaliana leaves only relatively short intergenic regions for potential cis-regulatory sequences. To learn more about the regulation of genes harbouring only very short upstream intergenic regions, this study investigates a recently identified novel microbe-associated molecular pattern (MAMP)-responsive cis-sequence located within the 101 bp long intergenic region upstream of the At1g13990 gene. It is shown that the cis-regulatory sequence is sufficient for MAMP-responsive reporter gene activity in the context of its native promoter. The 3' UTR of the upstream gene has a quantitative effect on gene expression. In context of a synthetic promoter, the cis-sequence is shown to achieve a strong increase in reporter gene activity as a monomer, dimer and tetramer. Mutation analysis of the cis-sequence determined the specific nucleotides required for gene expression activation. In transgenic A. thaliana the synthetic promoter harbouring a tetramer of the cis-sequence not only drives strong pathogen-responsive reporter gene expression but also shows a high background activity. The results of this study contribute to our understanding how genes with very short upstream intergenic regions are regulated and how these regions can serve as a source for MAMP-responsive cis-sequences for synthetic promoter design. PMID:26833485

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

    SciTech Connect

    Toth-Fejel, S.; Magenis, R.E.; Leff, S.

    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.

  10. Molecular Analysis of Promoter and Intergenic Region Attenuator of the Vibrio vulnificus prx1ahpF Operon.

    PubMed

    Lee, Hyun Sung; Lim, Jong Gyu; Han, Kook; Lee, Younghoon; Choi, Sang Ho

    2015-08-01

    Prx1, an AhpF-dependent 2-Cys peroxiredoxin (Prx), was previously identified in Vibrio vulnificus, a facultative aerobic pathogen. In the present study, transcription of the V. vulnificus prx1ahpF genes, which are adjacently located on the chromosome, was evaluated by analyzing the promoter and intergenic region of the two genes. Northern blot analyses revealed that transcription of prx1ahpF results in two transcripts, the prx1 and prx1ahpF transcripts. Primer extension analysis and a point mutational analysis of the promoter region showed that the two transcripts are generated from a single promoter. In addition, the 3' end of the prx1 transcript at the prx1ahpF intergenic region was determined by a 3'RACE assay. These results suggested that the prx1ahpF genes are transcribed as an operon, and the prx1 transcript was produced by transcriptional termination in the intergenic region. RNA secondary structure prediction of the prx1ahpF intergenic region singled out a stem-loop structure without poly(U) tract, and a deletion analysis of the intergenic region showed that the atypical stem-loop structure acts as the transcriptional attenuator to result in the prx1 and prx1ahpF transcripts. The combined results demonstrate that the differential expression of prx1 and ahpF is accomplished by the cis-acting transcriptional attenuator located between the two genes and thereby leads to the production of a high level of Prx1 and a low level of AhpF. PMID:25824432

  11. Star-forming regions of the Aquila rift cloud complex. II. Turbulence in molecular cores probed by NH3 emission

    NASA Astrophysics Data System (ADS)

    Levshakov, S. A.; Henkel, C.; Reimers, D.; Wang, M.

    2014-07-01

    Aims: We intend to derive statistical properties of stochastic gas motion inside the dense, low-mass star-forming molecular cores that are traced by NH3(1, 1) and (2, 2) emission lines. Methods: We use the spatial two-point autocorrelation (ACF) and structure functions calculated from maps of the radial velocity fields. Results: The observed ammonia cores are characterized by complex intrinsic motions of stochastic nature. The measured kinetic temperature ranges between 8.8 K and 15.1 K. From NH3 excitation temperatures of 3.5-7.3 K, we determine H2 densities with typical values of nH2~ (1-6) × 104 cm-3. The ammonia abundance, X = [NH3]/[H2], varies from 2 × 10-8 to 1.5 × 10-7. We find oscillating ACFs, which eventually decay to zero with increasing lags on scales of 0.04 ≲ ℓ ≲ 0.5 pc. The current paradigm supposes that the star-formation process is controlled by the interplay between gravitation and turbulence with the latter preventing molecular cores from a rapid collapse due to their own gravity. Thus, oscillating ACFs may indicate a damping of the developed turbulent flows surrounding the dense but less turbulent core, a transition to dominating gravitational forces and, hence, to gravitational collapse. Appendix A is available in electronic form at http://www.aanda.org

  12. DEVELOPMENT AND UTILITY OF A ‘ONE-STEP’ SPECIES-SPECIFIC MOLECULAR DIAGNOSTIC MARKER FOR GONATOCERUS MORRILLI DESIGNED TOWARD THE INTERNAL TRANSCRIBED SPACER REGION 2 (ITS2) TO MONITOR ESTABLISHMENT IN CALIFORNIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In addition to the ‘one-step’ species-specific molecular diagnostic ISSR-PCR DNA fingerprinting method, we developed an additional ‘one-step’ molecular diagnostic marker ‘gmtx’ toward Gonatocerus morrilli (Howard) designed toward the ribosomal internal transcribed spacer region 2 (ITS2) to aid in mo...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Molecular Epidemiology and Genetic Diversity of Orientia tsutsugamushi from Patients with Scrub Typhus in 3 Regions of India

    PubMed Central

    Janardhanan, Jeshina; Mahajan, Sanjay K.; Tariang, David; Trowbridge, Paul; Prakash, John A.J.; David, Thambu; Sathendra, Sowmya; Abraham, O.C.

    2015-01-01

    Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus–endemic geographic regions of India: South India, Northern India, and Northeast India. Eschar samples collected during September 2010–August 2012 from patients with scrub typhus were subjected to 56-kDa type-specific PCR and sequencing to identify their genotypes. Kato-like strains predominated (61.5%), especially in the South and Northeast, followed by Karp-like strains (27.7%) and Gilliam and Ikeda strains (2.3% each). Neimeng-65 genotype strains were also observed in the Northeast. Clarifying the genotypic diversity of O. tsutsugamushi in India enhances knowledge of the regional diversity among circulating strains and provides potential resources for future region-specific diagnostic studies and vaccine development. PMID:25530231

  15. Molecular epidemiology and genetic diversity of Orientia tsutsugamushi from patients with scrub typhus in 3 regions of India.

    PubMed

    Varghese, George M; Janardhanan, Jeshina; Mahajan, Sanjay K; Tariang, David; Trowbridge, Paul; Prakash, John A J; David, Thambu; Sathendra, Sowmya; Abraham, O C

    2015-01-01

    Scrub typhus, an acute febrile illness that is widespread in the Asia-Pacific region, is caused by the bacterium Orientia tsutsugamushi, which displays high levels of antigenic variation. We conducted an investigation to identify the circulating genotypes of O. tsutsugamushi in 3 scrub typhus-endemic geographic regions of India: South India, Northern India, and Northeast India. Eschar samples collected during September 2010-August 2012 from patients with scrub typhus were subjected to 56-kDa type-specific PCR and sequencing to identify their genotypes. Kato-like strains predominated (61.5%), especially in the South and Northeast, followed by Karp-like strains (27.7%) and Gilliam and Ikeda strains (2.3% each). Neimeng-65 genotype strains were also observed in the Northeast. Clarifying the genotypic diversity of O. tsutsugamushi in India enhances knowledge of the regional diversity among circulating strains and provides potential resources for future region-specific diagnostic studies and vaccine development. PMID:25530231

  16. A novel mRNA and a low molecular weight polypeptide encoded in the transforming region of adenovirus DNA.

    PubMed Central

    Katze, M G; Persson, H; Philipson, L

    1982-01-01

    Immunoprecipitation was used to identify adenovirus type 2 (ad2) tumor antigens synthesized in vivo. The antisera, prepared from tumor-bearing animals, reacted with a wide spectrum of ad2 early proteins including a 11 000-dalton (11 K) polypeptide. The gene for this polypeptide was mapped to the transforming region of the viral genome by hybridization selection followed by in vitro translation and immunoprecipitation. Hybrid arrest translation revealed that the 11 K RNA was transcribed from the leftward reading strand (1-strand) in contrast to other mRNAs from this region. Sucrose gradient analysis of the selected 11 K mRNA revealed that the size of the mRNA was 20S corresponding to approximately 2000 nucleotides. Novel 1-strand transcripts of this length from the transforming region were identified by S1 endonuclease analysis. Taken together, these results suggest that both strands of the transforming region of ad2 DNA are actively transcribed into functional mRNA early after viral infection. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:6985356

  17. Novel Molecular Tumor Cell Markers in Regional Lymph Nodes and Blood Samples from Patients Undergoing Surgery for Non-Small Cell Lung Cancer

    PubMed Central

    Nordgård, Oddmund; Singh, Gurpartap; Solberg, Steinar; Jørgensen, Lars; Halvorsen, Ann Rita; Smaaland, Rune; Brustugun, Odd Terje; Helland, Åslaug

    2013-01-01

    Introduction Recent evidence suggests that microscopic lymph node metastases and circulating tumor cells may have clinical importance in lung cancer. The purpose of this study was to identify new molecular markers for tumor cells in regional lymph nodes (LNs) and peripheral blood (PB) from patients with non-small cell lung cancer (NSCLC). Methods Candidate markers were selected based on digital transcript profiling and previous literature. KRT19, CEACAM5, EPCAM, DSG3, SFTPA, SFTPC and SFTPB mRNA levels were initially validated by real-time reverse transcription PCR-based quantification in 16 NSCLC tumors and 22 LNs and 12 PB samples from individuals without known cancer. Five of the candidate markers were selected for secondary validation by quantification in parallel tumor biopsies, regional LNs and PB samples from 55 patients undergoing surgery for NSCLC. LN and PB marker status were compared to clinicopathological patient data. Results All selected markers except DSG3 were present at high levels in the primary tumors and at very low or non-detectable levels in normal LNs and PB in the first round of validation, indicating a potential for detecting tumor cells in NSCLC patients. The expression profiles of KRT19, CEACAM5, DSG3, SFTPA and SFTPC mRNA were confirmed in the larger group during the secondary validation. Using the highest normal LN level of each marker as threshold, 39 (71%) of the 55 patients had elevated levels of at least one marker in regional LNs. Similarly, 26 (47%) patients had elevated levels of at least one marker in PB. A significantly higher number of patients with adenocarcinomas had positive LN status for these markers, compared with other histological types (P = 0.004). Conclusions Several promising molecular tumor cell markers in regional LNs and PB were identified, including the new SFTPA and SFTPC mRNAs. Clinical follow-up in a larger cohort is needed to elucidate their prognostic value. PMID:23671585

  18. Classical Wolf-Hirschhorn Syndrome confirmed molecularly despite normal results using commercially available probes: Redefinition of critical region

    SciTech Connect

    Zackai, E.H.; McDonald-McGinn, D.M.; Spinner, N.

    1994-09-01

    Wolf-Hirschhorn Syndrome, WHS, (4p-) is a clinically recognized entity where the deletion ranges from one half of the short arm of 4p to being subtle and cytogenetically undetectable. Because such variations do not result in significant differences in the WMS phenotype it has been suggested that them is a critical region involved in the distal portion of chromosome 4, within 4p16.3. This has been recently localized to a 2.5 Mb segment 100-300 kb from the telomere. A cosmid probe, pC847.351, that maps to distal 4p16.3 (locus D4F26) is commercially available for diagnostic use. We present a child with classical feature of Wolf-Hirschhorn Syndrome whose chromosome analyses, including high resolution banding, looking specifically at the 4p region, were normal, and in whom FISH using the commercially available cosmid probe for the 4p16.3 region did not demonstrate a deletion. Insistence on the clinician`s part that the child`s features were classic for WHS prompted further investigation. Four additional cosmid clones distal to the HD gene were tested by FISH on metaphase chromosomes from the proband. Cosmids representing the loci D4S95 and D4S43, which are {approximately}3.5 and 2.5 Mb, Respectively, proximal to D4F26 were present. However, cosmids for the loci D4S98 and FGFR3, which are within 100 kb of each other and {approximately}300 kb distal to D4S43 were deleted. This deletion is the smallest reported to date in a patient with typical WHS. Previous studies of patients both lacking the WHS phenotype and deleted using cosmid probe pC847.351 have suggested that the most distal region (150 kb) of 4p16.3 is not part of the WHS critical region. This is confirmed by our study. Estabrooks` report, together with our case, suggests redefinition of the WHS critical region proximal to D4F26 and distal to D4S43. We caution against ruling out WHS with the above probe since there may be other cases where the most distal region is intact.

  19. Molecular topography of the secondary constriction region (qh) of human chromosome 9 with an unusual euchromatic band

    SciTech Connect

    Verma, R.S.; Luk, S.; Brennan, J.P.; Mathews, T.; Conte, R.A.; Macera, M.J. )

    1993-05-01

    Heterochromatin confined to pericentromeric (c) and secondary constriction (qh) regions plays a major role in morphological variation of chromosome 9, because of its size and affinity for pericentric inversion. Consequently, pairing at pachytene may lead to some disturbances between homologous chromosomes having such extreme variations and may result in abnormalities involving bands adjacent to the qh region. The authors encountered such a case, where a G-positive band has originated de nova, suggesting a maternal origin from the chromosome 9 that has had a complete pericentric inversion. In previously reported cases, the presence of an extra G-positive band within the 9qh region has been familial, and in the majority of those cases it was not associated with any clinical consequences. Therefore, this anomaly has been referred to as a [open quotes]rare[close quotes] variant. The qh region consists of a mixture of various tandemly repeated DNA sequences, and routine banding techniques have failed to characterize the origin of this extra genetic material. By the chromosome in situ suppression hybridization technique using whole chromosome paint, the probe annealed with the extra G-band, suggesting a euchromatic origin from chromosome 9, presumably band p12. By the fluorescence in situ hybridization technique using alpha- and beta-satellite probes, the dicentric nature was further revealed, supporting the concept of unequal crossing-over during maternal meiosis I, which could account for a duplication of the h region. The G-positive band most likely became genetically inert when it was sandwiched between two blocks of heterochromatin, resulting in a phenotypically normal child. Therefore, an earlier hypothesis, suggesting its origin from heterochromatin through so-called euchromatinization, is refuted here. If the proband's progeny inherit this chromosome, it shall be envisaged as a rare familial variant whose clinical consequences remain obscure. 52 refs., 3 figs.

  20. Molecular gas toward the Bright-Rimmed Cloud BRC 82 illuminated by NGC6231; Triggered star formation associated with HII regions

    NASA Astrophysics Data System (ADS)

    Fukui, Yasuo; Torii, Kazufumi; Akio, Ohama; Soga, Sho

    2012-04-01

    High-mass stars are very energetic and give significant effects on their surroundings. The most remarkable effect among them is triggered star formation by UV radiation from high-mass stars. Bright-rimmed cloud BRC 82, located at ~1.6 kpc from the Sun, is illuminated on its sides by the UV radiation from the remarkable cluster NGC 6231 which contain a number of OB stars. Previous studies indicated that there is on-going star forming regions at the rim of BRC 82, likely triggered by the UV. However, only a few molecular line studies are known to date, and detailed gas distribution have never been revealed yet. Our recent search of molecular gas by using NANTEN2 reveals the dense CO peak in BRC 82, which coincides a high-mass ZAMS star. In this proposal, we intend to investigate the star formation activity and its mechanism in BRC 82 by observing molecular emission lines CO, HCO+, H13CO+, HCN, N2H+, SiO, etc. These observations will reveal the detailed distributions of small and dense condensations related to the star formation. We request 24 hours in total.

  1. Molecular clouds in the Carina arm - The largest objects, associated regions of star formation, and the Carina arm in the Galaxy

    NASA Technical Reports Server (NTRS)

    Grabelsky, D. A.; Cohen, R. S.; Bronfman, L.; Thaddeus, P.

    1988-01-01

    The Columbia CO survey of the southern Galactic plane is used to identify giant molecular clouds and cloud complexes in the Vela-Carina-Centaurus section of the Galaxy. Twenty-seven giant molecular clouds between l = 270 and 300 deg are catalogued and their heliocentric distances given. In addition, 16 clouds at l greater than 300 deg beyond the solar circle extend the catalog to include the very distant portion of the Carina arm. The most massive clouds in the catalog trace the Carina arm over 23 kpc in the plane of the Galaxy. The average mass of these objects is 1.4 x 10 to the 6th solar, and their average spacing along the arm is 700 pc. The composite distribution projected onto the Galactic plane of the largest molecular clouds in the Carina arm and of similarly massive clouds in the first and second quadrants strongly suggests that the Carina and Sagittarius arms form a single spiral arm about 40 kpc in length wrapping two-thirds of the way around the Galaxy. Descriptions of each cloud, including identification of associated star-forming regions, are presented in an appendix.

  2. SCUBA-Diving In Nearby Molecular Clouds: Large-Area Mapping of Star-Forming Regions at Sub-millimeter Wavelengths

    NASA Astrophysics Data System (ADS)

    Johnstone, D.

    Wide area sub-millimeter mapping of nearby molecular clouds allows for the study of large scale structures such as the Integral Shaped Filament in the Orion A cloud. Examination of these regions suggests that they are not equilibrium isothermal structures but rather require significant, and radially dependent, non-thermal support such as produced by helical magnetic fields Also observed in the large area maps are dense condensations with masses typical for stars. The mass distribution of these clumps is similar to the stellar initial mass function; however, the clumps appear stable against collapse. The clumps are clustered within the cores of molecular clouds and restricted to those locations where the molecular cloud column density is high (A_v > 4). As well, the typical sub-millimeter clump reveals little or no emission from isotopes of CO, likely indicating that the combination of high density and low temperatures within the clumps provides an environment in which these molecules freeze-out onto dust grain surfaces.

  3. [Morphologic and molecular characterization of Phomopsis longicolla(teleomorph unknown: Diaporthales) from tempered and subtropical regions of Argentina].

    PubMed

    Hernández, Facundo E; Pioli, Rosanna N; Peruzzo, Alejandra M; Formento, Ángela N; Pratta, Guillermo R

    2015-09-01

    Diaporthe (teleomorpho)-Phomopsis - (anamorph) (DP) is a fungal group of great genetic diversity with over 900 species associated to a wide host range that includes cultivated and uncultivated species, forest, fruit trees and weeds. DP isolates are hemibiotrophs and have different sources of primary inoculum as stubble and seeds to restart cycles of parasitism - saprophytism. They colonize host tissues from early plant stages and establish different nutritional relationships, acting as endophytic and necrotrophic fungi. The plasticity of the Phomopsis genus has favored its expansion to different agro-ecosystems and various hosts constituting an epidemiological risk. The objective was to validate the identity and evaluate the biological relationships among 12 isolates of P longicolla and D. phaseolorum var. sojae (anamorph P phaseoli var. sojae) obtained in different tempered and subtropical agro-environments of Argentina, in order to analyze the variability and strategies for preserving fungal biodiversity. Macromorphological attributes (such as texture and color of colonies, stroma shape and distribution, pycnidia and perythecia shape and distribution) and micro-morphological characteristics (such as size and shape of conidia, asci and ascospores) allowed identifying three new isolates as P longicolla. A complementary molecular analysis was also made to overcome the limitations derived from the morphological analysis, thus the AFP.8413 isolate was finally identified as P longicolla. The molecular characterization was useful to identify the evaluated isolates and to group them in four taxa of the Diaporthe-Phomopsis complex: ten isolates were included in P. longicolla, one isolate was included in D. phaseolorum var. sojae (anamorph P. phaseoli var. sojae), one isolate was identified as D. phaseolorum var. caulivora and two isolates were included in D. phaseolorum var. meridionalis. The use of phenotipic and molecular tools have contributed to an accurate

  4. Mapping to molecular resolution in the T to H-2 region of the mouse genome with a nested set of meiotic recombinants.

    PubMed Central

    King, T R; Dove, W F; Herrmann, B; Moser, A R; Shedlovsky, A

    1989-01-01

    We describe a meiotic fine-structure mapping strategy for achieving molecular access to developmental mutations in the mouse. The induction of lethal point mutations with the potent germ-line mutagen N-ethyl-N-nitrosourea has been reported. One lethal mutation of prime interest is an allele at the quaking locus on chromosome 17. To map this mutation, quaking(lethal-1), we have intercrossed hybrid mice that carry distinct alleles at many classical and DNA marker loci on proximal chromosome 17. From this cross we have obtained 337 animals recombinant in the T to H-2 region. This number of crossovers provides a mapping resolution in the size range of single mammalian genes if recombinational hot spots are absent. DNA samples obtained from these recombinant animals can be used retrospectively to map any restriction fragment length polymorphism in the region. This set of DNA samples has been used to map the molecular marker D17RP17 just distal of quaking(lethal-1). With the nested set of crossover DNA samples and appropriate cloning techniques, this tightly linked marker can be used to clone the quaking locus. Images PMID:2911572

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

    NASA Astrophysics Data System (ADS)

    Rangwala, Naseem; Maloney, Philip R.; Wilson, Christine D.; Glenn, Jason; Kamenetzky, Julia; Spinoglio, Luigi

    2015-06-01

    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\\buildrel{\\prime\\prime}\\over{.} 39× 0\\buildrel{\\prime\\prime}\\over{.} 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 substantial line center optical depth and a large gradient in the excitation temperature. The red/blue asymmetries and line-to-continuum offset are likely produced by absorption of the blue (SW) sides of the two nuclei by blueshifted, foreground molecular gas; the mass of the absorber is comparable to the nuclear warm gas mass (˜{{10}8} {{M}⊙ }). We measure an unusually high {{L}CO}/{{L}FIR} ratio in the eastern nucleus, suggesting there is an additional energy source, such as mechanical energy from shocks, present in this nucleus.

  6. Serological and molecular survey of toxoplasmosis in renal transplant recipients and hemodialysis patients in Kashan and Qom regions, central Iran.

    PubMed

    Rasti, Sima; Hassanzadeh, Malihe; Soliemani, Alireza; Hooshyar, Hossein; Mousavi, Seyed Gholam Abbas; Nikoueinejad, Hassan; Abdoli, Amir

    2016-07-01

    Toxoplasma gondii is one of the important opportunistic pathogen among solid-organ transplant recipients and hemodialysis patients (HD). This study was aimed to detect toxoplasmosis among 50 renal transplant recipients (RTR), 135 HD and 120 healthy individuals in two cities (Kashan and Qom) that located in the center of Iran, from 2014 to 2015. Serological detection (IgG and IgM antibodies) was performed among all individuals in case and control groups. Molecular detection was performed on all IgM positive individuals or IgG positive with moderate to high (>51 IU/mL) antibody titers in HD (n = 42) and control groups (n = 21). In RTR patients, molecular detection was conducted among all seropositive or seronegative individuals (n = 50). IgG seropositivity was detected in 52% (26/50) of RTR, 63% (85/135) of HD and 33.3% (40/120) of the control group. The rate of anti-T. gondii IgG antibody was significantly elevated in RTR and HD patients than the control group (p = 0.023 and p < 0.001, respectively). IgM seropositivity was only detected in one HD patient. T. gondii DNA was detected in 12% (6/50) of RTR and 7.1% (3/42) of HD patients. The results of this study suggested that the screening of toxoplasmosis should be given greater consideration among RTR and hemodialysis patients. PMID:27097530

  7. An AT-rich region in the APC gene may cause misinterpretation of familial adenomatous polyposis molecular screening.

    PubMed

    Palmirotta, Raffaele; De Marchis, Maria Laura; Ludovici, Giorgia; Leone, Barbara; Valente, Maria Giovanna; Alessandroni, Jhessica; Spila, Antonella; Della-Morte, David; Guadagni, Fiorella

    2012-05-01

    Familial adenomatous polyposis (FAP) is an autosomal-dominant condition mainly due to a mutation of the adenomatous polyposis coli (APC) gene. The present study reports evidence of a technical issue occurring during the mutational analysis of APC exon 4. Genetic conventional direct sequence analysis of a repetitive AT-rich region in the splice acceptor site of APC intron 3 could be misinterpreted as a pathogenetic frameshift result. However, this potential bias may be bypassed adopting a method for random mutagenesis of DNA based on the use of a triphosphate nucleoside analogues mixture. Using this method as a second-level analysis, we also demonstrated the nonpathogenic nature of the variant in the poly A trait in APC exon 4 region (c.423-4delA) that do not result in aberrant splicing of APC exons 3-4; conversely, we did not find a previously reported T deletion/insertion polymorphism. PMID:22447671

  8. Hydration, structure, and molecular interactions in the headgroup region of dioleoylphosphatidylcholine bilayers: an electron spin resonance study.

    PubMed

    Ge, Mingtao; Freed, Jack H

    2003-12-01

    The relationship between bilayer hydration and the dynamic structure of headgroups and interbilayer water in multilamellar vesicles is investigated by electron spin resonance methods. Temperature variations of the order parameter of a headgroup spin label DPP-Tempo in DOPC in excess water and partially dehydrated (10 wt % water) show a cusp-like pattern around the main phase transition, Tc. This pattern is similar to those of temperature variations of the quadrupolar splitting of interbilayer D2O in PC and PE bilayers previously measured by 2H NMR, indicating that the ordering of the headgroup and the interbilayer water are correlated. The cusp-like pattern of these and other physical properties around Tc are suggestive of quasicritical fluctuations. Also, an increase (a decrease) in ordering of DPP-Tempo is correlated with water moving out of (into) interbilayer region into (from) the bulk water phase near the freezing point, Tf. Addition of cholesterol lowers Tf, which remains the point of increasing headgroup ordering. Using the small water-soluble spin probe 4-PT, it is shown that the ordering of interbilayer water increases with bilayer dehydration. It is suggested that increased ordering in the interbilayer region, implying a lowering of entropy, will itself lead to further dehydration of the interbilayer region until its lowered pressure resists further flow, i.e., an osmotic phenomenon. PMID:14645091

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

    SciTech Connect

    Perry, D.S.

    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. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments.

    PubMed

    Calvaresi, Matteo; Eckhart, Leopold; Alibardi, Lorenzo

    2016-06-01

    The hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known. PMID:26965557

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

    PubMed Central

    Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J.

    2013-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions/Significance 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. PMID:23805195

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

    PubMed

    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. PMID:26852275

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:26243695

  15. Sequence and molecular characterization of a DNA region encoding the dibenzothiophene desulfurization operon of Rhodococcus sp. strain IGTS8.

    PubMed Central

    Piddington, C S; Kovacevich, B R; Rambosek, J

    1995-01-01

    Dibenzothiophene (DBT), a model compound for sulfur-containing organic molecules found in fossil fuels, can be desulfurized to 2-hydroxybiphenyl (2-HBP) by Rhodococcus sp. strain IGTS8. Complementation of a desulfurization (dsz) mutant provided the genes from Rhodococcus sp. strain IGTS8 responsible for desulfurization. A 6.7-kb TaqI fragment cloned in Escherichia coli-Rhodococcus shuttle vector pRR-6 was found to both complement this mutation and confer desulfurization to Rhodococcus fascians, which normally is not able to desulfurize DBT. Expression of this fragment in E. coli also conferred the ability to desulfurize DBT. A molecular analysis of the cloned fragment revealed a single operon containing three open reading frames involved in the conversion of DBT to 2-HBP. The three genes were designated dszA, dszB, and dszC. Neither the nucleotide sequences nor the deduced amino acid sequences of the enzymes exhibited significant similarity to sequences obtained from the GenBank, EMBL, and Swiss-Prot databases, indicating that these enzymes are novel enzymes. Subclone analyses revealed that the gene product of dszC converts DBT directly to DBT-sulfone and that the gene products of dszA and dszB act in concert to convert DBT-sulfone to 2-HBP. PMID:7574582

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

    PubMed

    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. PMID:26763394

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

    SciTech Connect

    Poidevin, Frédérick; Ade, Peter A. R.; Hargrave, Peter C.; Nutter, David; Angile, Francesco E.; Devlin, Mark J.; Klein, Jeffrey; Benton, Steven J.; Netterfield, Calvin B.; Chapin, Edward L.; Fissel, Laura M.; Gandilo, Natalie N.; Fukui, Yasuo; Gundersen, Joshua O.; Korotkov, Andrei L.; Matthews, Tristan G.; Novak, Giles; Moncelsi, Lorenzo; Mroczkowski, Tony K.; Olmi, Luca; 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.

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

    PubMed

    Zhang, Jiapu; Zhang, Yuanli

    2013-06-01

    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 'mad-cow' 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 (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)). 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. PMID:23563221

  19. Molecular and isotopic compositions and origin of natural gases from Cambrian and Carboniferous-Lower Permian reservoirs of the onshore Polish Baltic region

    NASA Astrophysics Data System (ADS)

    Kotarba, Maciej J.; Nagao, Keisuke

    2015-01-01

    Natural gases from Middle Cambrian and Carboniferous-Lower Permian reservoirs of the onshore Polish Baltic region were studied for their molecular and stable isotope compositions. The following gas species were analysed: 12,13C in CH4, C2H6, C3H8, n-C4H10, i-C4H10 and CO2, 1,2H in CH4, 14,15N in N2, and stable isotopes of all noble gases. Due to significantly different geological settings and genetic types of source rocks of Eastern and Western Pomerania, the molecular and isotopic compositions of natural gases of these two regions exhibit distinct differences. Hydrocarbon gases associated with oil accumulated in the Middle Cambrian reservoir of Eastern Pomerania were generated during low-temperature thermogenic processes from a single source rock containing Type-II kerogen at one phase of petroleum generation. Non-associated hydrocarbon gases accumulated in the Carboniferous (Mississippian and Pennsylvanian)-Lower Permian (Rotliegend) reservoirs of Western Pomerania originated during at least two phases of gas generation by thermogenic processes from mainly Type-III kerogen and a small component of mixed Type-III/II kerogen. Noble gases are in general heavily enriched in radiogenic and nucleogenic isotopes such as 4He, 40Ar and 21Ne accumulated in the reservoirs. Weak contributions of mantle-derived He and Ne are observed. Radiogenic 4He/40Ar ratios are higher than the average production rate ratio of about 5 for radiogenic 4He/40Ar in crustal materials, which might have been caused by a selective supply of 4He that is lighter than 40Ar from crustal rocks, or (U + Th)/K ratio might be higher than the average in crustal block. Carbon dioxide from gases of both the Western and Eastern Pomerania were mainly generated during thermogenic processes of transformation of organic matter, although gases of Western Pomerania can contain an endogenic component. Molecular nitrogen from the Eastern Pomeranian natural gases was mainly generated during low-temperature thermal

  20. SUBMILLIMETER ARRAY OBSERVATIONS OF THE MOLECULAR OUTFLOW IN HIGH-MASS STAR-FORMING REGION G240.31+0.07

    SciTech Connect

    Qiu Keping; Zhang Qizhou; Wu Jingwen; Chen, H.-R.

    2009-05-01

    We present Submillimeter Array observations toward the 10{sup 4.7} L {sub sun} star-forming region G240.31+0.07, in the J = 2-1 transition of {sup 12}CO and {sup 13}CO and at 1.3 mm continuum, as well as the {sup 12}CO and {sup 13}CO observations from the Caltech Submillimeter Observatory to recover the extended emission filtered out by the interferometer. Maps of the {sup 12}CO and {sup 13}CO emission show a bipolar, wide-angle, quasi-parabolic molecular outflow, roughly coincident with an infrared nebula revealed by the Spitzer 3.6 and 4.5 {mu}m emission. The outflow has {approx}98 M {sub sun} molecular gas, making it one of the most massive molecular outflows known, and resulting in a very high mass-loss rate of 4.1 x 10{sup -3} M {sub sun} yr{sup -1} over a dynamical timescale of 2.4 x 10{sup 4} yr. The 1.3 mm continuum observations with a 4'' x 3'' beam reveal a flattened dusty envelope of {approx}150 M {sub sun}, which is further resolved with a 1.''2 x 1'' beam into three dense cores with a total mass of {approx}40 M {sub sun}. The central mm core, showing evidence of active star formation, approximately coincides with the geometric center of the bipolar outflow thus most likely harbors the powering source of the outflow. Overall, our observations provide the best case to date of a well defined wide-angle molecular outflow in a higher than 10{sup 4} L {sub sun} star-forming region. The outflow is morphologically and kinematically similar to low-mass protostellar outflows but has two to three orders of magnitude greater mass, momentum, and energy, and is apparently driven by an underlying wide-angle wind, hence further supports that high-mass stars up to late-O types, even in a crowded clustering environment, can form as a scaled-up version of low-mass star formation.

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

    SciTech Connect

    Christian, S.L.; Huang, B.; Ledbetter, D.H.

    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.

  2. Molecular epidemiology of hepatitis B and hepatitis delta viruses circulating in the Western Amazon region, North Brazil

    PubMed Central

    2014-01-01

    Background Hepatitis B virus (HBV) and hepatitis D virus (HDV) represent important public health problems in the Western Amazon region with reported cases of fulminant hepatitis. This cross sectional study describes HBV and HDV genotypes circulating in the Brazilian Amazon region. Methods HBsAg positive individuals (n = 224) were recruited in Manaus/Amazonas State (130 blood donors from the Hematology and Hemotherapy Foundation from Amazonas/HEMOAM; 60 subjects from outpatient clinic) and in Eirunepe city (n = 34) from 2003–2009. Most participants (n = 153) lived in Manaus, 63 were from 20 remote isolated municipalities, 8 lived outside Amazonas State. Genotyping was based on PCR products: HBV genotype A-F specific primers, restricted length polymorphism for HDV. HDV isolates were directly sequenced (delta antigen 405 nucleotide fragment) and phylogenetic analysis performed (MEGA; neighbor-joining, Kimura’s two parameter). Results Most participants were young adult males and HBV mono-infection predominated (70.5%, 158/224). Among blood donors, outpatient subjects and individuals from Eirunepe, HBV/A prevailed followed by HBV/D and F (p > 0.05). HBV/A was more frequent in blood donors (p < 0.05). HBV-HDV coinfection rate was 8.5% in blood donors (11/130), 65.0% (39/60) in outpatient subjects and 47.0% (16/34) in individuals from Eirunepe. Compared to blood donors, coinfection was higher in outpatient subjects (65.0% versus 8.5%; RR = 5.0; CI 3.4-7.9; p < 0.0001) and in subjects from Eirunepe (47.0% versus 8.5%; RR = 5.5; CI 3.0-9.9; p < 0.0001). HBV-HDV coinfection rates were higher in patients from highly endemic remote cities. Only HDV genotype 3 was detected, HBV/F-HDV/3 predominated (20/38; 52.7%), followed by HBV/A-HDV/3 (31.6%; 12/38) and HBV/D-HDV/3 (15.8%; 6/38). Conclusions The description of HBV and HDV genotypes circulating in the western Amazon can contribute to a better understanding of their relevance on the

  3. Molecular Archaeology of Flaviviridae Untranslated Regions: Duplicated RNA Structures in the Replication Enhancer of Flaviviruses and Pestiviruses Emerged via Convergent Evolution

    PubMed Central

    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. PMID:24647143

  4. Deletion of the gene encoding the adenovirus 5 early region 1b 21,000-molecular-weight polypeptide leads to degradation of viral and host cell DNA.

    PubMed Central

    Pilder, S; Logan, J; Shenk, T

    1984-01-01

    The adenovirus 5 mutant H5dl337 lacks 146 base pairs within early region 1B. The deletion removes a portion of the region encoding the E1B 21,000-molecular-weight (21K) polypeptide, but does not disturb the E1B-55K/17K coding region. The virus is slightly defective for growth in cultured HeLa cells, in which its final yield is reduced ca. 10-fold compared with wild-type virus. The mutant displays a striking phenotype in HeLa cells. The onset of cytopathic effect is dramatically accelerated, and both host cell and viral DNAs are extensively degraded late after infection. This defect has been described previously for a variety of adenovirus mutants and has been termed a cytocidal (cyt) phenotype. H5dl337 serves to map this defect to the loss of E1B-21K polypeptide function. In addition to its defect in the productive growth cycle, H5dl337 is unable to transform rat cells at normal efficiency. Images PMID:6492257

  5. Chx10 functions as a regulator of molecular pathways controlling the regional identity in the primordial retina.

    PubMed

    Wang, Zi; Yasugi, Sadao; Ishii, Yasuo

    2016-05-01

    The light-sensitive neural retina (NR) and the retinal pigmented epithelium (RPE) develop from a common primordium, the optic vesicle, raising the question of how they acquire and maintain distinct identities. Here, we demonstrate that sustained misexpression of the Chx10 homeobox gene in the presumptive RPE in chick suppresses accumulation of melanin pigments and promotes ectopic NR-like neural differentiation. This phenotypic change involved ectopic expression of NR transcription factor genes, Sox2, Six3, Rx1 and Optx2, which, when misexpressed, counteracted RPE development without upregulating Chx10. These results suggest that Chx10 can function as a cell autonomous regulator of the regional identity in the primordial retina, presumably through a downstream transcriptional cascade. PMID:27001188

  6. Strain typing of Zygosaccharomyces yeast species using a single molecular method based on polymorphism of the intergenic spacer region (IGS).

    PubMed

    Wrent, Petra; Rivas, Eva-María; Peinado, José M; de Silóniz, María-Isabel

    2010-08-15

    Unlike previously reported methods that need a combination of several typing techniques, we have developed a single method for strain typing of the Zygosaccharomyces bailii, Z. mellis and Z. rouxii spoilage species. Strains belonging to other species have also been included for comparison. We have demonstrated that the IGS-PCR RFLP method has a high discriminative power. Considering the three endonucleases used in this work, we have obtained a variability of 100% for Z. mellis and Z. rouxii strains and up to 70% for Z. bailii. We have also detected two misidentified Z. mellis strains (CBS 711 and CBS 7412) which have RFLP patterns with a set of bands characteristic of Z. rouxii strains. Sequencing of 26S rDNA D1/D2 domains and the 5.8-ITS rDNA region confirmed these strains as Z. rouxii. The method also groups three certified hybrid strains of Zygosaccharomyces in a separate cluster. PMID:20619910

  7. Association of TAG-1 with Caspr2 is essential for the molecular organization of juxtaparanodal regions of myelinated fibers.

    PubMed

    Traka, Maria; Goutebroze, Laurence; Denisenko, Natalia; Bessa, Maria; Nifli, Artemisia; Havaki, Sophia; Iwakura, Yoichiro; Fukamauchi, Fumihiko; Watanabe, Kazutada; Soliven, Betty; Girault, Jean-Antoine; Karagogeos, Domna

    2003-09-15

    Myelination results in a highly segregated distribution of axonal membrane proteins at nodes of Ranvier. Here, we show the role in this process of TAG-1, a glycosyl-phosphatidyl-inositol-anchored cell adhesion molecule. In the absence of TAG-1, axonal Caspr2 did not accumulate at juxtaparanodes, and the normal enrichment of shaker-type K+ channels in these regions was severely disrupted, in the central and peripheral nervous systems. In contrast, the localization of protein 4.1B, an axoplasmic partner of Caspr2, was only moderately altered. TAG-1, which is expressed in both neurons and glia, was able to associate in cis with Caspr2 and in trans with itself. Thus, a tripartite intercellular protein complex, comprised of these two proteins, appears critical for axo-glial contacts at juxtaparanodes. This complex is analogous to that described previously at paranodes, suggesting that similar molecules are crucial for different types of axo-glial interactions. PMID:12975355

  8. Association of TAG-1 with Caspr2 is essential for the molecular organization of juxtaparanodal regions of myelinated fibers

    PubMed Central

    Traka, Maria; Goutebroze, Laurence; Denisenko, Natalia; Bessa, Maria; Nifli, Artemisia; Havaki, Sophia; Iwakura, Yoichiro; Fukamauchi, Fumihiko; Watanabe, Kazutada; Soliven, Betty; Girault, Jean-Antoine; Karagogeos, Domna

    2003-01-01

    Myelination results in a highly segregated distribution of axonal membrane proteins at nodes of Ranvier. Here, we show the role in this process of TAG-1, a glycosyl-phosphatidyl-inositol–anchored cell adhesion molecule. In the absence of TAG-1, axonal Caspr2 did not accumulate at juxtaparanodes, and the normal enrichment of shaker-type K+ channels in these regions was severely disrupted, in the central and peripheral nervous systems. In contrast, the localization of protein 4.1B, an axoplasmic partner of Caspr2, was only moderately altered. TAG-1, which is expressed in both neurons and glia, was able to associate in cis with Caspr2 and in trans with itself. Thus, a tripartite intercellular protein complex, comprised of these two proteins, appears critical for axo–glial contacts at juxtaparanodes. This complex is analogous to that described previously at paranodes, suggesting that similar molecules are crucial for different types of axo–glial interactions. PMID:12975355

  9. Characterizing Molecular Mechanisms of Imidacloprid Resistance in Select Populations of Leptinotarsa decemlineata in the Central Sands Region of Wisconsin.

    PubMed

    Clements, Justin; Schoville, Sean; Peterson, Nathan; Lan, Que; Groves, Russell L

    2016-01-01

    The Colorado potato beetle, Leptinotarsa decemlineata (Say), is a major agricultural pest in the Central Sands region of Wisconsin. Imidacloprid, a neonicotinoid insecticide, has commonly been used for control of L. decemlineata since its registration in 1995. In the last 10 years, many field populations of L. decemlineata have begun to show increasing imidacloprid resistance. We studied resistance phenotype as a phenomenon that reduces neonicotinoid efficacy and has practical consequences for potato pest management. Although we have not observed complete field failure following the use of these products, multiple studies have demonstrated that the lethal concentration to kill 50% of the test organisms (LC50) in different field populations of L. decemlineata varies greatly which may suggest that resistance of L. decemlineata is heritable and involves genetic changes. An important challenge in understanding resistance is assessing the genetic mechanisms associated with resistance and classifying up-regulated genes that may be involved in combating an insecticide insult. In this study we uncovered trends in imidacloprid phenotypic response that have developed in the region by estimating the LC50 values among different field populations against a range of imidacloprid doses. The LC50 values collected in 2008-2011, and more recently in 2013 and 2014, show that some field locations remain susceptible to imidacloprid, while nearby fields (<100km) have developed high levels of resistance. We also sought to uncover potential mechanisms of resistance at each field location. We compiled a transcriptome for populations, characterized as phenotypically 'susceptible' and 'resistant', by isolating mRNA from adult beetles and analyzing gene expression level differences. Strong differences were observed in constituently up and down-regulated genes among different field populations. Most significantly, the up-regulation of 3 cytochrome p450s and a glutathione synthetase related

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

    PubMed Central

    2013-01-01

    Background Multidrug-resistant Salmonella strains are frequently encountered problems worldwide with considerable increased occurrences in recent years. The aim of this study was to investigate the occurrence and frequency of antimicrobial resistance and associated resistance genes 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, and characterized for antimicrobial resistance genes associated to the phenotype. Pulsed-field gel electrophoresis (PFGE) was applied for comparison of genetic relatedness. Two serovars were detected among the isolates; Salmonella enterica serovar Infantis (75%) and S. Enteritidis (25%). Thirty-four (94%) of the isolates exhibited resistance to nalidixic acid and ciprofloxacin caused by a single mutation in the quinolone resistance-determining region (QRDR) of gyrA. For all strains this mutation occurred in the codon of Asp87 leading to a Asp87-Tyr, Asp87-Gly or Asp87-Asn substitutions. All S. Infantis (n = 27) 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. PMID:23561048

  11. Characterizing Molecular Mechanisms of Imidacloprid Resistance in Select Populations of Leptinotarsa decemlineata in the Central Sands Region of Wisconsin

    PubMed Central

    Clements, Justin; Schoville, Sean; Peterson, Nathan; Lan, Que; Groves, Russell L.

    2016-01-01

    The Colorado potato beetle, Leptinotarsa decemlineata (Say), is a major agricultural pest in the Central Sands region of Wisconsin. Imidacloprid, a neonicotinoid insecticide, has commonly been used for control of L. decemlineata since its registration in 1995. In the last 10 years, many field populations of L. decemlineata have begun to show increasing imidacloprid resistance. We studied resistance phenotype as a phenomenon that reduces neonicotinoid efficacy and has practical consequences for potato pest management. Although we have not observed complete field failure following the use of these products, multiple studies have demonstrated that the lethal concentration to kill 50% of the test organisms (LC50) in different field populations of L. decemlineata varies greatly which may suggest that resistance of L. decemlineata is heritable and involves genetic changes. An important challenge in understanding resistance is assessing the genetic mechanisms associated with resistance and classifying up-regulated genes that may be involved in combating an insecticide insult. In this study we uncovered trends in imidacloprid phenotypic response that have developed in the region by estimating the LC50 values among different field populations against a range of imidacloprid doses. The LC50 values collected in 2008–2011, and more recently in 2013 and 2014, show that some field locations remain susceptible to imidacloprid, while nearby fields (<100km) have developed high levels of resistance. We also sought to uncover potential mechanisms of resistance at each field location. We compiled a transcriptome for populations, characterized as phenotypically ‘susceptible’ and ‘resistant’, by isolating mRNA from adult beetles and analyzing gene expression level differences. Strong differences were observed in constituently up and down-regulated genes among different field populations. Most significantly, the up-regulation of 3 cytochrome p450s and a glutathione synthetase

  12. Molecular requirements for immunoglobulin heavy chain constant region gene switch-recombination revealed with switch-substrate retroviruses.

    PubMed

    Ott, D E; Marcu, K B

    1989-01-01

    We have employed a retroviral vector, ZN(Smu/S gamma 2b)tk1, as a means of introducing immunoglobulin heavy chain (IgH) switch (S) region sequences into B cell lines to directly measure their switch-recombinase activities. In an earlier study, we demonstrated that retrovector Smu-S gamma 2b recombination events occurred in two thymidine kinase (tk)-negative murine pre-B cell lines (18-8 and 38B9) upon selection in bromodeoxyuridine (BUdR) media for the loss of an Htk gene inserted in between the vector's Smu and S gamma 2b sequences. Here we have used this assay system to show that the 300-18 murine pre-B cell line possesses a very high level of switch-recombinase activity (greater than 1 event in 2500 cells/generation) while a terminally differentiated, antibody-secreting hybridoma line (A39R 1.1) has no detectable recombinase activity. Both S mu and S gamma 2b segments are required for switch region-mediated deletions. Retrovectors harboring only an Smu segment or an Smu segment and a portion of the murine c-myc gene in place of S gamma 2b sequences were both non-recombinagenic in this assay system. Nucleotide sequence analysis of six retrovector S segment recombinants, recovered from ZN(Smu/S gamma 2b) tk1-infected 18-8 and 39B9 pre-B lines, did not reveal homology at their sites of recombination. We conclude that: (1) S segment repetitive sequences play an essential but indirect role in IgCH gene switch-recombination, which occurs by an illegitimate, non-homologous mechanism; (2) the c-myc gene is not a significant target for switch-recombination; and (3) since endogenous Smu and S gamma 2b rearrangements were not observed in populations and clones of pre-B cells expressing a high level of switch-recombinase activity, multiple factors (presumably contributed in part by the degree of S segment accessibility) in addition to S recombinase activity are required for CH class switching. PMID:2489045

  13. Chagas' disease in Aboriginal and Creole communities from the Gran Chaco Region of Argentina: Seroprevalence and molecular parasitological characterization.

    PubMed

    Lucero, R H; Brusés, B L; Cura, C I; Formichelli, L B; Juiz, N; Fernández, G J; Bisio, M; Deluca, G D; Besuschio, S; Hernández, D O; Schijman, A G

    2016-07-01

    Most indigenous ethnias from Northern Argentina live in rural areas of "the Gran Chaco" region, where Trypanosoma cruzi is endemic. Serological and parasitological features have been poorly characterized in Aboriginal populations and scarce information exist regarding relevant T. cruzi discrete typing units (DTU) and parasitic loads. This study was focused to characterize T. cruzi infection in Qom, Mocoit, Pit'laxá and Wichi ethnias (N=604) and Creole communities (N=257) inhabiting rural villages from two highly endemic provinces of the Argentinean Gran Chaco. DNA extracted using Hexadecyltrimethyl Ammonium Bromide reagent from peripheral blood samples was used for conventional PCR targeted to parasite kinetoplastid DNA (kDNA) and identification of DTUs using nuclear genomic markers. In kDNA-PCR positive samples from three rural Aboriginal communities of "Monte Impenetrable Chaqueño", minicircle signatures were characterized by Low stringency single primer-PCR and parasitic loads calculated using Real-Time PCR. Seroprevalence was higher in Aboriginal (47.98%) than in Creole (27.23%) rural communities (Chi square, p=4.e(-8)). A low seroprevalence (4.3%) was detected in a Qom settlement at the suburbs of Resistencia city (Fisher Exact test, p=2.e(-21)).The kDNA-PCR positivity was 42.15% in Aboriginal communities and 65.71% in Creole populations (Chi square, p=5.e(-4)). Among Aboriginal communities kDNA-PCR positivity was heterogeneous (Chi square, p=1.e(-4)). Highest kDNA-PCR positivity (79%) was detected in the Qom community of Colonia Aborigen and the lowest PCR positivity in two different surveys at the Wichi community of Misión Nueva Pompeya (33.3% in 2010 and 20.8% in 2014). TcV (or TcII/V/VI) was predominant in both Aboriginal and Creole communities, in agreement with DTU distribution reported for the region. Besides, two subjects were infected with TcVI, one with TcI and four presented mixed infections of TcV plus TcII/VI. Most minicircle signatures

  14. A Multi-Scale Continuum and Line Exploration of the Most Luminous Star Formation Region in the Milky Way. I. The Mass Structure of the Giant Molecular Cloud.

    NASA Astrophysics Data System (ADS)

    Galvan-Madrid, R.; Liu, H. B.; 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.

    2013-07-01

    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~10^7.2 Lsun) star-formation region in the Milky Way. The project has multiple components that cover the entire GMC at different scales and angular resolutions, from 0.1 to 100 pc. We present a new all-configuration SMA mosaic of the central 10 pc (known as W49N), plus PMO mapping of the full GMC up to scales of 110 pc. We derive the mass structure of the GMC at all scales, revealing that the central ~0.1% of the volume, which contains ~20% of the total GMC mass, is forming a system of young massive clusters (YMCs). We compare our results with other possible sites of YMC formation in the Galaxy.

  15. Molecular evolution and variability of ITS1 -ITS2 in populations of Deschampsia antarctica from two regions of the maritime Antarctic

    NASA Astrophysics Data System (ADS)

    Volkov, R. A.; Kozeretska, I. A.; Kyryachenko, S. S.; Andreev, I. O.; Maidanyuk, D. N.; Parnikoza, I. Yu.; Kunakh, V. A.

    2010-12-01

    Only two vascular plants, Deschampsia antarctica Desv. (Poaceae) and Colobanthus quitensis Kunth. Bartl. (Caryophyllaceae), inhabit the Antarctic. To clarify the taxonomic position, phylogeographic origin, genetic heterogeneity, and population dynamics of D. antarctica, we comparatively analyzed the ITS1 and ITS2 sequences for several populations from two geographically distant regions of the maritime Antarctic (the South Shetland Islands and the Argentine archipelago). All accessions of D. antarctica formed a strongly supported clade in the phylogenetic dendrograms constructed. Despite the high degree of sequence similarity at ITS1 -ITS2 (97%-100%), the populations of D. antarctica in Tierra del Fuego, Falkland Islands and Antarctic can be discriminated at the molecular level. Our data indicate that the majority of D. antarctica populations originated from South America. Different populations may have invaded Antarctic at different times. Genetically distinct plants may coexist within the same or adjacent populations on Antarctic islands.

  16. Molecular dynamics simulation of liquid methanol. II. Unified assignment of infrared, raman, and sum frequency generation vibrational spectra in methyl C-H stretching region

    NASA Astrophysics Data System (ADS)

    Ishiyama, Tatsuya; Sokolov, Vladimir V.; Morita, Akihiro

    2011-01-01

    Vibrational spectra of methyl C-H stretching region are notoriously complicated, and thus a theoretical method of systematic assignment is strongly called for in condensed phase. Here we develop a unified analysis method of the vibrational spectra, such as infrared (IR), polarized and depolarized Raman, and ssp polarized sum frequency generation (SFG), by flexible and polarizable molecular dynamics simulation. The molecular model for methanol has been developed by charge response kernel model to allow for analyzing the methyl C-H stretching vibrations. The complicated spectral structure by the Fermi resonance has been unraveled by empirically shifting potential parameters, which provides clear information on the coupling mechanism. The analysis confirmed that for the IR, polarized Raman, and SFG spectra, two-band structure at about 2830 and 2950 cm^{-1} results from the Fermi resonance splitting of the methyl C-H symmetric stretching and bending overtones. In the IR spectrum, the latter, higher-frequency band is overlapped with prominent asymmetric C-H stretching bands. In the depolarized Raman spectrum, the high frequency band at about 2980 cm^{-1} is assigned to the asymmetric C-H stretching mode. In the SFG spectrum, the two bands of the splitted symmetric C-H stretching mode have negative amplitudes of imaginary nonlinear susceptibility χ ^{(2)}, while the higher-frequency band is partly cancelled by positive imaginary components of asymmetric C-H stretching modes.

  17. Molecular dynamics simulation of liquid methanol. II. Unified assignment of infrared, Raman, and sum frequency generation vibrational spectra in methyl C-H stretching region.

    PubMed

    Ishiyama, Tatsuya; Sokolov, Vladimir V; Morita, Akihiro

    2011-01-14

    Vibrational spectra of methyl C-H stretching region are notoriously complicated, and thus a theoretical method of systematic assignment is strongly called for in condensed phase. Here we develop a unified analysis method of the vibrational spectra, such as infrared (IR), polarized and depolarized Raman, and ssp polarized sum frequency generation (SFG), by flexible and polarizable molecular dynamics simulation. The molecular model for methanol has been developed by charge response kernel model to allow for analyzing the methyl C-H stretching vibrations. The complicated spectral structure by the Fermi resonance has been unraveled by empirically shifting potential parameters, which provides clear information on the coupling mechanism. The analysis confirmed that for the IR, polarized Raman, and SFG spectra, two-band structure at about 2830 and 2950 cm(-1) results from the Fermi resonance splitting of the methyl C-H symmetric stretching and bending overtones. In the IR spectrum, the latter, higher-frequency band is overlapped with prominent asymmetric C-H stretching bands. In the depolarized Raman spectrum, the high frequency band at about 2980 cm(-1) is assigned to the asymmetric C-H stretching mode. In the SFG spectrum, the two bands of the splitted symmetric C-H stretching mode have negative amplitudes of imaginary nonlinear susceptibility χ(2), while the higher-frequency band is partly cancelled by positive imaginary components of asymmetric C-H stretching modes. PMID:21241123

  18. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

    SciTech Connect

    Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

    2013-07-07

    Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

  19. Evaluation of internal transcribed spacer region of ribosomal DNA sequence analysis for molecular characterization of Candida albicans and Candida dubliniensis isolates from HIV-infected patients.

    PubMed

    Millon, L; Piarroux, R; Drobacheff, C; Monod, M; Grenouillet, F; Bulle, B; Bole, J; Blancard, A; Meillet, D

    2002-12-01

    Molecular typing systems have been needed to study Candida colonization in HIV-infected patients, particularly for investigating virulence and fluconazole resistance. Three methods--electrophoretic karyotyping (EK), detection of restriction fragment length polymorphisms (RFLP) and randomly amplified polymorphic DNA analysis (RAPD)--have been most frequently used. In this study, comparative sequence analysis of the internal transcribed spacer (ITS) region of rDNA was evaluated for delineation of Candida isolates from 14 HIV-infected patients. EK, ITS sequence analysis, RFLP and RAPD resulted in 11, 10, 9 and 8 DNA genotypes, respectively, from 39 Candida albicans isolates. The 10 genotypes observed using ITS sequence analysis were defined by six variation sites in the sequence. Molecular typing of sequential oral isolates showed the persistence of the same genotype of C. albicans in nine patients, and genotype variation in one patient. EK and RAPD showed that another patient was co-infected by two distinct genotypes and ITS analysis identified one of the two genotypes as Candida dubliniensis. Comparative ITS sequence analysis is a quick and reproducible method that provides clear and objective results, and it also identifies C. dubliniensis. The discriminatory power of this new typing approach could be improved by concomitant analysis of other DNA polymorphic sequences. PMID:12521117

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

    PubMed

    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. PMID:26809512

  1. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  2. Molecular identification of isolated fungi from unopened containers of greek yogurt by DNA sequencing of internal transcribed spacer region.

    PubMed

    Sulaiman, Irshad M; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

    2014-01-01

    In our previous study, we described the development of an internal transcribed spacer (ITS)1 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. PMID:25438008

  3. Human monoclonal antibodies targeting carbonic anhydrase IX for the molecular imaging of hypoxic regions in solid tumours

    PubMed Central

    Ahlskog, J K J; Schliemann, C; Mårlind, J; Qureshi, U; Ammar, A; Pedley, R B; Neri, D

    2009-01-01

    Background: Hypoxia, which is commonly observed in areas of primary tumours and of metastases, influences response to treatment. However, its characterisation has so far mainly been restricted to the ex vivo analysis of tumour sections using monoclonal antibodies specific to carbonic anhydrase IX (CA IX) or by pimonidazole staining, after the intravenous administration of this 2-nitroimidazole compound in experimental animal models. Methods: In this study, we describe the generation of high-affinity human monoclonal antibodies (A3 and CC7) specific to human CA IX, using phage technology. Results: These antibodies were able to stain CA IX ex vivo and to target the cognate antigen in vivo. In one of the two animal models of colorectal cancer studied (LS174T), CA IX imaging closely matched pimonidazole staining, with a preferential staining of tumour areas characterised by little vascularity and low perfusion. In contrast, in a second animal model (SW1222), distinct staining patterns were observed for pimonidazole and CA IX targeting. We observed a complementary pattern of tumour regions targeted in vivo by the clinical-stage vascular-targeting antibody L19 and the anti-CA IX antibody A3, indicating that a homogenous pattern of in vivo tumour targeting could be achieved by a combination of the two antibodies. Conclusion: The new human anti-CA IX antibodies are expected to be non-immunogenic in patients with cancer and may serve as broadly applicable reagents for the non-invasive imaging of hypoxia and for pharmacodelivery applications. PMID:19623173

  4. Molecular and technological characterization of lactic acid bacteria from traditional fermented sausages of Basilicata region (Southern Italy).

    PubMed

    Bonomo, M G; Ricciardi, A; Zotta, T; Parente, E; Salzano, G

    2008-12-01

    Lactic acid bacteria (LAB) from traditional fermented sausages of the Basilicata region were investigated by ARDRA-PCR and RAPD-PCR for taxonomic identification at species and strain level and characterized on the basis of the growth and acidification at different temperatures, incubation times, levels of NaCl and KNO(2), hydrolysis of sarcoplasmatic and myofibrillar proteins and antimicrobial, peptide/amino acid release and nitrate reductase activities. Lactobacillus sakei was the predominant species (67%) followed by Pediococcus pentosaceus (16%), Leuconostoc carnosum (8%), Lactobacillus plantarum (4%), Lactobacillus brevis (2%) and Leuconostoc pseudomesenteroides (2%). The technological characterization revealed that most of the isolates had good acidifying and proteolytic properties. Moreover, Lb. sakei strains showed antimicrobial ability, while Leuconostoc strains the highest reduction of nitrates. This work was a preliminary study in the formulation of autochthonous starter cultures in order to standardize the production process of sausages, to preserve their typical organoleptic and sensory characteristics and to improve the quality of final product. PMID:22063864

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

    PubMed Central

    Sulaiman, Irshad M.; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

    2014-01-01

    In our previous study, we described the development of an internal transcribed spacer (ITS)1 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. PMID:25438008

  6. Cholecystokinin in White Sea Bream: Molecular Cloning, Regional Expression, and Immunohistochemical Localization in the Gut after Feeding and Fasting

    PubMed Central

    D’Ascola, Angela; Guerrera, M. Cristina; Levanti, M. Beatrice; Germanà, Antonino; Muglia, Ugo

    2012-01-01

    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. PMID:23285038

  7. Development of molecular markers, based on chloroplast and ribosomal DNA regions, to discriminate three popular medicinal plant species, Cynanchum wilfordii, Cynanchum auriculatum, and Polygonum multiflorum.

    PubMed

    Han, Eun-Heui; Cho, KyeMan; Goo, YoungMin; Kim, ManBae; Shin, Young-Wook; Kim, Yun-Hee; Lee, Shin-Woo

    2016-04-01

    Identification of plant species is important for standardizing herbal medicine. Cynanchum wilfordii (Baekshuoh in Korean) and Polygonum multiflorum (Hashuoh in Korean) are important oriental medicinal herbs in Korea, Japan, and China. Cynanchum auriculatum is a faster growing and more productive plant than C. wilfordii; and, it is not recognized as a medicinal plant in the Korean Pharmacopoeia. C. wilfordii, P. multiflorum, and C. auriculatum are often misidentified in the Korean herbal medicine marketplace due to their morphological similarities and similar names. In this study, we investigated molecular authentication of these three medicinal plants using DNA sequences in the TrnL-F chloroplast intergenic region. Specific species identification was achieved by detecting allelic variations of single nucleotide polymorphisms (SNPs) using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and high resolution melting curve analysis. Our results demonstrate that the intraspecific genetic distance between C. wilfordii and C. auriculatum is relatively low. We also developed a quantitative PCR assay using species-specific TrnL-F primers, which allowed us to estimate the ratio of C. wilfordii and C. auriculatum using varying ratios of mixed genomic DNA template from the two species. Additionally, to identify species in hybrid plants produced by cross-fertilization, we analyzed nuclear ribosomal DNA internal transcribed spacer regions in C. wilfordii and C. auriculatum by ARMS-PCR. Our results indicate that SNP-based molecular markers, usable to barcode tools could provide efficient and rapid authentication of these closely related medicinal plant species, and will be useful for preventing the distribution of products contaminated with adulterants. PMID:26902862

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

    PubMed

    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 < 50% may be needed to detect differences < 50% between experimental and control groups when six subjects (n = 6) or more are used and statistical power is adequate (80%). Surprisingly high variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes. PMID:23526701

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

    PubMed Central

    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 < 50% may be needed to detect differences < 50% between experimental and control groups when six subjects (n = 6) or more are used and statistical power is adequate (80%). Surprisingly high variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes. PMID:23526701

  10. HIERARCHICAL FRAGMENTATION OF THE ORION MOLECULAR FILAMENTS

    SciTech Connect

    Takahashi, Satoko; Ho, Paul T. P.; Su, Yu-Nung; Teixeira, Paula S.; Zapata, Luis A.

    2013-01-20

    We present a high angular resolution map of the 850 {mu}m continuum emission of the Orion Molecular Cloud-3 (OMC 3) obtained with the Submillimeter Array (SMA); the map is a mosaic of 85 pointings covering an approximate area of 6.'5 Multiplication-Sign 2.'0 (0.88 Multiplication-Sign 0.27 pc). We detect 12 spatially resolved continuum sources, each with an H{sub 2} mass between 0.3-5.7 M {sub Sun} and a projected source size between 1400-8200 AU. All the detected sources are on the filamentary main ridge (n{sub H{sub 2}}{>=}10{sup 6} cm{sup -3}), and analysis based on the Jeans theorem suggests that they are most likely gravitationally unstable. Comparison of multi-wavelength data sets indicates that of the continuum sources, 6/12 (50%) are associated with molecular outflows, 8/12 (67%) are associated with infrared sources, and 3/12 (25%) are associated with ionized jets. The evolutionary status of these sources ranges from prestellar cores to protostar phase, confirming that OMC-3 is an active region with ongoing embedded star formation. We detect quasi-periodical separations between the OMC-3 sources of Almost-Equal-To 17''/0.035 pc. This spatial distribution is part of a large hierarchical structure that also includes fragmentation scales of giant molecular cloud ( Almost-Equal-To 35 pc), large-scale clumps ( Almost-Equal-To 1.3 pc), and small-scale clumps ( Almost-Equal-To 0.3 pc), suggesting that hierarchical fragmentation operates within the Orion A molecular cloud. The fragmentation spacings are roughly consistent with the thermal fragmentation length in large-scale clumps, while for small-scale cores it is smaller than the local fragmentation length. These smaller spacings observed with the SMA can be explained by either a helical magnetic field, cloud rotation, or/and global filament collapse. Finally, possible evidence for sequential fragmentation is suggested in the northern part of the OMC-3 filament.

  11. Molecular bases of genetic diversity and evolution of the immunoglobulin heavy chain variable region (IGHV) gene locus in leporids

    PubMed Central

    Pinheiro, Ana; Lanning, Dennis; Alves, Paulo C.; Mage, Rose G.; Knight, Katherine L.; van der Loo, Wessel; Esteves, Pedro J.

    2012-01-01

    The rabbit has long been a model for studies of the immune system. Work using rabbits contributed both to the battle against infectious diseases such as rabies and syphilis, and to our knowledge of antibodies' structure, function, and regulated expression. With the description of rabbit Ig allotypes, the discovery of different gene segments encoding immunoglobulins became possible. This challenged the “one gene-one protein” dogma. The observation that rabbit allotypic specificities of the variable regions were present on IgM and IgG molecules also led to the hypothesis of Ig class switching. Rabbit allotypes contributed to the documentation of phenomena such as allelic exclusion and imbalance in production of allelic gene products. During the last 30 years, the rabbit Ig allotypes revealed a number of unique features, setting them apart from mice, humans and other mammals. Here, we review the most relevant findings concerning the rabbit IGHV. Among these are the preferential usage of one VH gene in VDJ rearrangements, the existence of trans-species polymorphism in the IGHV locus revealed by serology and confirmed by sequencing IGHV genes in Lepus, the unusually large genetic distances between allelic lineages and the fact that the antibody repertoire is diversified in this species only after birth. The Whole Genome Sequence of rabbit, plus re-sequencing of additional strains and related genera, will allow further evolutionary investigations of antibody variation. Continued research will help define the roles that genetic, allelic and population diversity at antibody loci may play in host-parasite interactions. PMID:21594770

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

    PubMed Central

    Monaco, Federica; Cosseddu, Gian Mario; Doumbia, Baba; Madani, Hafsa; El Mellouli, Fatiha; Jiménez-Clavero, Miguel Angel; Sghaier, Soufien; Marianneau, Philippe; Cetre-Sossah, Catherine; Polci, Andrea; Lacote, Sandra; Lakhdar, Magtouf; Fernandez-Pinero, Jovita; Sari Nassim, Chabane; Pinoni, Chiara; Capobianco Dondona, Andrea; Gallardo, Carmina; Bouzid, Taoufiq; Conte, Annamaria; Bortone, Grazia; Savini, Giovanni; Petrini, Antonio; Puech, Lilian

    2015-01-01

    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 currently

  13. Genetic Variability in Probe Binding Regions Explains False Negative Results of a Molecular Assay for the Detection of Dengue Virus.

    PubMed

    Koo, Carmen; Kaur, Simrandeep; Teh, Zhi-Yong; Xu, Helen; Nasir, Amna; Lai, Yee-Ling; Khan, Erum; Ng, Lee-Ching; Hapuarachchi, Hapuarachchige C

    2016-07-01

    Dengue fever is currently the most prevalent disease caused by mosquito-borne flaviviruses. Despite being potentially fatal, there are no specific antiviral therapies for Dengue virus (DENV) infections. Therefore, early, accurate, and rapid diagnosis plays an important role in proper patient management. In this study, we evaluated the performance of a probe-based real-time RT-PCR (rRT-PCR) assay against that of a conventional RT-PCR assay in three sample cohorts from Pakistan (n = 94) and Singapore (first cohort; n = 559, second cohort; n = 123). The Pakistan cohort also included a comparison with virus isolation. The rRT-PCR assay showed relatively lower overall sensitivity (20.2%) in the Pakistan cohort than that in first (90.8%) and second (80.5%) Singapore cohorts. Surprisingly, the overall sensitivity of rRT-PCR assay was lower compared with the virus isolation (26.6%) among Pakistan samples, indicating a high percentage (79.8%) of false negatives due to rRT-PCR assay. The analysis of sequences of failed and successful DENV isolates indicated mismatches in probe binding regions as the likely cause of rRT-PCR assay failure. Our observations testify the importance of utilizing a combination of methods for dengue diagnostics and surveillance. We emphasize that a thorough understanding of the genetic composition of local DENV populations as well as regular monitoring of the performance and reviewing of probe/primer sequences are essential to maintain a consistently high diagnostic accuracy of PCR-based assays. PMID:27172387

  14. Molecular line survey of the high-mass star-forming region NGC 6334I with Herschel/HIFI and the Submillimeter Array

    NASA Astrophysics Data System (ADS)

    Zernickel, A.; Schilke, P.; Schmiedeke, A.; Lis, D. C.; Brogan, C. L.; Ceccarelli, C.; Comito, C.; Emprechtinger, M.; Hunter, T. R.; Möller, T.

    2012-10-01

    Aims: We aim at deriving the molecular abundances and temperatures of the hot molecular cores in the high-mass star-forming region NGC 6334I and consequently deriving their physical and astrochemical conditions. Methods: In the framework of the Herschel guaranteed time key program CHESS (Chemical HErschel Surveys of Star forming regions), NGC 6334I is investigated by using the Heterodyne Instrument for the Far-Infrared (HIFI) aboard the Herschel Space Observatory. A spectral line survey is carried out in the frequency range 480-1907 GHz, and further auxiliary interferometric data from the Submillimeter Array (SMA) in the 230 GHz band provide spatial information for disentangling the different physical components contributing to the HIFI spectrum. The spectral lines in the processed Herschel data are identified with the aid of former surveys and spectral line catalogs. The observed spectrum is then compared to a simulated synthetic spectrum, assuming local thermal equilibrium, and best fit parameters are derived using a model optimization package. Results: A total of 46 molecules are identified, with 31 isotopologues, resulting in about 4300 emission and absorption lines. High-energy levels (Eu > 1000 K) of the dominant emitter methanol and vibrationally excited HCN (ν2 = 1) are detected. The number of unidentified lines remains low with 75, or <2% of the lines detected. The modeling suggests that several spectral features need two or more components to be fitted properly. Other components could be assigned to cold foreground clouds or to outflows, most visible in the SiO and H2O emission. A chemical variation between the two embedded hot cores is found, with more N-bearing molecules identified in SMA1 and O-bearing molecules in SMA2. Conclusions: Spectral line surveys give powerful insights into the study of the interstellar medium. Different molecules trace different physical conditions like the inner hot core, the envelope, the outflows or the cold foreground

  15. Analysis of the sequence diversity of the P1, HC, P3, NIb and CP genomic regions of several yam mosaic potyvirus isolates: implications for the intraspecies molecular diversity of potyviruses.

    PubMed

    Aleman-Verdaguer, M E; Goudou-Urbino, C; Dubern, J; Beachy, R N; Fauquet, C

    1997-06-01

    Partial sequences from serologically characterized yam mosaic potyvirus (YMV) isolates were determined in conserved (helper-component proteinase, HC; nuclear inclusion b, NIb) and variable (first protein, P1; third protein, P3; and coat protein, CP) regions of the potyviral genome in order to investigate the intraspecies molecular diversity of YMV. Multiple sequence alignments and pairwise comparisons were used to quantify the sequence polymorphism in these regions. Two levels of diversity were observed among YMV isolates: above 90% nucleotide (nt) sequence identities were found between YMV isolates of the same group (intragroup) regardless of the region considered, whereas identities between isolates from different groups (intergroup) were lower and depended upon the protein chosen. For instance, the average intergroup nt sequence identity between YMV isolates was about 65% in the P1 protein and the N terminus of the CP while there was more than 80% nt identity in the HC, P3 and NIb proteins. Thus P3 appeared to be conserved between YMV isolates even though this region was variable between potyvirus species. Similar analysis of the intraspecies molecular diversity of other potyviruses (potato virus Y, zucchini yellow mosaic virus, plum pox virus, pea seed-borne mosaic virus) led to the same results: (i) two levels of intraspecies molecular diversity were found (intragroup and intergroup); (ii) intraspecies molecular diversity differed from interspecies molecular diversity in the P3, P1 and N-terminal regions. PMID:9191916

  16. In situ mask designed for selective growth of InAs quantum dots in narrow regions developed for molecular beam epitaxy system

    SciTech Connect

    Ohkouchi, Shunsuke; Nakamura, Yusui; Ikeda, Naoki; Sugimoto, Yoshimasa; Asakawa, Kiyoshi

    2007-07-15

    We have developed an in situ mask that enables the selective formation of molecular beam epitaxially grown layers in narrow regions. This mask can be fitted to a sample holder and removed in an ultrahigh-vacuum environment; thus, device structures can be fabricated without exposing the sample surfaces to air. Moreover, this mask enables the observation of reflection high-energy electron diffraction during growth with the mask positioned on the sample holder and provides for the formation of marker layers for ensuring alignment in the processes following the selective growth. To explore the effectiveness of the proposed in situ mask, we used it to grow quantum dot (QD) structures in narrow regions and verified the perfect selectivity of the QD growth. The grown QDs exhibited high optical quality with a photoluminescence peak at approximately 1.30 {mu}m and a linewidth of 30 meV at room temperature. The proposed technique can be applied for the integration of microstructures into optoelectronic functional devices.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Cichlid fishes in the Angolan headwaters region: molecular evidence of the ichthyofaunal contact between the Cuanza and Okavango-Zambezi systems.

    PubMed

    Musilová, Zuzana; Kalous, Lukáš; Petrtýl, Miloslav; Chaloupková, Petra

    2013-01-01

    The headwaters of five large African river basins flow through the Bié Plateau in Angola and still remain faunistically largely unexplored. We investigated fish fauna from the Cuanza and Okavango-Zambezi river systems from central Angola. We reconstructed molecular phylogenies of the most common cichlid species from the region, Tilapia sparrmanii and Serranochromis macrocephalus, using both mitochondrial and nuclear markers. We found evidence for ichthyofaunal contact and gene flow between the Cuanza and Okavango-Zambezi watersheds in the Bié Plateau in central Angola. Waterfalls and rapids also appeared to restrict genetic exchange among populations within the Cuanza basin. Further, we found that the Angolan Serranochromis cichlid fishes represent a monophyletic lineage with respect to other haplochromines, including the serranochromines from the Congo and Zambezi rivers. This study represents an important initial step in a biodiversity survey of this extremely poorly explored region, as well as giving further understanding to species distributions and gene flow both between and within river basins. PMID:23724120

  19. Cichlid Fishes in the Angolan Headwaters Region: Molecular Evidence of the Ichthyofaunal Contact between the Cuanza and Okavango-Zambezi Systems

    PubMed Central

    Musilová, Zuzana; Kalous, Lukáš; Petrtýl, Miloslav; Chaloupková, Petra

    2013-01-01

    The headwaters of five large African river basins flow through the Bié Plateau in Angola and still remain faunistically largely unexplored. We investigated fish fauna from the Cuanza and Okavango-Zambezi river systems from central Angola. We reconstructed molecular phylogenies of the most common cichlid species from the region, Tilapia sparrmanii and Serranochromis macrocephalus, using both mitochondrial and nuclear markers. We found evidence for ichthyofaunal contact and gene flow between the Cuanza and Okavango-Zambezi watersheds in the Bié Plateau in central Angola. Waterfalls and rapids also appeared to restrict genetic exchange among populations within the Cuanza basin. Further, we found that the Angolan Serranochromis cichlid fishes represent a monophyletic lineage with respect to other haplochromines, including the serranochromines from the Congo and Zambezi rivers. This study represents an important initial step in a biodiversity survey of this extremely poorly explored region, as well as giving further understanding to species distributions and gene flow both between and within river basins. PMID:23724120

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

    PubMed

    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

  1. A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes

    PubMed Central

    Perry, Gregory; DiNatale, Claudia; Xie, Weilong; Navabi, Alireza; Reinprecht, Yarmilla; Crosby, William; Yu, Kangfu; Shi, Chun; Pauls, K. Peter

    2013-01-01

    Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared. These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). However, fifty-nine genes unique to OAC Rex were identified, with resistance gene homologues making up the largest category (10 genes identified). Two unique genes in OAC-Rex located within the SU91 resistance QTL have homology to P. acutifolius ESTs and may be potential sources of CBB resistance. As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean. PMID:24009615

  2. A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes.

    PubMed

    Perry, Gregory; Dinatale, Claudia; Xie, Weilong; Navabi, Alireza; Reinprecht, Yarmilla; Crosby, William; Yu, Kangfu; Shi, Chun; Pauls, K Peter

    2013-01-01

    Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared. These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). However, fifty-nine genes unique to OAC Rex were identified, with resistance gene homologues making up the largest category (10 genes identified). Two unique genes in OAC-Rex located within the SU91 resistance QTL have homology to P. acutifolius ESTs and may be potential sources of CBB resistance. As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean. PMID:24009615

  3. Molecular characterization, sexually dimorphic expression, and functional analysis of 3'-untranslated region of vasa gene in half-smooth tongue sole (Cynoglossus semilaevis).

    PubMed

    Huang, Jinqiang; Chen, Songlin; Liu, Yang; Shao, Changwei; Lin, Fan; Wang, Na; Hu, Qiaomu

    2014-07-15

    Vasa is a highly conserved ATP-dependent RNA helicase expressed mainly in germ cells. The vasa gene plays a crucial role in the development of germ cell lineage and has become an excellent molecular marker in identifying germ cells in teleosts. However, little is known about the structure and function of the vasa gene in flatfish. In this study, the vasa gene (Csvasa) was isolated and characterized in half-smooth tongue sole (Cynoglossus semilaevis), an economically important flatfish in China. In the obtained 6425-bp genomic sequence, 23 exons and 22 introns were identified. The Csvasa gene encodes a 663-amino acid protein, including highly conserved domains of the DEAD-box protein family. The amino acid sequence also shared a high homology with other teleosts. Csvasa expression was mainly restricted to the gonads, with little or no expression in other tissues. Real-time quantitative polymerase chain reaction analysis revealed that Csvasa expression levels decreased during embryonic and early developmental stages and increased with the primordial germ cell proliferation. A typical sexually dimorphic expression pattern of Csvasa was observed during early development and sex differentiation, suggesting that the Csvasa gene might play a differential role in the proliferation and differentiation of male and female primordial germ cells (PGCs). Csvasa mRNA expression levels in neomales were significantly lower than those in normal males and females, indicating that the Csvasa gene might be implicated in germ cell development after sex reversal by temperature treatment. In addition, medaka (Oryzias latipes) PGCs could be transiently labeled by microinjection of synthesized mRNA containing the green fluorescence protein gene and 3'-untranslated region of Csvasa, which confirmed that the Csvasa gene has the potential to be used as a visual molecular marker of germ cells and laid a foundation for manipulation of PGCs in tongue sole reproduction. PMID:24768058

  4. Molecular diagnosis of Fragile X syndrome in subjects with intellectual disability of unknown origin: implications of its prevalence in regional Pakistan.

    PubMed

    Kanwal, Madiha; Alyas, Saadia; Afzal, Muhammad; Mansoor, Atika; Abbasi, Rashda; Tassone, Flora; Malik, Sajid; Mazhar, Kehkashan

    2015-01-01

    Fragile-X syndrome (FXS) is the most common form of inherited intellectual disability (ID) and affects 0.7-3.0% of intellectually compromised population of unknown etiology worldwide. It is mostly caused by repeat expansion mutations in the FMR1 at chromosome Xq27.3. The present study aimed to develop molecular diagnostic tools for a better detection of FXS, to assess implementation of diagnostic protocols in a developing country and to estimate the prevalence of FXS in a cohort of intellectually disabled subjects from Pakistan. From a large pool of individuals with below normal IQ range, 395 subjects with intellectual disability of unknown etiology belonging to different regions of the country were recruited. Conventional-PCR, modified-PCR and Southern blot analysis methods were employed for the detection of CGG repeat polymorphisms in the FMR1 gene. Initial screening with conventional-PCR identified 13 suspected patients. Subsequent investigations through modified PCR and Southern blot analyses confirmed the presence of the FMR1 mutation, suggesting a prevalence of 3.5% and 2.8% (mean 3.3%) among the male and female ID patients, respectively. These diagnostic methods were further customized with the in-house conditions to offer robust screening of referral patients/families for diagnostics and genetic counseling. Prescreening and early diagnosis are crucial for designing a prudent strategy for the management of subjects with ID. Outcome of the study recommends health practitioners for implementation of molecular based FXS diagnosis in routine clinical practice to give a better care for patients similar to the ones included in the study. PMID:25875842

  5. Molecular Diagnosis of Fragile X Syndrome in Subjects with Intellectual Disability of Unknown Origin: Implications of Its Prevalence in Regional Pakistan

    PubMed Central

    Kanwal, Madiha; Alyas, Saadia; Afzal, Muhammad; Mansoor, Atika; Abbasi, Rashda; Tassone, Flora; Malik, Sajid; Mazhar, Kehkashan

    2015-01-01

    Fragile-X syndrome (FXS) is the most common form of inherited intellectual disability (ID) and affects 0.7–3.0% of intellectually compromised population of unknown etiology worldwide. It is mostly caused by repeat expansion mutations in the FMR1 at chromosome Xq27.3. The present study aimed to develop molecular diagnostic tools for a better detection of FXS, to assess implementation of diagnostic protocols in a developing country and to estimate the prevalence of FXS in a cohort of intellectually disabled subjects from Pakistan. From a large pool of individuals with below normal IQ range, 395 subjects with intellectual disability of unknown etiology belonging to different regions of the country were recruited. Conventional-PCR, modified-PCR and Southern blot analysis methods were employed for the detection of CGG repeat polymorphisms in the FMR1 gene. Initial screening with conventional-PCR identified 13 suspected patients. Subsequent investigations through modified PCR and Southern blot analyses confirmed the presence of the FMR1 mutation, suggesting a prevalence of 3.5% and 2.8% (mean 3.3%) among the male and female ID patients, respectively. These diagnostic methods were further customized with the in-house conditions to offer robust screening of referral patients/families for diagnostics and genetic counseling. Prescreening and early diagnosis are crucial for designing a prudent strategy for the management of subjects with ID. Outcome of the study recommends health practitioners for implementation of molecular based FXS diagnosis in routine clinical practice to give a better care for patients similar to the ones included in the study. PMID:25875842

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

    PubMed Central

    Taktaz Hafshejani, Taghi; Nekoei, Shahin; Vazirian, Behnam; Doosti, Abbas; Khamesipour, Faham; Anyanwu, Madubuike Umunna

    2015-01-01

    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. PMID:26421307

  7. Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

    PubMed Central

    Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

    2014-01-01

    Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

  8. Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10.

    PubMed

    Nagasawa, Koo; Hirano, Eiko; Kobayashi, Miho; Ryo, Akihide; Oishi, Kazunori; Obuchi, Masatsugu; Ishiwada, Naruhiko; Noda, Masahiro; Kuroda, Makoto; Shimojo, Naoki; Kimura, Hirokazu

    2015-12-01

    We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period. PMID:26408340

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

    PubMed

    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. PMID:23406568

  10. Binding hotspots on K-Ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis

    PubMed Central

    Prakash, Priyanka; Hancock, John F.; Gorfe, Alemayehu A.

    2015-01-01

    We have used probe-based molecular dynamics (pMD) simulations to search for interaction hotspots on the surface of the therapeutically highly relevant oncogenic K-Ras G12D. Combining the probe-based query with an ensemble-based pocket identification scheme and an analysis of existing Ras-ligand complexes, we show that (i) pMD is a robust and cost-effective strategy for binding site identification, (ii) all four of the previously reported ligand binding sites are suitable for structure-based ligand design, and (iii) in some cases probe binding and expanded sampling of configurational space enable pocket expansion and increase the likelihood of site identification. Furthermore, by comparing the distribution of hotspots in non-pocket-like regions with known protein- and membrane-interacting interfaces, we propose that pMD has the potential to predict surface patches responsible for protein-biomolecule interactions. These observations have important implications for future drug design efforts and will facilitate the search for potential interfaces responsible for the proposed transient oligomerization or interaction of Ras with other biomolecules in the cellular milieu. PMID:25740554

  11. Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants

    PubMed Central

    Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard

    2015-01-01

    ABSTRACT The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X‐ray crystallographic structure of higher plant PsbQ residues S14‐Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this “missing link”, we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N‐terminal residues 1–45 the solution structure deviates significantly from the X‐ray crystallographic one, while the four‐helix bundle core found previously is confirmed. A short α‐helix is observed in the solution structure at the location where a β‐strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N‐terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β‐strand are found. Proteins 2015; 83:1677–1686. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:26138376

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

    PubMed

    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. PMID:27436470

  13. Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

    PubMed

    Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

    2015-09-01

    The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. PMID:26138376

  14. Identification and gene mapping of a 14,700-molecular-weight protein encoded by region E3 of group C adenoviruses.

    PubMed Central

    Tollefson, A E; Wold, W S

    1988-01-01

    Early region E3 of adenovirus type 5 should encode at least nine proteins as judged by the DNA sequence and the spliced structures of the known mRNAs. Only two E3 proteins have been proved to exist, a glycoprotein (gp19K) and an 11,600-molecular-weight protein (11.6K protein). Here we describe an abundant 14.7K protein coded by a gene in the extreme 3' portion of E3. To identify this 14.7K protein, we constructed a bacterial vector which synthesized a TrpE-14.7K fusion protein, then we prepared antiserum against the fusion protein. This antiserum immunoprecipitated the 14.7K protein from cells infected with adenovirus types 5 and 2, as well as with a variety of E3 deletion mutants. Synthesis of the 14.7K protein correlated precisely with the presence or absence of the 14.7K gene and with the synthesis of the mRNA (mRNA h) which encodes the 14.7K protein. The 14.7K protein appeared as a triplet on immunoprecipitation gels and Western blots (immunoblots). Images PMID:3275435

  15. Molecular confirmation of Trichomonas gallinae and other parabasalids from Brazil using the 5.8S and ITS-1 rRNA regions.

    PubMed

    Ecco, Roselene; Preis, Ingred S; Vilela, Daniel A R; Luppi, Marcela M; Malta, Marcelo C C; Beckstead, Robert B; Stimmelmayr, Raphaela; Stimmelmayer, Raphaela; Gerhold, Richard W

    2012-11-23

    Clinical, gross, and histopathology lesions and molecular characterization of Trichomonas spp. infection were described in two striped owls (Asio (Rhinoptynx) clamator), one American kestrel (Falco sparverius), two green-winged saltators (Saltator similis), and in a toco toucan (Ramphastos toco) from Brazil. These birds presented clinical signs including emaciation, ruffled feathers, abundant salivation and open mouth breathing presumably due to abundant caseous material. Gross lesions were characterized by multifocal yellow friable plaques on the surface of the tongue, pharynx and/or caseous masses partially occluding the laryngeal entrance. In the owls, the caseous material extended into the mandibular muscles and invaded the sinuses of the skull. Histopathologically, marked necrotic and inflammatory lesions were associated with numerous round to oval, pale eosinophilic structures (6-10μm) with basophilic nuclei, consistent with trichomonads. Organisms similar to those described above also were found in the liver of the two green-winged saltators. To the authors' knowledge, this is the first report of trichomonosis in a striped owl and a toco toucan. Sequence analysis of the Trichomonas spp. internal transcribed spacer 1 (ITS-1) region and partial 5.8S of the ribosomal RNA (rRNA) disclosed significant genetic diversity. Two sequences had 100% identity to Trichomonas gallinae, whereas two sequences had a 99% and 92% identity to a Trichomonas vaginalis-like sequence, respectively. One sequence (green-winged saltator 502-08) had a 100% identity to a newly recognized genus Simplicomonas. PMID:22749289

  16. Molecular and Cytogenetic Analysis of the Heterochromatin-Euchromatin Junction Region of the Drosophila Melanogaster X Chromosome Using Cloned DNA Sequences

    PubMed Central

    Yamamoto, M. T.; Mitchelson, A.; Tudor, M.; O'Hare, K.; Davies, J. A.; Miklos, GLG.

    1990-01-01

    We have used three cloned DNA sequences consisting of (1) part of the suppressor of forked transcription unit, (2) a cloned 359-bp satellite, and (3), a type I ribosomal insertion, to examine the structure of the base of the X chromosome of Drosophila melanogaster where different chromatin types are found in juxtaposition. A DNA probe from the suppressor of forked locus hybridizes exclusively to the very proximal polytenized part of division 20, which forms part of the β-heterochromatin of the chromocenter. The cloned 359-bp satellite sequence, which derives from the proximal mitotic heterochromatin between the centromere and the ribosomal genes, hybridizes to the under replicated α-heterochromatin of the chromocenter. The type I insertion sequence, which has major locations in the ribosomal genes and in the distal mitotic heterochromatin of the X chromosome, hybridizes as expected to the nucleolus but does not hybridize to the β-heterochromatic division 20 of the polytene X chromosome. Our molecular data reveal that the suppressor of forked locus, which on cytogenetic grounds is the most proximal ordinary gene on the X chromosome, is very close to the junction of the polytenized and non-polytenized region of the X chromosome. The data have implications for the structure of β-heterochromatin-α-heterochromatin junction zones in both mitotic and polytene chromosomes, and are discussed with reference to models of chromosome structure. PMID:2118871

  17. Molecular epidemiology of canine GM1 gangliosidosis in the Shiba Inu breed in Japan: relationship between regional prevalence and carrier frequency

    PubMed Central

    2013-01-01

    Background Canine GM1 gangliosidosis is a fatal disease in the Shiba Inu breed, which is one of the most popular traditional breeds in Japan and is maintained as a standard breed in many countries. Therefore, it is important to control and reduce the prevalence of GM1 gangliosidosis for maintaining the quality of this breed and to ensure supply of healthy dogs to prospective breeders and owners. This molecular epidemiological survey was performed to formulate an effective strategy for the control and prevention of this disease. Results The survey was carried out among 590 clinically unaffected Shiba Inu dogs from the 8 districts of Japan, and a genotyping test was used to determine nation-wide and regional carrier frequencies. The number and native district of affected dogs identified in 16 years from 1997 to June 2013 were also surveyed retrospectively. Of the 590 dogs examined, 6 dogs (1.02%, 6/590) were carriers: 3 dogs (2.27%, 3/132) from the Kinki district and the other 3 dogs from the Hokkaido, Kanto, and Shikoku districts. The retrospective survey revealed 23 affected dogs, among which, 19 dogs (82.6%) were born within the last 7 years. Of the 23 affected dogs, 12 dogs (52.2%) were from the Kinki district. Pedigree analysis demonstrated that all the affected dogs and carriers with the pedigree information have a close blood relationship. Conclusions Our results showed that the current carrier frequency for GM1 gangliosidosis is on the average 1.02% in Japan and rather high in the Kinki district, which may be related to the high prevalence observed over the past 16 years in this region. This observation suggests that carrier dogs are distributed all over Japan; however, kennels in the Kinki district may face an increased risk of GM1 gangliosidosis. Therefore, for effective control and prevention of this disease, it is necessary to examine as many breeding dogs as possible from all regions of Japan, especially from kennels located in areas with high prevalence

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

    PubMed

    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. PMID

  19. Liposomal vaccines incorporating molecular adjuvants and intrastructural T-cell help promote the immunogenicity of HIV membrane-proximal external region peptides

    PubMed Central

    Hanson, Melissa C.; Abraham, Wuhbet; Crespo, Monica P.; Chen, Stephanie H.; Liu, Haipeng; Szeto, Greg Lee; Kim, Mikyung; Reinherz, Ellis L.; Irvine, Darrell J.

    2015-01-01

    An HIV vaccine capable of inducing high and durable levels of broadly neutralizing antibodies has thus far proven elusive. A promising antigen is the membrane-proximal external region (MPER) from gp41, a segment of the viral envelope recognized by a number of broadly neutralizing antibodies. Though an attractive vaccine target due to the linear nature of the epitope and its highly conserved sequence, MPER peptides are poorly immunogenic and may require display on membranes to achieve a physiological conformation matching the native virus. Here we systematically explored how the structure and composition of liposomes displaying MPER peptides impacts the strength and durability of humoral responses to this antigen as well as helper T-cell responses in mice. Administration of MPER peptides anchored to the surface of liposomes induced MPER-specific antibodies whereas MPER administered in oil-based emulsion adjuvants or alum did not, even when combined with Toll like receptor agonists. High-titer IgG responses to liposomal MPER required the inclusion of molecular adjuvants such as monophosphoryl lipid A. Anti-MPER humoral responses were further enhanced by incorporating high-Tm lipids in the vesicle bilayer and optimizing the MPER density to a mean distance of ~10–15 nm between peptides on the liposomes' surfaces. Encapsulation of helper epitopes within the vesicles allowed efficient “intrastructural” T-cell help, which promoted IgG responses to MPER while minimizing competing B-cell responses against the helper sequence. These results define several key properties of liposome formulations that promote durable, high-titer antibody responses against MPER peptides, which will be a prerequisite for a successful MPER-targeting vaccine. PMID:25559188

  20. The molecular origin of a loading-induced black layer in the deep region of articular cartilage at the magic angle

    PubMed Central

    Wang, Nian; Kahn, David; Badar, Farid; Xia, Yang

    2014-01-01

    Purpose To investigate the molecular origin of an unusual low-intensity layer in the deep region of articular cartilage as seen in MRI when the tissue is imaged under compression and oriented at the magic angle. Materials and Methods Microscopic MRI (μMRI) T2 and T1ρ experiments were carried out for both native and degraded (treated with trypsin) 18 specimens. The glycosaminoglycan (GAG) concentrations in the specimens were quantified by both sodium ICP-OES and μMRI Gd(DTPA)2--contrast methods. The mechanical modulus of the specimens was also measured. Results Native tissue shows no load-induced layer, while the trypsin-degraded tissue shows clearly the low-intensity line at the deep part of tissue. The GAG reductions are confirmed by the sodium ICP-OES (from 81.7 ± 5.4 mg/ml to 9.2 ± 3.4 mg/ml), MRI GAG quantification (from 72.4 ± 6.7 mg/ml to 11.2 ± 2.9 mg/ml). The modulus reduction is confirmed by biomechanics (from 4.3 ± 0.7 MPa to 0.3 ± 0.1 MPa). Conclusion Both T2 and T1ρ profiles in native and degraded cartilage show strongly strain-, depth-, and angle-dependent using high resolution MRI. The GAG reduction is responsible for the visualization of a low-intensity layer in deep cartilage when it is loaded and orientated at 55°. PMID:24833266

  1. Molecular fountain.

    SciTech Connect

    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.

  2. 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.

    PubMed

    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

  3. 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

    SciTech Connect

    Sebastio, G.; Perone, L.; Guzzetta, V.

    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.

  4. Virulence and molecular diversity of the Puccinia striiformis f. sp. tritici population in Xinjiang in relation to other regions of western China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, wheat stripe rust caused severe yield losses in western China, especially the Xinjiang Autonomous Region. The population of the stripe rust fungus, Puccinia striiformis f. sp. tritici (Pst), in the vast region had not been well studied. To determine the population structure and comp...

  5. Bean yellow mosaic, clover yellow vein, and pea mosaic are distinct potyviruses: evidence from coat protein gene sequences and molecular hybridization involving the 3' non-coding regions.

    PubMed

    Tracy, S L; Frenkel, M J; Gough, K H; Hanna, P J; Shukla, D D

    1992-01-01

    The sequences of the 3' 1019 nucleotides of the genome of an atypical strain of bean yellow mosaic virus (BYMV-S) and of the 3' 1018 nucleotides of the clover yellow vein virus (CYVV-B) genome have been determined. These sequences contain the complete coding region of the viral coat protein followed by a 3' non-coding region of 173 and 178 nucleotides for BYMV-S and CYVV-B, respectively. When the deduced amino acid sequences of the coat protein coding regions were compared, a sequence identity of 77% was found between the two viruses, and optimal alignment of the 3' untranslated regions of BYMV-S and CYVV-B gave a 65% identity. However, the degree of homology of the amino acid sequences of coat proteins of BYMV-S with the published sequences for three other strains of BYMV ranged from 88% to 94%, while the sequence homology of the 3' untranslated regions between the four strains of BYMV ranged between 86% and 95%. Amplified DNA probes corresponding to the 3' non-coding regions of BYMV-S and CYVV-B showed strong hybridization only with the strains of their respective viruses and not with strains of other potyviruses, including pea mosaic virus (PMV). The relatively low sequence identities between the BYMV-S and CYVV-B coat proteins and their 3' non-coding regions, together with the hybridization results, indicate that BYMV, CYVV, and PMV are distinct potyviruses. PMID:1731696

  6. Molecular cloning of amyloid cDNA derived from mRNA of the Alzheimer disease brain: coding and noncoding regions of the fetal precursor mRNA are expressed in the cortex

    SciTech Connect

    Zain, S.B.; Salim, M.; Chou, W.G.; Sajdel-Sulkowska, E.M.; Majocha, R.E.; Marotta, C.A.

    1988-02-01

    To gain insight into factors associated with the excessive accumulation of ..beta..-amyloid in the Alzheimer disease (AD) brain, the present studies were initiated to distinguish between a unique primary structure of the AD-specific amyloid precursor mRNA vis a vis other determinants that may affect amyloid levels. Previous molecular cloning experiments focused on amyloid derived from sources other than AD cases. In the present work, the authors cloned and characterized amyloid cDNA derived directly from AD brain mRNA. Poly(A)/sup +/ RNA from AD cortices was used for the preparation of lambdagt11 recombinant cDNA libraries. An insert of 1564 nucleotides was isolated that included the ..beta..-amyloid domain and corresponded to 75% of the coding region and approx. = 70% of the 3'-noncoding region of the fetal precursor amyloid cDNA reported by others. On RNA blots, the AD amyloid mRNA consisted of a doublet of 3.2 and 3.4 kilobases. In control and AD cases, the amyloid mRNA levels were nonuniform and were independent of glial-specific mRNA levels. Based on the sequence analysis data, they conclude that a segment of the amyloid gene is expressed in the AD cortex as a high molecular weight precursor mRNA with major coding and 3'-noncoding regions that are identical to the fetal brain gene product.

  7. Molecular Genetics of the Posterior Sex Combs/Suppressor 2 of Zeste Region of Drosophila: Aberrant Expression of the Suppressor 2 of Zeste Gene Results in Abnormal Bristle Development

    PubMed Central

    Brunk, B. P.; Martin, E. C.; Adler, P. N.

    1991-01-01

    We report the molecular characterization of the Posterior sex combs-Suppressor 2 of zeste region of Drosophila melanogaster. The distal breakpoint of the Aristapedioid inversion divides the region into two parts. We have molecularly mapped the lesions associated with several loss of function mutations in the Polycomb group gene Posterior sex combs (Psc) proximal to this breakpoint. In addition, we have found that lesions associated with several loss of function mutations in the Suppressor 2 of zeste [Su(z)2] gene lie distal to this breakpoint. Since the breakpoint does not cause a loss of function in either gene, no essential sequences are shared by these two neighboring genes. There are three dominant gain of function mutations in the region that result in abnormal bristle development. We find that all three juxtapose foreign DNA sequences upstream of the Su(z)2 gene, and that at least two of these mutations (Arp(1) and vg(D)) behave genetically as gain of function mutations in Su(z)2. Northern and in situ hybridization analyses show that the mutations result in increased accumulation of the Su(z)2 mRNA, which we argue is responsible for the bristle loss phenotype. PMID:1905661

  8. Molecular Characterization of Pre-Core/Core and S Region of Hepatitis B Virus in Hemodialysis Patients With Occult Hepatitis B Infection

    PubMed Central

    Rastegarvand, Nasrin; Makvandi, Manoochehr; Samarbafzadeh, Alireza; Rasti, Mojtaba; Neisi, Niloofar; Pouremamali, Amir; Teimoori, Ali; Shabani, Abdolnabi

    2015-01-01

    Background: Occult hepatitis B infection (OBI) is a major public health problem worldwide, which harbors potential risk of hepatitis B virus (HBV) transmission through blood transfusion and transplantation. OBI is characterized by the presence of HBV-DNA in the blood or liver tissue without detectable hepatitis B surface antigen (HBsAg) in the serum. An important cause of OBI is the occurrence of mutations in the HBV genome, especially in the S region. Objectives: The study aims to analyze mutations in S and pre-core/core regions of HBV-DNA in hemodialysis patients. Patients and Methods: Sera of 216 hemodialysis patients were tested for HBsAg and hepatitis B core antibody (HBcAb) by ELISA. Sera of patients that tested negative for HBsAg were evaluated by PCR for the detection of HBV-DNA in the S and pre-core/core regions. In total, six PCR products were sequenced, aligned, and compared with the HBV reference sequence. Amino acid deletion and nucleotide substitution were considered mutations in S and pre-core/core regions of HBV-DNA. Results: Among 216 patients, 203 (93.98%) and 175 (81.01%) sera samples tested negative for HBsAg and HBcAb, respectively. Among all HBsAg-negative samples, six (2.9%) tested positive for HBV-DNA, including four (1.97%) for S and two (0.98%) for pre-core regions. All four (1.97%) samples that tested positive for the S region belonged to HBV-subtype awy. The amino acid sequence of all four samples showed the YMDD motif in position 204 (rtM204). There were three amino acid substitutions in the S region (T127P, P153L, and F170S) and one substitution in the RT region (Y135S). Moreover, two (0.98%) pre-core/core positive patients had an unexpected stop codon in position 1896. Conclusions: This study indicates that 2.9% of hemodialysis patients had OBI, which is considered as a major public health problem worldwide. Moreover, we observed three mutations in S region, including T127P, P153L, and F170S, which caused OBI. This study is first to

  9. Molecular Evolution of the Duplicated Amy Locus in the Drosophila Melanogaster Species Subgroup: Concerted Evolution Only in the Coding Region and an Excess of Nonsynonymous Substitutions in Speciation

    PubMed Central

    Shibata, H.; Yamazaki, T.

    1995-01-01

    From the analysis of restriction maps of the Amy region in eight sibling species belonging to the Drosophila melanogaster species subgroup, we herein show that the patterns of duplication of the Amy gene are almost the same in all species. This indicates that duplication occurred before speciation within this species subgroup. From the nucleotide sequence data, we show a strong within-species similarity between the duplicated loci in the Amy coding region. This is in contrast to a strong similarity in the 5' and 3' flanking regions within each locus (proximal or distal) throughout the species subgroup. This means that concerted evolution occurred only in the Amy coding region and that differentiated evolution between the duplication occurred in the flanking regions. Moreover, when comparing the species, we also found a significant excess of nonsynonymous substitutions. In particular, all the fixed substitutions specific to D. erecta were found to be nonsynonymous. We thus conclude that adaptive protein evolution occurred in the lineage of D. erecta that is a ``specialist'' species for host plants and probably also occurs in the process of speciation in general. PMID:8536970

  10. Molecular basis for expression of the A48 regulatory idiotope on antibodies encoded by immunoglobulin variable-region genes from various families.

    PubMed Central

    Zaghouani, H; Bonilla, F A; Meek, K; Bona, C

    1989-01-01

    The idiotype defined by the levan-specific BALB/c myeloma protein ABPC48 (A48) has previously been encountered only in antibodies the variable regions of which derive from the VHX24 and V kappa 10 gene families. We have demonstrated expression of the idiotope recognized by the monoclonal anti-A48 idiotype antibody IDA10 on five monoclonal antibodies from different mouse strains, with different specificities including foreign and self antigens and deriving their variable regions from families other than VHX24 and V kappa 10. We analyzed variable region protein structure (deduced from nucleotide sequences) and hydrophilicity profiles of idiotype+ and idiotype- antibodies. We identified four surface-exposed areas (one in the heavy chain and three in the light chain) that may contribute to expression of the idiotope defined by antibody IDA10. Images PMID:2494665

  11. Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize.

    PubMed

    Almeida, Gustavo Dias; Nair, Sudha; Borém, Aluízio; Cairns, Jill; Trachsel, Samuel; Ribaut, Jean-Marcel; Bänziger, Marianne; Prasanna, Boddupalli M; Crossa, Jose; Babu, Raman

    2014-01-01

    Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize. PMID:25076840

  12. Involvement of the glucose moiety in the molecular recognition of methyl beta-lactoside by ricin: synthesis, conformational analysis, and binding studies of different derivatives at the C-3 region.

    PubMed

    Fernández, P; Jiménez-Barbero, J; Martín-Lomas, M; Solís, D; Díaz-Mauriño, T

    1994-04-01

    Syntheses of the 3-aminodeoxy (4), 3-deoxy-3-methyl (5), and 3-epi (6) derivatives of methyl beta-lactoside (1) have been achieved from 1 in a straightforward way, and their solution conformations in water and dimethyl sulfoxide analysed through molecular mechanics and dynamics calculations and nuclear magnetic resonance data. The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low energy region with phi = 15 +/- 45 degrees and psi = -25 +/- 30 degrees, that is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. The binding of the different compounds to ricin, the galactose-specific toxin from Ricinus communis, has been investigated. The results confirm the involvement of the C-3 region in a nonpolar interaction with the protein at the periphery of the combining site. PMID:8187100

  13. B- AND A-TYPE STARS IN THE TAURUS-AURIGA STAR-FORMING REGION

    SciTech Connect

    Mooley, Kunal; Hillenbrand, Lynne; Rebull, Luisa; Padgett, Deborah; Knapp, Gillian

    2013-07-10

    We describe the results of a search for early-type stars associated with the Taurus-Auriga molecular cloud complex, a diffuse nearby star-forming region noted as lacking young stars of intermediate and high mass. We investigate several sets of possible O, B, and early A spectral class members. The first is a group of stars for which mid-infrared images show bright nebulae, all of which can be associated with stars of spectral-type B. The second group consists of early-type stars compiled from (1) literature listings in SIMBAD, (2) B stars with infrared excesses selected from the Spitzer Space Telescope survey of the Taurus cloud, (3) magnitude- and color-selected point sources from the Two Micron All Sky Survey, and (4) spectroscopically identified early-type stars from the Sloan Digital Sky Survey coverage of the Taurus region. We evaluated stars for membership in the Taurus-Auriga star formation region based on criteria involving: spectroscopic and parallactic distances, proper motions and radial velocities, and infrared excesses or line emission indicative of stellar youth. For selected objects, we also model the scattered and emitted radiation from reflection nebulosity and compare the results with the observed spectral energy distributions to further test the plausibility of physical association of the B stars with the Taurus cloud. This investigation newly identifies as probable Taurus members three B-type stars: HR 1445 (HD 28929), {tau} Tau (HD 29763), 72 Tau (HD 28149), and two A-type stars: HD 31305 and HD 26212, thus doubling the number of stars A5 or earlier associated with the Taurus clouds. Several additional early-type sources including HD 29659 and HD 283815 meet some, but not all, of the membership criteria and therefore are plausible, though not secure, members.

  14. B- and A-Type Stars in the Taurus-Auriga Star-Forming Region

    NASA Technical Reports Server (NTRS)

    Mooley, Kunal; Hillenbrand, Lynne; Rebull, Luisa; Padgett, Deborah; Knapp, Gillian

    2013-01-01

    We describe the results of a search for early-type stars associated with the Taurus-Auriga molecular cloud complex, a diffuse nearby star-forming region noted as lacking young stars of intermediate and high mass. We investigate several sets of possible O, B, and early A spectral class members. The first is a group of stars for which mid-infrared images show bright nebulae, all of which can be associated with stars of spectral-type B. The second group consists of early-type stars compiled from (1) literature listings in SIMBAD, (2) B stars with infrared excesses selected from the Spitzer Space Telescope survey of the Taurus cloud, (3) magnitude- and color-selected point sources from the Two Micron All Sky Survey, and (4) spectroscopically identified early-type stars from the Sloan Digital Sky Survey coverage of the Taurus region. We evaluated stars for membership in the Taurus-Auriga star formation region based on criteria involving: spectroscopic and parallactic distances, proper motions and radial velocities, and infrared excesses or line emission indicative of stellar youth. For selected objects, we also model the scattered and emitted radiation from reflection nebulosity and compare the results with the observed spectral energy distributions to further test the plausibility of physical association of the B stars with the Taurus cloud. This investigation newly identifies as probable Taurus members three B-type stars: HR 1445 (HD 28929), t Tau (HD 29763), 72 Tau (HD 28149), and two A-type stars: HD 31305 and HD 26212, thus doubling the number of stars A5 or earlier associated with the Taurus clouds. Several additional early-type sources including HD 29659 and HD 283815 meet some, but not all, of the membership criteria and therefore are plausible, though not secure, members.

  15. Molecular Characterization of a Foot-and-Mouth Disease Virus (FMDV) Containing a 57-Nucleotide Insertion in the 3' Untranslated Region (3'UTR)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A foot-and-mouth disease virus (FMDV) virus containing a 57 nt insertion in the 3’ untranslated region (3’UTR) was generated by a transposon (tn) mediated mutagenesis. Characterization of the mutant virus (A24-3’UTR8110) revealed no significant differences in virus growth, translation efficiency and...

  16. Photodissociation Regions

    NASA Technical Reports Server (NTRS)

    Hollenbach, David J.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The interstellar medium of galaxies is the reservoir out of which stars are born and into which stars inject newly created elements as they age. The physical properties of the interstellar medium are governed in part by the radiation emitted by these stars. Far-ultraviolet (6 eV< hNu < 13.6 eV) photons from massive stars dominate the heating and influence the chemistry of the neutral atomic gas and much of the molecular gas in galaxies. Predominantly neutral regions of the interstellar medium in which the heating and chemistry are regulated by far ultraviolet photons are termed Photodissociation Regions (PDRs). These regions are the origin of most of the non-stellar infrared (IR) and the millimeter and submillimeter CO emission from galaxies. The importance of PDRs has become increasingly apparent with the advances in IR and submillimeter astronomy. The IR emission from PDRs includes fine structure lines of C, C(+) and O; rovibrational lines of H2; rotational lines of CO; broad mid-IR features of polycyclic aromatic hydrocarbons; and a luminous underlying IR continuum from interstellar dust. The transition of H to H2 and C(+) to CO occurs within PDRs. Comparison of observations with theoretical models of PDRs enables one to determine the density and temperature structure, the elemental abundances, the level of ionization, and the radiation field. PDR models have been applied to interstellar clouds near massive stars, planetary nebulae, red giant outflows, photoevaporating planetary disks around newly formed stars, diffuse clouds, the neutral intercloud medium, and molecular clouds in the interstellar radiation field-in summary, much of the interstellar medium in galaxies. Theoretical PDR models explain the observed correlations of the [CII] 158, micrometers with the CO J=1-0 emission, the CO J=1-0 luminosity with the interstellar molecular mass, and the [CII] 158 micrometers plus [OI] 63 micrometers luminosity with the IR continuum luminosity. On a more global

  17. Molecular mapping of uncharacteristically small 5q deletions in two patients with the 5q-syndrome: Delineation of the critical region on 5q and identification of a 5q-breakout

    SciTech Connect

    Boultwood, J.; Fidler, C.; Lewis, S.; Littlewood, T.J.; Wainscoat, J.S.; Buckle, V.J. ); Kelly, S. ); Sheridan, H. )

    1994-02-01

    Molecular mapping techniques have defined the region of gene loss in two patients with the 5q-syndrome and uncharacteristically small 5q deletions (5q31-q33). The allelic loss of 10 genes localized to 5q23-qter (centromere-CSF2-EGR1-FGFA-GRL-ADRB2-CSF1R-SPARC-GLUH1-NKSF1-FLT4-telomere) was investigated in peripheral blood cell fractions. Gene dosage experiments demonstrated that CSF2, EGR1, NKSF1, and FLT4 were retained on the 5q-chromosome in both patients and that FGFA was retained in one patient, thus placing these genes outside the critical region. GRL, ADRB2, CSF1R, SPARC, and GLUH1 were shown to be deleted in both patients. The proximal breakpoint is localized between EGR1 and FGFA in one patient and between FGFA and ADRB2 in the other, and the distal breakpoint is localized between GLUH1 and NKSF1 in both patients. Pulsed-field gel electrophoresis was used to map the 5q deletion breakpoints, and breakpoint-specific fragments were detected with FGFA in the granulocyte but not the lymphocyte fraction of one patient. This study has established the critical region of gene loss of the 5q-chromosome in the 5q-syndrome, giving the location for a putative tumor-suppressor gene in the 5.6-Mb region between FGFA and NKSF1. 54 refs., 3 figs., 2 tabs.

  18. Molecular and pigment studies of the picophytoplankton in a region of the Southern Ocean (42 54°S, 141 144°E) in March 1998

    NASA Astrophysics Data System (ADS)

    Wilmotte, A.; Demonceau, C.; Goffart, A.; Hecq, J.-H.; Demoulin, V.; Crossley, A. C.

    Seven filtered seawater samples (depths between 30 and 55 m) collected during the SAZ project of the Austral summer of 1997-1998 were used for a simultaneous study of the picophytoplankton pigments based on high-performance liquid chromatography (HPLC) analyses and flow cytometry, and of the molecular diversity of the picophytoplankton based on their rDNA sequences. The sampling sites could be divided into three temperature zones, distinguished by their proximity to the Sub-Antarctic and Polar Fronts. HPLC analysis of total chlorophylls and carotenoids showed fairly low phytoplankton concentrations (77-262 ng chl a l -1), with minimal values of the pigments in the two samples of the Polar Front Zone around 54°S (water temperature of 4°C at time of collection). In this zone, a similar decrease of particles, identified as cyanobacteria on the basis of their fluorescence, was observed by flow cytometry. Sequences very similar to the 16S rDNA sequence of Synechococcus WH8103 were present in all samples. This Synechococcus genotype is thus found in the Southern Ocean in addition to the Atlantic and Pacific locations where it has been previously observed. The yield of PCR products was lower in the two samples taken in the Polar Front Zone, showing a good agreement between molecular and pigment data. 16S rDNA sequences of plastids of eukaryotic algae also were retrieved, mostly related to those of an environmental clone called OM164, which has not been cultivated but has phylogenetic affinities to the Raphidophyceae.

  19. Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene.

    PubMed Central

    Higuchi, M; Kazazian, H H; Kasch, L; Warren, T C; McGinniss, M J; Phillips, J A; Kasper, C; Janco, R; Antonarakis, S E

    1991-01-01

    Hemophilia A is an X chromosome-linked disorder resulting from deficiency of factor VIII, an important protein in blood coagulation. A large number of disease-producing mutations have been reported in the factor VIII gene. However, a comprehensive analysis of the mutations has been difficult because of the large gene size, its many scattered exons, and the high frequency of de novo mutations. Recently, we have shown that nearly all mutations resulting in mild-to-moderate hemophilia A can be detected by PCR and denaturing gradient gel electrophoresis (DGGE). In this study, we attempted to discover the mutations causing severe hemophilia A by analyzing 47 unselected patients, 30 of whom had severe hemophilia and 17 of whom had mild-to-moderate disease. Using DGGE as a screening method, we analyzed 99% of the coding region, 94% of the splice junctions, the promoter region, and the polyadenylylation site of the gene. We found the mutation in 16 of 17 (94%) patients with mild-to-moderate disease but in only 16 of 30 (53%) patients with severe hemophilia A. Since DGGE after computer analysis appears to detect all mutations in a given fragment, the lower-than-expected yield of mutations in patients with severe disease is likely not due to failure of the detection method; it is probably due to the presence of mutations in DNA sequences outside the regions studied. Such sequences may include locus-controlling regions, other sequences within introns or outside the gene that are important for its expression, or another gene involved in factor VIII expression that is very closely linked to the factor VIII gene. Images PMID:1908096

  20. Molecular analysis of the replication region of the theta-replicating plasmid pUCL287 from Tetragenococcus (Pediococcus) halophilus ATCC33315.

    PubMed

    Benachour, A; Frère, J; Flahaut, S; Novel, G; Auffray, Y

    1997-08-01

    The complete nucleotide sequence of the 8.7-kb theta-replicating plasmid pUCL287 from Tetragenococcus halophilus (formerly Pediococcus halophilus) ATCC33315 has been determined. The replication region was identified and analyzed. Its nucleotide sequence contains an untranslated region, the replication origin, followed by two open reading frames (ORFs) encoding two proteins of 311 (RepA287) and 168 (RepB287) amino acids, respectively. Evidence is presented to show that RepA287 represents the plasmid replication protein. RepB287, which is non-essential for replication, is involved in the plasmid copy-number control and segregational stability. The roles of lactococcal proteins homologous to RepB287 have not been defined so far. Nevertheless, the structural organization of the pUCL287 replication region is remarkably similar to those of well known theta-replicating lactococcal plasmids despite the absence of homology of the replication origin and of the replication protein, and this suggests that pUCL287 uses the same mechanism of replication. Nucleotide sequence comparisons show that pSMB74, a pediococcal plasmid encoding bacteriocin production, is a member of the pUCL287 replicon family. PMID:9294035

  1. Molecular evolution of a central region containing B cell epitopes in the gene encoding the p67 sporozoite antigen within a field population of Theileria parva.

    PubMed

    Obara, Isaiah; Ulrike, Seitzer; Musoke, Tony; Spooner, Paul R; Jabbar, Ahmed; Odongo, David; Kemp, Stephen; Silva, Joana C; Bishop, Richard P

    2015-05-01

    Protective immunity induced by the infective sporozoite stage of Theileria parva indicates a potential role for antibodies directed against conserved serologically reactive regions of the major sporozoite surface antigen p67 in vaccination to control the parasite. We have examined the allelic variation and determined the extent of B cell epitope polymorphism of the gene encoding p67 among field isolates originating from cattle exposed to infected ticks in the Marula area of the rift valley in central Kenya where the African cape buffalo (Syncerus caffer) and cattle co-graze. In the first of two closely juxtaposed epitope sequences in the central region of the p67 protein, an in-frame deletion of a seven-amino acid segment results in a truncation that was observed in parasites derived from cattle that co-grazed with buffalo. In contrast, the variation in the second epitope was primarily due to nonsynonymous substitutions, resulting in relatively low overall amino acid conservation in this segment of the protein. We also observed polymorphism in the region of the protein adjacent to the two defined epitopes, but this was not sufficient to provide statistically significant evidence for positive selection. The data indicates that B cell epitopes previously identified within the p67 gene are polymorphic within the Marula field isolates. Given the complete sequence identity of the p67 gene in all previously characterized T. parva isolates that are transmissible between cattle by ticks, the diversity observed in p67 from the Marula isolates in combination with the clinical reaction of the infected cattle is consistent with them originating from ticks that had acquired T. parva from buffalo. PMID:25673078

  2. High-Resolution Soft X-Ray Spectral Analysis in the CK Region of Titanium Carbide (TiC) using the DV-X alpha Molecular Orbital Method

    SciTech Connect

    Shimomura, Kenta; Muramatsu, Yasuji; Denlinger, Jonathan D.; Gullikson, Eric M.

    2008-10-31

    We used the DV-X alpha method to analyze the high-resolution soft X-ray emission and absorption spectra in the CK region of titanium carbide (TiC). The spectral profiles of the X-ray emission and absorption can be ssuscfucelly reproduced by the occupied and unoccupied density of states (DOS ), respectively, in the C2p orbitals of the center carbon atoms in a Ti62C63 cluster model, suggesting that the center carbon atom in a large cluster model expanded to the cubic-structured 53 (= 125) atoms provides sufficient DOS for the X-ray spectral analysis of rock-salt structured metal carbides.

  3. The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria.

    PubMed

    Tramuto, Fabio; Orsi, Andrea; Maida, Carmelo Massimo; Costantino, Claudio; Trucchi, Cecilia; Alicino, Cristiano; Vitale, Francesco; Ansaldi, Filippo

    2016-01-01

    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. PMID:27089319

  4. Preferential binding of anti-cancer drug adriamycin to the Sp1 binding site in c-met promoter region: A spectroscopic and molecular modeling study

    NASA Astrophysics Data System (ADS)

    Singhal, Garima; Rajeswari, Moganty R.

    2009-02-01

    The c-met gene encodes a transmembrane glycoprotein receptor with tyrosine kinase activity and overexpression of MET receptor is found in a number of common human malignancies. Regulation of c-met oncogene expression in general can be controlled by several DNA binding anti-cancer drugs. Interaction of adriamycin with a short oligonucleotide (24RY), which is part of the positive regulatory element (-233 to -68) in c-met gene was studied using UV-Vis absorption and fluorescence spectroscopy, UV-thermal melting, and molecular modeling. Strong binding of adriamycin to 24RY (overall binding constant K, 1- 3 × 10 5 M -1) is thermodynamically favored and is accompanied by the following: a marked increase in the melting temperature of 24RY by +15 °C and ˜60% decrease in absorption at 480 nm, ˜80% quenching of fluorescence at 555 nm along with a blue shift of the λemimax to 522 nm of adriamycin. Present data reveals that adriamycin binds to ˜ 5 bp (GCGGG) of the Sp1 binding site in 24RY and thus competes with Sp1 binding to the promoter site which results in down-regulation of kinase. Therefore, targeting c-met is a promising approach as it is an attractive novel oncogene for cancer therapeutics.

  5. Molecular and Stable Carbon Isotope Composition of Organic Compounds from Particles Sampled from the Lower Fraser Valley, BC Urban and Regional Air Shed

    NASA Astrophysics Data System (ADS)

    Whiticar, M. J.; Gray, S. L.

    2001-12-01

    This study examines the character of specific non-volatile organic compounds (N-VOCs) extracted from total suspended particulates. Aerosols are collected on filters by HiVol samplers on monthly intervals, at well-characterized meteorological sites throughout the Lower Fraser Valley. Filters are solvent-extracted , then separated into different compound classes by Silica-gel Chromatography. Selected fractions are analysed for their individual compound molecular compositions by Gas Chromatography-Mass Spectrometry (GC/MS) and by Continuous Flow-Isotope Ratio Mass Spectrometry (CF-IRMS) for their stable carbon isotope ratio. The purpose is to identify spatial and temporal variations in N-VOCs, with the long-term goal of understanding their sources, transport processes and atmospheric chemistry. This Health Canada, Toxic Substance Research Initiative offers insights into the levels and signatures of N-VOCs exposed to humans in congested urban settings. The program is also part of the Pacific 2001 field study. This paper presents the initial year's results on our N-VOCs, including alkanes, organic acids, in comparison with bulk isotope analyses.

  6. The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010–2015: The Experience of Sicily and Liguria

    PubMed Central

    Tramuto, Fabio; Orsi, Andrea; Maida, Carmelo Massimo; Costantino, Claudio; Trucchi, Cecilia; Alicino, Cristiano; Vitale, Francesco; Ansaldi, Filippo

    2016-01-01

    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. PMID:27089319

  7. Molecular characterization of Rhodococcus equi Isolates of horse breeding farms from an endemic region in South of Brazil by multiplex PCR

    PubMed Central

    Krewer, Cristina da Costa; Spricigo, Dênis Augusto; de Avila Botton, Sônia; da Costa, Mateus Matiuzzi; Schrank, Irene; de Vargas, Agueda Castagna

    2008-01-01

    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 vapApositive R. equi from adult horse feces, which is an evidence for other routes of dissemination of this pathogen in the farms. PMID:24031201

  8. Molecular Cloning of Spergen-4, Encoding a Spermatogenic Cell-Specific Protein Associated with Sperm Flagella and the Acrosome Region in Rat Spermatozoa.

    PubMed

    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. PMID:27032685

  9. Molecular cloning of a full-length cDNA for dentatorubral-pallidoluysian atrophy and regional expressions of the expanded alleles in the CNS

    SciTech Connect

    Onodera, Osamu; Oyake, Mutsuo; Takano, Hiroki

    1995-11-01

    Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder characterized by genetic anticipation and variable combinations of symptoms including myoclonus, epilepsy, cerebellar ataxia, choreoathetosis, and dementia. Recently, we discovered that DRPLA is caused by unstable expansion of a CAG repeat of a gene on the short arm of chromosome 12. We determined the consensus DRPLA cDNA sequence containing the complete coding region for 1,185 amino acids. The CAG repeat, which is expanded in DRPLA, is located 1,462 bp downstream from the putative methionine initiation codon and encodes a poly-glutamine tract. Although poly-serine and proline tracts exist near the CAG repeats, these poly-serine or proline tracts did not show any polymorphisms, which is in strong contrast to the high heterogeneity in the length of the CAG repeat. Northern blot analysis revealed a 4.7-kb transcript that is widely expressed in various tissues including heart, lung, kidney, placenta, skeletal muscle, and brain. Reverse transcription-PCR analysis revealed that the expanded alleles are transcribed to levels comparable to those of normal alleles. These results indicate that there is no difference in transcriptional efficiency between expanded and normal alleles. Furthermore, mRNA from cerebellar hemispheres of DRPLA patients showed smaller sizes of CAG repeats compared with other regions of the brain, which reflects somatic mosaicism of the expanded alleles of the DRPLA gene. 49 refs., 6 figs.

  10. Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene

    SciTech Connect

    Higuchi, Miyoko; Kazazian, H.H. Jr.; Kasch, L.; Warren, T.C.; McGinniss, M.J.; Antonarakis, S.E. ); Phillips, J.A. III; Janco, R. ); Kasper, C. )

    1991-08-15

    Hemophilia A is an X chromosome-linked disorder resulting from deficiency of factor VIII, an important protein in blood coagulation. A large number of disease-producing mutations have been reported in the factor VIII gene. However, a comprehensive analysis of the mutations has been difficult because of the larger gene size, its many scattered exons, and the high frequency of de novo mutations. Recently, the authors have shown that nearly all mutations resulting in mild-to-moderate hemophilia A can be detected by PCR and denaturing gradient gel electrophoresis (DGGE). In this study, they attempted to discover the mutations causing severe hemophilia A by analyzing 47 unselected patients, 30 of whom had severe hemophilia and 17 of whom had mild-to-moderate disease. Using DGGE as a screening method, they analyzed 99% of the coding region, 94% of the splice junctions, the promoter region, and the polyadenylylation site of the gene. They found the mutation in 16 of 17 (94%) patients with mild-to-moderate disease but in only 16 of 30 (53%) patients with severe hemophilia A.

  11. Molecular findings from influenza A(H1N1)pdm09 detected in patients from a Brazilian equatorial region during the pandemic period

    PubMed Central

    Oliveira, Maria José Couto; Motta, Fernando do Couto; Siqueira, Marilda M; Resende, Paola Cristina; Born, Priscilla da Silva; Souza, Thiago Moreno L; Mesquita, Milene; Oliveira, Maria de Lourdes Aguiar; Carney, Sharon; de Mello, Wyller Alencar; Magalhães, Vera

    2014-01-01

    After the World Health Organization officially declared the end of the first pandemic of the XXI century in August 2010, the influenza A(H1N1)pdm09 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(H1N1)pdm09 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. PMID:25410995

  12. Ninety-Nine Is Not Enough: Molecular Characterization of Inhibitor-Resistant Human Immunodeficiency Virus Type 1 Protease Mutants with Insertions in the Flap Region

    SciTech Connect

    Koiek, Milan; Saskova, Klara Grantz; Rezaova, Pavlina; Brynda, Jii; van Maarseveen, Noortje M.; De Jong, Dorien; Boucher, Charles A.; Kagan, Ron M.; Nijhuis, Monique; Konvalinka, Jan

    2008-07-21

    While the selection of amino acid insertions in human immunodeficiency virus (HIV) reverse transcriptase (RT) is a known mechanism of resistance against RT inhibitors, very few reports on the selection of insertions in the protease (PR) coding region have been published. It is still unclear whether these insertions impact protease inhibitor (PI) resistance and/or viral replication capacity. We show that the prevalence of insertions, especially between amino acids 30 to 41 of HIV type 1 (HIV-1) PR, has increased in recent years. We identified amino acid insertions at positions 33 and 35 of the PR of HIV-1-infected patients who had undergone prolonged treatment with PIs, and we characterized the contribution of these insertions to viral resistance. We prepared the corresponding mutated, recombinant PR variants with or without insertions at positions 33 and 35 and characterized them in terms of enzyme kinetics and crystal structures. We also engineered the corresponding recombinant viruses and analyzed the PR susceptibility and replication capacity by recombinant virus assay. Both in vitro methods confirmed that the amino acid insertions at positions 33 and 35 contribute to the viral resistance to most of the tested PIs. The structural analysis revealed local structural rearrangements in the flap region and in the substrate binding pockets. The enlargement of the PR substrate binding site together with impaired flap dynamics could account for the weaker inhibitor binding by the insertion mutants. Amino acid insertions in the vicinity of the binding cleft therefore represent a novel mechanism of HIV resistance development.

  13. Molecular characterization of Staphylococcus aureus isolates from skin and soft tissue infections samples and healthy carriers in the Central Slovenia region.

    PubMed

    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. PMID:26781044

  14. Molecular Characterization of the ORF3 and S1 Genes of Porcine Epidemic Diarrhea Virus Non S-INDEL Strains in Seven Regions of China, 2015

    PubMed Central

    Wang, Enyu; Guo, Donghua; Li, Chunqiu; Wei, Shan; Wang, Zhihui; Liu, Qiujin; Zhang, Bei; Kong, Fanzhi; Feng, Li; Sun, Dongbo

    2016-01-01

    In an effort to trace the evolution of porcine epidemic diarrhea virus (PEDV), S1 and ORF3 genes of viruses identified in 41 pig farms from seven regions (North, Northeast, Northwest, Central, East, South West, and South, respectively) of China in 2015 were sequenced and analyzed. Sequence analysis revealed that the 41 ORF3 genes and 29 S1 genes identified in our study exhibited nucleotide homologies of 98.2%–100% and 96.6%–100%, respectively; these two genes exhibited low nucleotide sequence similarities with classical CV777 strain and early Chinese strain LZC. Phylogenetic analysis indicated that the identified PEDV strains belonged to global non S-INDEL strains, and exhibited genetic diversity; S1 gene of the HLJ2015/DP1-1 strain harbored an unique deletion of 12 nucleotides (A1130CAACTCCACTG1141); while the Chinese PEDV S-INDEL reference strains included two types of the “CV777” S-INDEL as well as the “US” S-INDEL, and all co-circulated with Chinese non S-INDEL strains. Of 29 identified S1 genes, the SS2 epitope (Y748SNIGVCK755) was highly conserved, while the SS6 epitope (L764QDGQVKI771) and pAPN receptor-binding region (aa 490–615) exhibited amino substitutions. Nine possible recombination events were identified between the 29 identifed S1 genes and the 3 S1 reference genes from early Chinese PEDV strains. The complete S genes of selected Chinese PEDV field strains (2011–2015) showed 5.18%–6.07% nucleotide divergence, which is far higher than the divergence observed in early Chinese PEDV strains (3.1%) (P<0.05). Our data provide evidence that PEDV non S-INDEL strains with genetic diversities and potential recombination circulate in seven regions of China in 2015; Chinese PEDV S-INDEL strains exhibit genetic diversity and co-circulate with non S-INDEL strains. PMID:27494026

  15. Molecular weight abnormalities of the CTCF transcription factor: CTCF migrates aberrantly in SDS-PAGE and the size of the expressed protein is affected by the UTRs and sequences within the coding region of the CTCF gene.

    PubMed Central

    Klenova, E M; Nicolas, R H; U, S; Carne, A F; Lee, R E; Lobanenkov, V V; Goodwin, G H

    1997-01-01

    CTCF belongs to the Zn finger transcription factors family and binds to the promoter region of c-myc. CTCF is highly conserved between species, ubiquitous and localised in nuclei. The endogenous CTCF migrates as a 130 kDa (CTCF-130) protein on SDS-PAGE, however, the open reading frame (ORF) of the CTCF cDNA encodes only a 82 kDa protein (CTCF-82). In the present study we investigate this phenomenon and show with mass-spectra analysis that this occurs due to aberrant mobility of the CTCF protein. Another paradox is that our original cDNA, composed of the ORF and 3'-untranslated region (3'-UTR), produces a protein with the apparent molecular weight of 70 kDa (CTCF-70). This paradox has been found to be an effect of the UTRs and sequences within the coding region of the CTCF gene resulting in C-terminal truncation of CTCF-130. The potential attenuator has been identified and point-mutated. This restored the electrophoretic mobility of the CTCF protein to 130 kDa. CTCF-70, the aberrantly migrating CTCF N-terminus per se, is also detected in some cell types and therefore may have some biological implications. In particular, CTCF-70 interferes with CTCF-130 normal function, enhancing transactivation induced by CTCF-130 in COS6 cells. The mechanism of CTCF-70 action and other possible functions of CTCF-70 are discussed. PMID:9016583

  16. Spectro-Imaging of the Asymmetric Inner Molecular and Dust Shell Region of the Mira Variable W Hya with MIDI/VLTI

    NASA Astrophysics Data System (ADS)

    Zhao-Geisler, R.; Köhler, R.; Kemper, F.; Kerschbaum, F.; Mayer, A.; Quirrenbach, A.; Lopez, B.

    2015-08-01

    We have observed W Hya, one of the closest and best-studied oxygen-rich evolved stars, in the dust sensitive mid-IR spectral domain with the interferometric instrument MIDI. Images could be obtained for the first time with MIDI in 25 wavelengths bins with the image reconstruction software MiRA using only the modulus of the visibilities. This still remains one of the few cases in which images could be successfully recovered due to the difficulties inherent to optical/infrared interferometry concerning the sparseness of the UV-plane and the missing Fourier phase information. Different regularization terms were compared and the influence of the UV-coverage was investigated. The lack of Fourier phase information, however, still limits the interpretation of the images. W Hya appears clearly nonsymmetric and the size is wavelength dependent. The photosphere, molecular layers, and dust formation zone could be resolved with an photospheric Gaussian FWHM diameter of 42 ± 2 mas (corresponding to 4.1 AU) and a dust layer of presumably amorphous aluminum oxide (Al2O3) at around two photospheric radii. The position angle of the major axis of the elongated structure could be determined to be (15 ± 10)° with a less well defined axis ratio between 0.4 and 0.6 showing that the dust forms primarily along a N-S axis. By comparing the elongated structure seen with MIDI with the Herschel/PACS 70 μm image at much larger scales, one can conclude that the asymmetry in the mass-loss most likely originates in the very close vicinity of the star and is thus not due to an interaction with the ambient media. Based on observations made with the Very Large Telescope Interferometer (VLTI) at the Paranal Observatory under program IDs 083.D-0294, 084.D-0334, and 085.D-0201.

  17. The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

    PubMed Central

    Hřibová, Eva; Čížková, Jana; Christelová, Pavla; Taudien, Stefan; de Langhe, Edmond; Doležel, Jaroslav

    2011-01-01

    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. PMID:21445344

  18. Molecular Epidemiology of Rabies Viruses Circulating in Two Rabies Endemic Provinces of Laos, 2011–2012: Regional Diversity in Southeast Asia

    PubMed Central

    Ahmed, Kamruddin; Phommachanh, Phouvong; Vorachith, Phengphet; Matsumoto, Takashi; Lamaningao, Pheophet; Mori, Daisuke; Takaki, Minako; Douangngeun, Bounlom; Khambounheuang, Bounkhouang; Nishizono, Akira

    2015-01-01

    Background Although rabies is endemic in Laos, genetic characterization of the viruses in this country is limited. There are growing concerns that development in the region may have increased transport of dog through Laos for regional dog meat consumption, and that this may cause spillover of the viruses from dogs brought here from other countries. This study was therefore undertaken to evaluate the current rabies situation and the genetic characteristics of rabies viruses currently circulating in Laos. Methods We determined the rate of rabies-positive samples by analyzing data from animal samples submitted to the Lao Ministry of Agriculture and Forestry’s National Animal Health Centre rabies laboratory from 2004 through 2011. Twenty-three rabies-positive samples were used for viral genetic characterization. Full genome sequencing was performed on two rabies viruses. Results Rabies-positive samples increased substantially from 40.5% in 2004 to 60.2% in 2009 and continued at this level during the study period. More than 99% of the samples were from dogs, followed by cats and monkeys. Phylogenetic analyses showed that three rabies virus lineages belonging to the Southeast Asian cluster are currently circulating in Laos; these are closely related to viruses from Thailand, Cambodia and Vietnam. Lineages of the circulating Laos rabies viruses diverged from common ancestors as recently as 44.2 years and as much as 55.3 years ago, indicating periodic virus invasions. Conclusion There is an increasing trend of rabies in Laotian animals. Similar to other rabies-endemic countries, dogs are the main viral reservoir. Three viral lineages closely related to viruses from neighboring countries are currently circulating in Laos. Data provide evidence of periodic historic exchanges of the viruses with neighboring countries, but no recent invasion. PMID:25825907

  19. 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.

    PubMed

    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

  20. Studies of the biosynthesis of 3,6-dideoxyhexoses: molecular cloning and characterization of the asc (ascarylose) region from Yersinia pseudotuberculosis serogroup VA.

    PubMed Central

    Thorson, J S; Lo, S F; Ploux, O; He, X; Liu, H W

    1994-01-01

    The 3,6-dideoxyhexoses are found in the lipopolysaccharides of gram-negative bacteria, where they have been shown to be the dominant antigenic determinants. Of the five 3,6-dideoxyhexoses known to occur naturally, four have been found in various strains of Salmonella enterica (abequose, tyvelose, paratose, and colitose) and all five, including ascarylose, are present among the serotypes of Yersinia pseudotuberculosis. Although there exists one report of the cloning of the rfb region harboring the abequose biosynthetic genes from Y. pseudotuberculosis serogroup HA, the detailed genetic principles underlying a 3,6-dideoxyhexose polymorphism in Y. pseudotuberculosis have not been addressed. To extend the available information on the genes responsible for 3,6-dideoxyhexose formation in Yersinia spp. and facilitate a comparison with the established rfb (O antigen) cluster of Salmonella spp., we report the production of three overlapping clones containing the entire gene cluster required for CDP-ascarylose biosynthesis. On the basis of a detailed sequence analysis, the implications regarding 3,6-dideoxyhexose polymorphism among Salmonella and Yersinia spp. are discussed. In addition, the functional cloning of this region has allowed the expression of Ep (alpha-D-glucose cytidylyltransferase), Eod (CDP-D-glucose 4,6-dehydratase), E1 (CDP-6-deoxy-L-threo-D-glycero-4- hexulose-3-dehydrase), E3 (CDP-6-deoxy-delta 3,4-glucoseen reductase), Eep (CDP-3,6-dideoxy-D-glycero-D- glycero-4-hexulose-5-epimerase), and Ered (CDP-3,6-dideoxy-L-glycero-D-glycero-4-hexulose-4-reductase), facilitating future mechanistic studies of this intriguing biosynthetic pathway. Images PMID:8071227

  1. Molecular Scanning of β-Thalassemia in the Southern Region of Central Java, Indonesia; a Step Towards a Local Prevention Program.

    PubMed

    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. PMID:26291967

  2. Generation and Molecular Mapping of a Sequence Characterized Amplified Region Marker Linked with the Bct Gene for Resistance to Beet curly top virus in Common Bean.

    PubMed

    Larsen, Richard C; Miklas, Phillip N

    2004-04-01

    ABSTRACT A random amplified polymorphic DNA (RAPD) marker directly linked (0.0 cM) with a resistance gene was identified in a snap bean recombinant inbred population (Moncayo x Primo) consisting of 94 F(5:7) recombinant inbred lines that had uniform segregation for disease reaction to Beet curly top virus (BCTV) across three field locations. Resistance was conditioned by a single dominant allele tentatively designated Bct. Seven hundred and fifty decamer primers were screened to obtain the linked RAPD marker that was then converted to a sequence characterized amplified region (SCAR) marker SAS8.1550. The SCAR mapped within a cluster of resistance genes on linkage group B7 of the core map. A survey of 103 BCTV-resistant and -susceptible snap and dry bean genotypes was conducted using SAS8.1550. Results showed that the SCAR would be highly useful for marker-assisted selection of Bct in snap and dry bean originating from the Andean gene pool. Marker-assisted selection for Bct will expedite the development of BCTV-resistant cultivars and minimize the need for cumbersome pathogen tests. PMID:18944106

  3. Molecular epidemiology of Mycobacterium avium subspecies paratuberculosis: IS900 PCR identification and IS1311 polymorphism analysis from ruminants in the Punjab region of India.

    PubMed

    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. PMID:21071087

  4. Molecular Insights into the Coding Region Determinant-binding Protein-RNA Interaction through Site-directed Mutagenesis in the Heterogeneous Nuclear Ribonucleoprotein-K-homology Domains*

    PubMed Central

    Barnes, Mark; van Rensburg, Gerrit; Li, Wai-Ming; Mehmood, Kashif; Mackedenski, Sebastian; Chan, Ching-Man; King, Dustin T.; Miller, Andrew L.; Lee, Chow H.

    2015-01-01

    The ability of its four heterogeneous nuclear RNP-K-homology (KH) domains to physically associate with oncogenic mRNAs is a major criterion for the function of the coding region determinant-binding protein (CRD-BP). However, the particular RNA-binding role of each of the KH domains remains largely unresolved. Here, we mutated the first glycine to an aspartate in the universally conserved GXXG motif of the KH domain as an approach to investigate their role. Our results show that mutation of a single GXXG motif generally had no effect on binding, but the mutation in any two KH domains, with the exception of the combination of KH3 and KH4 domains, completely abrogated RNA binding in vitro and significantly retarded granule formation in zebrafish embryos, suggesting that any combination of at least two KH domains cooperate in tandem to bind RNA efficiently. Interestingly, we found that any single point mutation in one of the four KH domains significantly impacted CRD-BP binding to mRNAs in HeLa cells, suggesting that the dynamics of the CRD-BP-mRNA interaction vary over time in vivo. Furthermore, our results suggest that different mRNAs bind preferentially to distinct CRD-BP KH domains. The novel insights revealed in this study have important implications on the understanding of the oncogenic mechanism of CRD-BP as well as in the future design of inhibitors against CRD-BP function. PMID:25389298

  5. Molecular and Isotopic Analysis of Earthworm Fecal Matter as a Tool for Determining Carbon Cycling Dynamics in two Great Lakes Region Forests

    NASA Astrophysics Data System (ADS)

    Top, S. M.; Filley, T. R.; Zurn-Birkhimer, S.

    2009-12-01

    Earthworms are frequently referred to as soil ecosystem engineers, reflecting their role as a potential major factor in controlling the dynamics of litter and soil organic matter transformations. Their significance is magnified when considering they are exotic in northern North American forests, humans acting as the main vector with transport of soil and recreational fishing. As a result of earthworm activity, forests can undergo significant changes to forest floor chemistry and soil structure, possibly increasing nutrient loss from both soil and leaf litter. The impact of earthworms on overall soil carbon stabilization/destabilization is largely unknown but likely a function of both species composition and edaphic soil properties. We are investigating the impacts of exotic earthworms on soils within two Great Lakes region forests; the Aspen free air CO2 enrichment (FACE) site, Rhinelander, WI, and forests in Red Lake Indian Reservation, MN. Aspen FACE provides an opportunity to document the changes that occur to forest chemistry and earthworm activity are a result of increased CO2, while the sites on the Red Lake Reservation are significant because of they contain a gradient of earthworm influence. At both sites earthworm populations were amassed from small pits and isolated to collect gut contents for isotopic and plant biopolymer chemistry analysis. Analysis are ongoing and will eventually include alkaline CuO extraction and isotopic analyses on the fecal matter, leaf litter, and soil to determine how plant biopolymers are vertically transported and mixed with soil from deeper horizons.

  6. Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826)

    PubMed Central

    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations. PMID:25003795

  7. Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions

    PubMed Central

    Pauciullo, Alfredo; Erhardt, Georg

    2015-01-01

    In the present paper, we report for the first time the characterization of llama (Lama glama) caseins at transcriptomic and genetic level. A total of 288 casein clones transcripts were analysed from two lactating llamas. The most represented mRNA populations were those correctly assembled (85.07%) and they encoded for mature proteins of 215, 217, 187 and 162 amino acids respectively for the CSN1S1, CSN2, CSN1S2 and CSN3 genes. The exonic subdivision evidenced a structure made of 21, 9, 17 and 6 exons for the αs1-, β-, αs2- and κ-casein genes respectively. Exon skipping and duplication events were evidenced. Two variants A and B were identified in the αs1-casein gene as result of the alternative out-splicing of the exon 18. An additional exon coding for a novel esapeptide was found to be cryptic in the κ-casein gene, whereas one extra exon was found in the αs2-casein gene by the comparison with the Camelus dromedaries sequence. A total of 28 putative phosphorylated motifs highlighted a complex heterogeneity and a potential variable degree of post-translational modifications. Ninety-six polymorphic sites were found through the comparison of the lama casein cDNAs with the homologous camel sequences, whereas the first description and characterization of the 5’- and 3’-regulatory regions allowed to identify the main putative consensus sequences involved in the casein genes expression, thus opening the way to new investigations -so far- never achieved in this species. PMID:25923814

  8. Molecular Characterization of the Llamas (Lama glama) Casein Cluster Genes Transcripts (CSN1S1, CSN2, CSN1S2, CSN3) and Regulatory Regions.

    PubMed

    Pauciullo, Alfredo; Erhardt, Georg

    2015-01-01

    In the present paper, we report for the first time the characterization of llama (Lama glama) caseins at transcriptomic and genetic level. A total of 288 casein clones transcripts were analysed from two lactating llamas. The most represented mRNA populations were those correctly assembled (85.07%) and they encoded for mature proteins of 215, 217, 187 and 162 amino acids respectively for the CSN1S1, CSN2, CSN1S2 and CSN3 genes. The exonic subdivision evidenced a structure made of 21, 9, 17 and 6 exons for the αs1-, β-, αs2- and κ-casein genes respectively. Exon skipping and duplication events were evidenced. Two variants A and B were identified in the αs1-casein gene as result of the alternative out-splicing of the exon 18. An additional exon coding for a novel esapeptide was found to be cryptic in the κ-casein gene, whereas one extra exon was found in the αs2-casein gene by the comparison with the Camelus dromedaries sequence. A total of 28 putative phosphorylated motifs highlighted a complex heterogeneity and a potential variable degree of post-translational modifications. Ninety-six polymorphic sites were found through the comparison of the lama casein cDNAs with the homologous camel sequences, whereas the first description and characterization of the 5'- and 3'-regulatory regions allowed to identify the main putative consensus sequences involved in the casein genes expression, thus opening the way to new investigations -so far- never achieved in this species. PMID:25923814

  9. Fluoroquinolone resistance and molecular characterization of gyrA and parC quinolone resistance-determining regions in Escherichia coli isolated from poultry.

    PubMed

    Vanni, M; Meucci, V; Tognetti, R; Cagnardi, P; Montesissa, C; Piccirillo, A; Rossi, A M; Di Bello, D; Intorre, L

    2014-04-01

    Escherichia coli are a common inhabitant of the gastrointestinal tract of mammals and birds; nevertheless, they may be associated with a variety of severe and invasive infections. Whereas fluoroquinolones (FQ) have been banned in the United States for use in poultry production, the use of these antimicrobials in poultry husbandry is still possible in the European Union, although with some restrictions. The aim of this study was to investigate the FQ resistance of 235 E. coli isolates recovered from chickens and turkeys. Minimum inhibitory concentrations were determined by a microdilution method, whereas mutations in the quinolone resistance-determining regions of the target genes, gyrA and parC, were detected by a PCR-based method. High resistance rates (>60%) were observed for nalidixic acid, flumequine, and difloxacin, whereas resistance to ciprofloxacin, danofloxacin, enrofloxacin, marbofloxacin, and sarafloxacin was less frequently reported (<40%). Sixty-four isolates (27.2%) showed full susceptibility toward the tested FQ, but 57 isolates (24.2%) were resistant to all tested FQ. The remaining 114 E. coli isolates (48.5%) were grouped in 5 different resistance patterns. Isolates resistant only to flumequine or nalidixic acid or both possessed 1 gyrA mutation, whereas isolates with further resistance to enrofloxacin, difloxacin, danofloxacin, and sarafloxacin had in addition 1 or 2 parC substitutions. Two gyrA mutations coupled with 1 substitution in parC were detected in isolates resistant to all tested FQ. The number of mutations and their correlation with the in vitro activity of FQ reflected the currently accepted model, according to which a single gyrA substitution is associated with resistance or decreased susceptibility to older quinolones, whereas further gyrA or parC substitutions are needed for a higher level of resistance. PMID:24706962

  10. Synthetic Human NOTCH1 EGF Modules Unraveled Molecular Mechanisms for the Structural and Functional Roles of Calcium Ions and O-Glycans in the Ligand-Binding Region.

    PubMed

    Hayakawa, Shun; Koide, Ryosuke; Hinou, Hiroshi; Nishimura, Shin-Ichiro

    2016-02-01

    The Notch signaling pathway is an evolutionarily highly conserved mechanism that operates across multicellular organisms and is critical for cell-fate decisions during development and homeostasis in most tissues. Notch signaling is modified by posttranslational glycosylations of the Notch extracellular EGF-like domain. To evaluate the structural and functional roles of various glycoforms at multiple EGF domains in the human Notch transmembrane receptor, we established a universal method for the construction of NOTCH1 EGF modules displaying the desired O-glycans at the designated glycosylation sites. The versatility of this strategy was demonstrated by the rapid and highly efficient synthesis of NOTCH1 EGF12 concurrently having a β-D-glucopyranose-initiated glycan (Xylα1 → 3Xylα1 → 3Glcβ1 →) at Ser458 and α-L-fucopyranose-initiated glycan (Neu5Acα2 → 3Galβ1 → 4GlcNAcβ1 → 3Fucα1 →) at Thr466. The efficiency of the proper folding of the glycosylated EGF12 was markedly enhanced in the presence of 5 mM CaCl2. A nuclear magnetic resonance study revealed the existence of strong nuclear Overhauser effects between key sugar moieties and neighboring amino acid residues, indicating that both O-glycans contribute independently to the intramolecular stabilization of the antiparallel β-sheet structure in the ligand-binding region of EGF12. A preliminary test using synthetic human NOTCH1 EGF modules showed significant inhibitory effects on the proliferation and adhesiveness of human breast cancer cell line MCF-7 and lung adenocarcinoma epithelial cell line A549, demonstrating for the first time evidence that exogenously applied synthetic EGF modules have the ability to interact with intrinsic Notch ligands on the surface of cancer cells. PMID:26765751

  11. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    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.

  12. Preferential Glutathione Conjugation of a Reverse Diol Epoxide Compared to a Bay Region Diol Epoxide of Phenanthrene in Human Hepatocytes: Relevance to Molecular Epidemiology Studies of Glutathione-S-Transferase Polymorphisms and Cancer

    PubMed Central

    Hecht, Stephen S.; Berg, Jeannette Zinggeler; Hochalter, J. Bradley

    2009-01-01

    Bay region diol epoxides are recognized ultimate carcinogens of polycyclic aromatic hydrocarbons (PAH), and in vitro studies have demonstrated that they can be detoxified by conjugation with glutathione, leading to the widely investigated hypothesis that individuals with low activity forms of glutathione-S-transferases are at higher risk of PAH induced cancer, a hypothesis that has found at most weak support in molecular epidemiology studies. A weakness in this hypothesis was that the mercapturic acids resulting from conjugation of PAH bay region diol epoxides had never been identified in human urine. We recently analyzed smokers’ urine for mercapturic acids derived from phenanthrene, the simplest PAH with a bay region. The only phenanthrene diol epoxide-derived mercapturic acid in smokers’ urine was produced from the reverse diol epoxide, anti-phenanthrene-3,4-diol-1,2-epoxide (11), not the bay region diol epoxide, anti-phenanthrene-1,2-diol-3,4-epoxide (10), which does not support the hypothesis noted above. In this study, we extended these results by examining the conjugation of phenanthrene metabolites with glutathione in human hepatocytes. We identified the mercapturic acid N-acetyl-S-(r-4,t-2,3-trihydroxy-1,2,3,4-tetrahydro-c-1-phenanthryl)-L-cysteine (14a), (0.33–35.9 pmol/mL at 10 µM 8, 24h incubation, N = 10) in all incubations with phenanthrene-3,4-diol (8) and the corresponding diol epoxide 11, but no mercapturic acids were detected in incubations with phenanthrene-1,2-diol (7) and only trace amounts were observed in incubations with the corresponding bay region diol epoxide 10. Taken together with our previous results, these studies clearly demonstrate that glutathione conjugation of a reverse diol epoxide of phenanthrene is favored over conjugation of a bay region diol epoxide. Since reverse diol epoxides of PAH are generally weakly or non-mutagenic/carcinogenic, these results, if generalizable to other PAH, do not support the widely held

  13. 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

    PubMed Central

    Hynniewta, Marlykynti; Malik, Surendra Kumar; Rao, Satyawada Rama

    2014-01-01

    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 clear that C

  14. 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

    PubMed Central

    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

  15. THE DARK MOLECULAR GAS

    SciTech Connect

    Wolfire, Mark G.; Hollenbach, David; McKee, Christopher F. E-mail: dhollenbach@seti.or

    2010-06-20

    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{sub 2} mass. However, a significant H{sub 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{sup +}. Here, H{sub 2} self-shields or is shielded by dust from UV photodissociation, whereas CO is photodissociated. This H{sub 2} gas is 'dark' in molecular transitions because of the absence of CO and other trace molecules, and because H{sub 2} emits so weakly at temperatures 10 K 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 is remarkably constant ({approx}0.3 for average visual extinction through the cloud A-bar{sub V{approx_equal}}8) and insensitive to the incident ultraviolet radiation field strength, the internal density distribution, and the mass of the molecular cloud as long as A-bar{sub V}, or equivalently, the product of the average hydrogen nucleus column and the metallicity through the cloud, is constant. We also find that the dark mass fraction increases with decreasing A-bar{sub V}, since relatively more molecular H{sub 2} material lies outside the CO region in this case.

  16. Molecular Plasmonics.

    PubMed

    Wilson, Andrew J; Willets, Katherine A

    2016-06-12

    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. PMID:27049633

  17. Comparison of Arm and Interarm Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Lee, Y.; Kim, H. G.; Moon, D. S.; Stark, A. A.

    1999-01-01

    The physical properties of the molecular clouds in the arm and interarm region of the inner Galalxy are compared. We used Bell Laboratories Galactic Plane 13CO Survey data and UMSB Galactic Plane 12CO Survey data. The LCO/M of the interarm molecular clouds is much smaller that of arm molecular clouds. Several physical properties, including abundance ratio of molecular clouds in two regions are discussed.

  18. Characterization of new monoclonal antibodies against porcine lymphocytes: molecular characterization of clone 7G3, an antibody reactive with the constant region of the T-cell receptor delta-chains.

    PubMed

    Tang, W-R; Shioya, N; Eguchi, T; Ebata, T; Matsui, J; Takenouchi, H; Honma, D; Yasue, H; Takagaki, Y; Enosawa, S; Itagaki, M; Taguchi, T; Kiyokawa, N; Amemiya, H; Fujimoto, J

    2005-01-10

    A battery of mouse monoclonal antibodies (mAbs) reactive with porcine peripheral blood (PB) leukocytes was generated. Among the mAbs, 6F10 was found to react probably with cluster of differentiation (CD)8 alpha-chain, while 7G3 and 3E12 were found to recognize gammadelta T-cells, as revealed by two-color flow cytometric and immunoprecipitation studies. 7G3 was shown to react with the constant (C) region of the T-cell receptor (TCR) delta-chain by the following facts: (1) 7G3 immunoprecipitated full-length TCR delta-chain protein fused with glutathione S-transferase (GST) produced by Esherichia coli and (2) 7G3 reacted with TCR delta-chain expressing Cos-7 cells transfected with either full-length or N-terminal deleted mutant cDNA, but did not react with Cos-7 cells transfected with C-terminal deleted mutant TCR delta-chain cDNA. All three mAbs produced high-quality immunostaining results on frozen sections, revealing a distinct distribution of gammadelta T-cells and CD8(+) cells. This report precisely characterizes mAbs against porcine TCR for the first time, facilitating molecular biological investigations of the porcine immune system. PMID:15626467

  19. Molecular dynamics

    SciTech Connect

    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.

  20. Molecular motors

    NASA Astrophysics Data System (ADS)

    Allemand, Jean François Desbiolles, Pierre

    2015-10-01

    How do we move? More precisely, what are the molecular mechanisms that can explain that our muscles, made of very small components can move at a osopic scale? To answer these questions we must introduce molecular motors. Those motors are proteins, or small protein assemblies that, in our cells, transform chemical energy into mechanical work. Then, like we could do for a oscopic motor, used in a car or in a fan, we are going to study the basic behavior of these molecular machines, present what are their energy sources, calculate their power, their yield. If molecular motors are crucial for our oscopic movements, we are going to see that they are also essential to cellular transport and that considering the activity of some enzymes as molecular motors bring some interesting new insights on their activity.

  1. Circumstellar radio molecular lines

    NASA Technical Reports Server (NTRS)

    NGUYEN-QUANG-RIEU

    1987-01-01

    Radio molecular lines appear to be useful probes into the stellar environment. Silicon oxide masers provide information on the physical conditions in the immediate vicinity of the stellar photosphere. Valuable information on the physics operating in the envelope of IRC + 10216 was recently obtained by high sensitivity observations and detailed theoretical analyses. Infrared speckle interferometry in the molecular lines and in the continuum is helpful in the investigation of the inner region of the envelope. These techniques are discussed in terms of late-type star mass loss.

  2. Warm and Dense Molecular Gas in the N 159 Region: 12CO J = 4-3 and 13CO J = 3-2 Observations with NANTEN2 and ASTE

    NASA Astrophysics Data System (ADS)

    Mizuno, Yoji; Kawamura, Akiko; Onishi, Toshikazu; Minamidani, Tetsuhiro; Muller, Erik; Yamamoto, Hiroaki; Hayakawa, Takahiro; Mizuno, Norikazu; Mizuno, Akira; Stutzki, Jürgen; Pineda, Jorge L.; Klein, Uli; Bertoldi, Frank; Koo, Bon-Chul; Rubio, Monica; Burton, Michael; Benz, Arnold; Ezawa, Hajime; Yamaguchi, Nobuyuki; Kohno, Kotaro; Hasegawa, Tetsuo; Tatematsu, Ken'ichi; Ikeda, Masafumi; Ott, Jürgen; Wong, Tony; Hughes, Annie; Meixner, Margaret; Indebetouw, Remy; Gordon, Karl D.; Whitney, Barbara; Bernard, Jean-Philippe; Fukui, Yasuo

    2010-02-01

    New 12CO J = 4-3 and 13CO J = 3-2 observations of the N 159 region, an active site of massive star formation in the Large Magellanic Cloud, have been made with the NANTEN2 and ASTE submillimeter telescopes, respectively. The 12CO J = 4-3 distribution is separated into three clumps, each associated with N 159 W, N 159 E, and N 159 S. These new measurements toward the three clumps are used in coupled calculations of molecular rotational excitation and line radiation transfer, along with other transitions of the 12CO J = 1-0, J = 2-1, J = 3-2, and J = 7-6 as well as the isotope transitions of 13CO J = 1-0, J = 2-1, J = 3-2, and J = 4-3. The 13CO J = 3-2 data were newly taken for the present work. The temperatures and densities were found to be ˜70-80 K and ˜3 × 10³ cm-3 in N 159 W and N 159 E, and ˜30 K and ˜1.6 × 10³ cm-3 in N 159 S. These results were compared with the star-formation activity based on data of young stellar clusters and HII regions as well as midinfrared emission obtained with the Spitzer MIPS. The N 159 E clump is associated with cluster(s) embedded, as observed at 24μm by the Spitzer MIPS, and the derived high temperature, 80 K, is interpreted as being heated by these sources. The N 159 E clump is likely to be responsible for a dark lane in a large HII region by dust extinction. On the other hand, the N 159 W clump is associated with clusters embedded mainly toward the eastern edge of the clump only. These clusters show offsets of 20''-40'' from the 12CO J = 4-3 peak, and are probably responsible for heating indicated by the derived high temperature, 70 K. The N 159 W clump exhibits no sign of star formation toward the 12CO J = 4-3 peak position and its western region that shows enhanced R4-3/1-0 and R3-2/1-0 ratios. We therefore suggest that the N 159 W peak represents a pre-star-cluster core of ˜105Modot which deserves further detailed studies. The N 159 S clump shows little sign of star formation, as is consistent with the lower

  3. 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

    PubMed Central

    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

  4. 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

    NASA Astrophysics Data System (ADS)

    Galván-Madrid, R.; Liu, H. B.; Zhang, Z.-Y.; Pineda, J. E.; Peng, T.-C.; Zhang, Q.; Keto, E. R.; Ho, P. T. P.; Rodríguez, L. F.; Zapata, L.; Peters, T.; De Pree, C. G.

    2013-12-01

    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 gas ~ 1.1 × 106 M ⊙ within a radius of 60 pc. Within a radius of 6 pc, the total gas mass is M gas ~ 2 × 105 M ⊙. 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 cl >~ 5 × 104 M ⊙) is still not enough to entirely disrupt the GMC, but further stellar mass growth could be enough to allow radiation pressure to clear the

  5. 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

    SciTech Connect

    Galván-Madrid, R.; Pineda, J. E.; Peng, T.-C.; Liu, H. B.; Ho, P. T. P.; Zhang, Z.-Y.; Zhang, Q.; Keto, E. R.; Rodríguez, L. F.; Zapata, L.; Peters, T.; De Pree, C. G.

    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 the GMC, but further stellar

  6. 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.

    PubMed

    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

  7. Molecular Descriptors

    NASA Astrophysics Data System (ADS)

    Consonni, Viviana; Todeschini, Roberto

    In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

  8. Molecular Haeckel.

    PubMed

    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. PMID:20549737

  9. Molecular printing

    PubMed Central

    Braunschweig, Adam B.; Huo, Fengwei; Mirkin, Chad A.

    2014-01-01

    Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography and soft lithography. Both are characterized by material and substrate flexibility, but dip-pen nanolithography has unlimited pattern design whereas soft lithography has limited pattern flexibility but is low in cost and has high throughput. Advances in DPN tip arrays and inking methods have increased the throughput and enabled applications such as multiplexed arrays. A new approach to molecular printing, polymer-pen lithography, achieves low-cost, high-throughput and pattern flexibility. This Perspective discusses the evolution and future directions of molecular printing. PMID:21378889

  10. Molecular Spintronics using Molecular Nanomagnets

    NASA Astrophysics Data System (ADS)

    Wernsdorfer, Wolfgang

    2009-03-01

    A revolution in electronics is in view, with the contemporary evolution of two novel disciplines, spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets [1], which combine the classic macroscale properties of a magnet with the quantum properties of a nanoscale entity. The resulting field, molecular spintronics aims at manipulating spins and charges in electronic devices containing one or more molecules. In this context, we want to fabricate, characterize and study molecular devices (molecular spin-transistor, molecular spin-valve and spin filter, molecular double-dot devices, carbon nanotube nano-SQUIDs, etc.) in order to read and manipulate the spin states of the molecule and to perform basic quantum operations. The talk will discuss this--still largely unexplored--field and present our the first important results [2,3].[4pt] [1] L. Bogani & W. Wernsdorfer, Nature Mat. 7, 179 (2008).[0pt] [2] J.-P. Cleuziou, W. Wernsdorfer, V. Bouchiat, T. Ondarcuhu, M. Monthioux, Nature Nanotech. 1, 53-59 (2006).[0pt] [3] N. Roch, S. Florens, V. Bouchiat, W. Wernsdorfer, F. Balestro, Nature 453, 633 (2008).

  11. Molecular Electronics

    NASA Astrophysics Data System (ADS)

    Petty, Michael

    The prospects of using organic materials in electronics and optoelectronics applications have attracted scientists and technologists since the 1970s. This field has become known as molecular electronics. Some successes have already been achieved, for example the liquid-crystal display. Other products such as organic light-emitting displays, chemical sensors and plastic transistors are developing fast. There is also a keen interest in exploiting technologies at the molecular scale that might eventually replace silicon devices. This chapter provides some of the background physics and chemistry to the interdisciplinary subject of molecular electronics. A review of some of the possible application areas for organic materials is presented and some speculation is provided regarding future directions.

  12. Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Wright, John D.

    1995-02-01

    This book describes the chemical and physical structure of molecular crystals, their optical and electronic properties, and the reactions between neighboring molecules in crystals. In the second edition, the author has taken into account research that has undergone extremely rapid development since the first edition was published in 1987. For instance, he gives extensive coverage to the applications of molecular materials in high-technology devices (e.g. optical communications, laser printers, photocopiers, liquid crystal displays, solar cells, and more). There is also an entirely new chapter on the recently discovered Buckminsterfullerene carbon molecule (C60) and organic non-linear optic materials.

  13. Molecular gastronomy

    NASA Astrophysics Data System (ADS)

    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.

  14. Molecular ion photofragment spectroscopy

    SciTech Connect

    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).

  15. Molecular astrophysics

    NASA Astrophysics Data System (ADS)

    Herzberg, G.

    1989-01-01

    A brief history of Molecular Astrophysics is presented. The first molecules in space were identified in the 1920s in comets followed soon after by those in planetary atmospheres. The recent identification by MCKELLAR of the dimer of H 2, that is, (H 2) 2 in the atmosphere of Jupiter as well as the discovery, by DROSSART, MAILLARD, WATSON and others, of the H 3+ ion in the auroral zone of Jupiter are described. In this laboratory there is a continuing interest in interstellar molecules. Several molecules and molecular ions were observed by collaboration of laboratory spectroscopists and astronomers. Only the most recent ones are discussed. Also a few of the molecules not yet observed but likely to be observed are mentioned.

  16. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  17. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  18. Molecular pathways in dystonia

    PubMed Central

    Bragg, D. Cristopher; Armata, Ioanna A.; Nery, Flavia C.; Breakefield, Xandra O.; Sharma, Nutan

    2011-01-01

    The hereditary dystonias comprise a set of diseases defined by a common constellation of motor deficits. These disorders are most likely associated with different molecular etiologies, many of which have yet to be elucidated. Here we discuss recent advances in three forms of hereditary dystonia, DYT1, DYT6 and DYT16, which share a similar clinical picture: onset in childhood or adolescence, progressive spread of symptoms with generalized involvement of body regions and a steady state affliction without treatment. Unlike DYT1, the genes responsible for DYT6 and DYT16 have only recently been identified, with relatively little information about the function of the encoded proteins. Nevertheless, recent data suggest that these proteins may fit together within interacting pathways involved in dopaminergic signaling, transcriptional regulation, and cellular stress responses. This review focuses on these molecular pathways, highlighting potential common themes among these dystonias which may serve as areas for future research. PMID:21134457

  19. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. 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.

    PubMed

    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. PMID:27333026

  1. Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When

  2. Molecular clocks.

    PubMed

    Lee, Michael S Y; Ho, Simon Y W

    2016-05-23

    In the 1960s, several groups of scientists, including Emile Zuckerkandl and Linus Pauling, had noted that proteins experience amino acid replacements at a surprisingly consistent rate across very different species. This presumed single, uniform rate of genetic evolution was subsequently described using the term 'molecular clock'. Biologists quickly realised that such a universal pacemaker could be used as a yardstick for measuring the timescale of evolutionary divergences: estimating the rate of amino acid exchanges per unit of time and applying it to protein differences across a range of organisms would allow deduction of the divergence times of their respective lineages (Figure 1). PMID:27218841

  3. Molecular Mechanics

    PubMed Central

    Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

  4. Molecular replacement.

    PubMed

    Toth, Eric A

    2007-01-01

    As more protein structures are solved, the likelihood that current structural investigations will involve proteins for which there exists no homologous structure continually decreases. The extraction of phase information from diffraction experiments is one of several great barriers that crystallographers must overcome on the path to structure solution. One means to overcome this obstacle, the technique of molecular replacement, uses the structural similarity between proteins with similar sequences to give a good first estimate of the phases for the diffraction data of the protein of interest. The programs that execute this technique currently come in many flavors, from traditional Patterson-based methods, to stochastic searches in greater than three dimensions, to maximum likelihood-enhanced molecular replacement, each possessing unique advantages that can shake loose a recalcitrant solution. As crystallographers aim to solve larger macromolecular complexes that more faithfully depict the actors in cellular events, having existing phase information for parts of those biological machines will reinforce the technological advancements in data collection and structure solution that have already produced mammoth structures like the ribosome, yielding an ever-clearer picture of the inner workings of biology. PMID:17172763

  5. Molecular Aggregation in Disodium Cromoglycate

    NASA Astrophysics Data System (ADS)

    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.

  6. Molecular-beam scattering

    SciTech Connect

    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.

  7. [CII] dynamics in the S140 region

    SciTech Connect

    Dedes, C.; Röllig, M.; Okada, Y.; Ossenkopf, V.; Mookerjea, B.; Collaboration: WADI Team

    2015-01-22

    We report the observation of [C II] emission in a cut through the S140 region together with single pointing observations of several molecular tracers, including hydrides, in key regions of the photon-dominated region (PDR) and molecular cloud [1]. At a distance of 910 pc, a BOV star ionizes the edge of the molecular cloud L1204, creating S140. In addition, the dense molecular cloud hosts a cluster of embedded massive young stellar objects only 75' from the H II region [e.g. 2, 3]. We used HIFI on Herschel to observe [CII] in a strip following the direction of the impinging radiation across the ionisation front and through the cluster of embedded YSOs. With [C II], we can trace the ionising radiation and, together with the molecular tracers such as CO isotopologues and HCO{sup +}, study the dynamical processes in the region. Combining HIFIs high spectral resolution data with ground based molecular data allows us to study the dynamics and excitation conditions both in the ionization front and the dense molecular star forming region and model their physical conditions [4].

  8. [CII] dynamics in the S140 region

    NASA Astrophysics Data System (ADS)

    Dedes, C.; Röllig, M.; Mookerjea, B.; Okada, Y.; Ossenkopf, V.; WADI Team

    2015-01-01

    We report the observation of [C II] emission in a cut through the S140 region together with single pointing observations of several molecular tracers, including hydrides, in key regions of the photon-dominated region (PDR) and molecular cloud [1]. At a distance of 910 pc, a BOV star ionizes the edge of the molecular cloud L1204, creating S140. In addition, the dense molecular cloud hosts a cluster of embedded massive young stellar objects only 75" from the H II region [e.g. 2, 3]. We used HIFI on Herschel to observe [CII] in a strip following the direction of the impinging radiation across the ionisation front and through the cluster of embedded YSOs. With [C II], we can trace the ionising radiation and, together with the molecular tracers such as CO isotopologues and HCO+, study the dynamical processes in the region. Combining HIFIs high spectral resolution data with ground based molecular data allows us to study the dynamics and excitation conditions both in the ionization front and the dense molecular star forming region and model their physical conditions [4].

  9. The utility of the internal transcribed spacer region 2 (ITS2) in confirming species boundaries in the genus Gonatocerus:comparison to the cytochrome oxidase subunit I(COI) gene and taxonomic data: molecular key based on ITS2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We sequenced the nuclear ribosomal internal transcribed spacer region 2(ITS2) from several glassy-winged sharpshooter (GWSS) [Homalodisca vitripennis Germar (=H.coagulata Say)] egg parasitoid species (Hymenoptera: Mymaridae) belonging to the genus Gonatocerus Nees to test the utility of this fragmen...

  10. Charge exchange molecular ion source

    DOEpatents

    Vella, Michael C.

    2003-06-03

    Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

  11. A correlated K-distribution model of the heating rates for H[sub 2]O and a molecular mixture in the 0-2500 cm[sup [minus]1] wavelength region in the atmosphere between 0 and 60 km

    SciTech Connect

    Grossman, A S; Grant, K E

    1992-11-16

    For this report a prototype infrared radiative transfer model using a correlated k-distribution technique to calculate the transmission between atmospheric levels has been used to calculate the radiative fluxes and heating rates for H[sub 2]O and a mixture of the major molecular absorbers in the atmosphere between 0 and 60 km. The mixture consists of H[sub 2]O, CO[sub 2], O[sub 3], CH[sub 4], and N[sub 2]O. The wave number range considered is 0-2500 cm[sup [minus]1]. The use of the k-distribution method allows 25 cm[sup [minus]1] wave number bins to produce fluxes and heating rates which are within ten percent of the results of detailed line by line calculations.

  12. H.E.S.S. detection of TeV emission from the interaction region between the supernova remnant G349.7+0.2 and a molecular cloud

    NASA Astrophysics Data System (ADS)

    H. E. S. S. Collaboration; Abramowski, A.; Aharonian, F.; Ait Benkhali, F.; Akhperjanian, A. G.; Angüner, E. O.; Backes, M.; Balenderan, S.; Balzer, A.; Barnacka, A.; Becherini, Y.; Becker Tjus, J.; Berge, D.; Bernhard, S.; Bernlöhr, K.; Birsin, E.; Biteau, J.; Böttcher, M.; Boisson, C.; Bolmont, J.; Bordas, P.; Bregeon, J.; Brun, F.; Brun, P.; Bryan, M.; Bulik, T.; Carrigan, S.; Casanova, S.; Chadwick, P. M.; Chakraborty, N.; Chalme-Calvet, R.; Chaves, R. C. G.; Chrétien, M.; Colafrancesco, S.; Cologna, G.; Conrad, J.; Couturier, C.; Cui, Y.; Davids, I. D.; Degrange, B.; Deil, C.; deWilt, P.; Djannati-Ataï, A.; Domainko, W.; Donath, A.; O'C. Drury, L.; Dubus, G.; Dutson, K.; Dyks, J.; Dyrda, M.; Edwards, T.; Egberts, K.; Eger, P.; Espigat, P.; Farnier, C.; Fegan, S.; Feinstein, F.; Fernandes, M. V.; Fernandez, D.; Fiasson, A.; Fontaine, G.; Förster, A.; Füßling, M.; Gabici, S.; Gajdus, M.; Gallant, Y. A.; Garrigoux, T.; Giavitto, G.; Giebels, B.; Glicenstein, J. F.; Gottschall, D.; Grondin, M.-H.; Grudzińska, M.; Hadasch, D.; Häffner, S.; Hahn, J.; Harris, J.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hervet, O.; Hillert, A.; Hinton, J. A.; Hofmann, W.; Hofverberg, P.; Holler, M.; Horns, D.; Ivascenko, A.; Jacholkowska, A.; Jahn, C.; Jamrozy, M.; Janiak, M.; Jankowsky, F.; Jung-Richardt, I.; Kastendieck, M. A.; Katarzyński, K.; Katz, U.; Kaufmann, S.; Khélifi, B.; Kieffer, M.; Klepser, S.; Klochkov, D.; Kluźniak, W.; Kolitzus, D.; Komin, Nu.; Kosack, K.; Krakau, S.; Krayzel, F.; Krüger, P. P.; Laffon, H.; Lamanna, G.; Lefaucheur, J.; Lefranc, V.; Lemière, A.; Lemoine-Goumard, M.; Lenain, J.-P.; Lohse, T.; Lopatin, A.; Lu, C.-C.; Marandon, V.; Marcowith, A.; Marx, R.; Maurin, G.; Maxted, N.; Mayer, M.; McComb, T. J. L.; Méhault, J.; Meintjes, P. J.; Menzler, U.; Meyer, M.; Mitchell, A. M. W.; Moderski, R.; Mohamed, M.; Morå, K.; Moulin, E.; Murach, T.; de Naurois, M.; Niemiec, J.; Nolan, S. J.; Oakes, L.; Odaka, H.; Ohm, S.; Opitz, B.; Ostrowski, M.; Oya, I.; Panter, M.; Parsons, R. D.; Paz Arribas, M.; Pekeur, N. W.; Pelletier, G.; Petrucci, P.-O.; Peyaud, B.; Pita, S.; Poon, H.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raab, S.; Reichardt, I.; Reimer, A.; Reimer, O.; Renaud, M.; de los Reyes, R.; Rieger, F.; Romoli, C.; Rosier-Lees, S.; Rowell, G.; Rudak, B.; Rulten, C. B.; Sahakian, V.; Salek, D.; Sanchez, D. A.; Santangelo, A.; Schlickeiser, R.; Schüssler, F.; Schulz, A.; Schwanke, U.; Schwarzburg, S.; Schwemmer, S.; Sol, H.; Spanier, F.; Spengler, G.; Spies, F.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stinzing, F.; Stycz, K.; Sushch, I.; Tavernet, J.-P.; Tavernier, T.; Taylor, A. M.; Terrier, R.; Tluczykont, M.; Trichard, C.; Valerius, K.; van Eldik, C.; van Soelen, B.; Vasileiadis, G.; Veh, J.; Venter, C.; Viana, A.; Vincent, P.; Vink, J.; Völk, H. J.; Volpe, F.; Vorster, M.; Vuillaume, T.; Wagner, S. J.; Wagner, P.; Wagner, R. M.; Ward, M.; Weidinger, M.; Weitzel, Q.; White, R.; Wierzcholska, A.; Willmann, P.; Wörnlein, A.; Wouters, D.; Yang, R.; Zabalza, V.; Zaborov, D.; Zacharias, M.; Zdziarski, A. A.; Zech, A.; Zechlin, H.-S.

    2015-02-01

    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 cloud. In this paper, the detection of very high energy (VHE, E> 100 GeV) γ-ray emission coincident with this SNR with the High Energy Stereoscopic System (H.E.S.S.) is reported. This makes it one of the farthest Galactic SNR ever detected in this domain. An integral flux F(E> 400 GeV) = (6.5 ± 1.1stat ± 1.3syst) × 10-13 ph cm-2 s-1 corresponding to ~0.7% of that of the Crab Nebula and to a luminosity of ~1034 erg s-1 above the same energy threshold, and a steep photon index ΓVHE = 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 ΓHE = 2.2 ± 0.04stat+0.13-0.31 sys. The combined γ-ray spectrum of G349.7+0.2 can be described by either a broken power-law (BPL) or a power-law with exponential (or sub-exponential) cutoff (PLC). In the former case, the photon break energy is found at Ebr,γ = 55+70-30 GeV, slightly higher than what is usually observed in the HE/VHE γ-ray emitting middle-aged SNRs known to be interacting with molecular clouds. In the latter case, the exponential (respectively sub-exponential) cutoff energy is measured at Ecut,γ = 1.4+1.6-0.55 (respectively 0.35+0.75-0.21) TeV. A pion-decay process resulting from the interaction of the accelerated protons and nuclei with the dense surrounding medium is clearly the preferred scenario to explain the γ-ray emission. The BPL with a spectral steepening of 0.5-1 and the PLC provide equally good fits to the data. The product of the average gas density and the total energy content of accelerated protons and nuclei amounts to nHWp ~ 5 × 1051 erg cm-3.

  13. The molecular matching problem

    NASA Technical Reports Server (NTRS)

    Kincaid, Rex K.

    1993-01-01

    Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

  14. Molecular spectroscopic analyses of gelatin

    NASA Astrophysics Data System (ADS)

    Ibrahim, Medhat; Mahmoud, Abdel Aziz; Osman, Osama; Abd El-Aal, Mohamed; Eid, May

    2011-10-01

    The molecular structure of gelatin was studied using Fourier transform infrared spectroscopy FTIR. The spectrum is subjected to deconvolution in order to elucidate the constituents of the molecular structure. B3LYP/6-31g** was used to study 13 amino acids then the scaled spectrum was compared to those of protein in order to describe the contribution of each amino acid into protein structure. A special interest was paid to the NH and C dbnd O region. The reactivity of each amino acid was studied in terms of some important physical parameters like total dipole moment and HOMO/LUMO which describe the interaction of amino acid with their surrounding molecules. Results indicated that B3LYP/6-31g** model is a suitable and precise method for studying molecular structure of protein.

  15. Physical conditions in molecular clouds

    NASA Technical Reports Server (NTRS)

    Evans, Neal J., II

    1989-01-01

    Recent developments have complicated the picture of the physical conditions in molecular clouds. The discoveries of widespread emission from high-J lines of CD and 12-micron IRAS emission have revealed the presence of considerably hotter gas and dust near the surfaces of molecular clouds. These components can complicate interpretation of the bulk of the cloud gas. Commonly assumed relations between column density or mean density and cloud size are called into question by conflicting results and by consideration of selection effects. Analysis of density and density structure through molecular excitation has shown that very high densities exist in star formation regions, but unresolved structure and possible chemical effects complicate the interpretation. High resolution far-IR and submillimeter observations offer a complementary approach and are beginning to test theoretical predictions of density gradients in clouds.

  16. Molecular dynamics simulations

    SciTech Connect

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.

  17. Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.

    PubMed

    Rodríguez-Blanco, Arturo; Lemos, Manuel L; Osorio, Carlos R

    2016-08-01

    Integrating conjugative elements (ICEs) of the SXT/R391 family have been identified in fish-isolated bacterial strains collected from marine aquaculture environments of the northwestern Iberian Peninsula. Here we analysed the variable regions of two ICEs, one preliminarily characterised in a previous study (ICEVscSpa3) and one newly identified (ICEPspSpa1). Bacterial strains harboring these ICEs were phylogenetically assigned to Vibrio scophthalmi and Pseudoalteromonas sp., thus constituting the first evidence of SXT/R391-like ICEs in the genus Pseudoalteromonas to date. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterised. Interestingly, the two ICEs contained 29 genes not found in variable DNA insertions of previously described ICEs. Most notably, variable gene content for ICEVscSpa3 showed similarity to genes potentially involved in housekeeping functions of replication, nucleotide metabolism and transcription. For these genes, closest homologues were found clustered in the genome of Pseudomonas psychrotolerans L19, suggesting a transfer as a block to ICEVscSpa3. Genes encoding antibiotic resistance, restriction modification systems and toxin/antitoxin systems were absent from hotspots of ICEVscSpa3. In contrast, the variable gene content of ICEPspSpa1 included genes involved in restriction/modification functions in two different hotspots and genes related to ICE maintenance. The present study unveils a relatively large number of novel genes in SXT/R391-ICEs, and demonstrates the major role of ICE elements as contributors to horizontal gene transfer. PMID:27230650

  18. Molecular phylogeny of the subfamily Gerbillinae (Muridae, Rodentia) with emphasis on species living in the Xinjiang-Uygur Autonomous Region of China and based on the mitochondrial cytochrome b and cytochrome c oxidase subunit II genes.

    PubMed

    Ito, Mamoru; Jiang, Wei; Sato, Jun J; Zhen, Qiang; Jiao, Wei; Goto, Kazuo; Sato, Hiroshi; Ishiwata, Kenji; Oku, Yuzaburo; Chai, June-Jie; Kamiya, Haruo

    2010-03-01

    Rodents belonging to the subfamily Gerbillinae and living in the Xinjiang-Uygur autonomous region of China were collected in field surveys between 2001 and 2003. We found four Meriones species, including M. chengi M. liycus, M. meridianus, and M. tamariscinus, as well as related species from different genera, Rhombomys opimus and Brachiones przewaliskii For phylogenetic analyses of these gerbilline species, DNA sequences of parts of the mitochondrial cytochrome b (Cytb) and cytochrome c oxidase subunit II (COII) genes were examined with the neighbor Joining, maximum parsimony, maximum likelihood, and Bayesian inference methods. Our phylogenetic analyses suggest that the genus Meriones is not monophyletic and place M. tamaricinus as the sister taxon to a clade comprising Brachiones, Psammomys, Rhombomys, and the other Meriones species. The remaining Meriones species separate into three lineages: M. meridianus (including M. chengi), Meriones unguiculatus, and a clade that includes multiple Meriones species originating from Asia, the Middle East, and Africa. The phylogenetic relationships among the genera Brachines, Meriones, Psammomys, and Rhombomys remain ambiguous, probably due to the saturation of mutations that occurs in fast-evolving mitochondrial DNA. In addition, intraspecific variation was observed for M. meridianus, and this mostly correlated with collection localities, i.e., the northern and southern parts of the Xinjiang region. This variation corresponded to interspecific levels of divergence among other lineages of Meriones. Interestingly, no differences were observed in either the Cytb or COII gene sequences isolated from M. chengi collected from the Turfan Basin in the north and those from M. meridianus in the south, suggesting that M. chengi may be a synonym of M. meridianus. PMID:20192696

  19. 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

    PubMed Central

    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

  20. Molecular implementation of molecular shift register memories

    NASA Technical Reports Server (NTRS)

    Beratan, David N. (Inventor); Onuchic, Jose N. (Inventor)

    1991-01-01

    An electronic shift register memory (20) at the molecular level is described. The memory elements are based on a chain of electron transfer molecules (22) and the information is shifted by photoinduced (26) electron transfer reactions. Thus, multi-step sequences of charge transfer reactions are used to move charge with high efficiency down a molecular chain. The device integrates compositions of the invention onto a VLSI substrate (36), providing an example of a molecular electronic device which may be fabricated. Three energy level schemes, molecular implementation of these schemes, optical excitation strategies, charge amplification strategies, and error correction strategies are described.

  1. Direct interactions between molecular chaperones heat-shock protein (Hsp) 70 and Hsp40: yeast Hsp70 Ssa1 binds the extreme C-terminal region of yeast Hsp40 Sis1.

    PubMed Central

    Qian, Xinguo; Hou, Wenbo; Zhengang, Li; Sha, Bingdong

    2002-01-01

    Heat-shock protein 40 (Hsp40) enables Hsp70 to play critical roles in a number of cellular processes, such as protein folding, assembly, degradation and translocation in vivo. Hsp40 recognizes and binds non-native polypeptides and delivers them to Hsp70. Then Hsp40 stimulates the ATPase activity of Hsp70 to fold the polypeptides. By using yeast Hsp40 Sis1 and yeast Hsp70 Ssa1 as our model proteins, we found that the Sis1 peptide-binding fragment interacts directly with the full-length Ssa1 in vitro. Further studies showed that the C-terminal lid domain of Ssa1 could interact with Sis1 peptide-binding domain physically in vitro. The Sis1 peptide-binding fragment forms a stable complex with the Ssa1 C-terminal lid domain in solution. The interactions between these two proteins appear to be charge-charge interactions because high-ionic-strength buffer can dissociate the complex. Further mapping studies showed that the Sis1 peptide-binding fragment binds the extreme C-terminal 15 amino acid residues of Ssa1. A flexible glycine-rich region is followed by these 15 residues in the Ssa1 primary sequence. Atomic force microscopy of the Sis1-Ssa1 complex showed that only one end of the Ssa1 lid domain binds the Sis1 peptide-binding-fragment dimer at the upper level of the huge groove within the Sis1 dimer. Based on the data, we propose an "anchoring and docking" model to illustrate the mechanisms by which Hsp40 interacts with Hsp70 and delivers the non-native polypeptide to Hsp70. PMID:11743879

  2. 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

    SciTech Connect

    Nishimura, Yoshifumi; Lee, Yuan-Pern; Irle, Stephan; Witek, Henryk A.

    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.

  3. Molecular clouds. [significance in stellar evolution

    NASA Technical Reports Server (NTRS)

    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.

  4. The molecular astrophysics of stars and galaxies.

    NASA Astrophysics Data System (ADS)

    Hartquist, T. W.; Williams, D. A.

    This book provides a comprehensive survey of modern molecular astrophysics. It gives an introduction to molecular spectroscopy and then addresses the main areas of current molecular astrophysics, including galaxy formation, star forming regions, mass loss from young as well as highly evolved stars and supernovae, starburst galaxies plus the tori and discs near the central engines of active galactic nuclei. With chapters written by leading experts, the book is unique in giving a detailed view of this wide-ranging subject. It will provide the standard introduction for research students in molecular astrophysics; it will also enable chemists to learn the astrophysics most related to chemistry as well as instruct physicists about the molecular processes most important in astronomy. This volume is dedicated to Alexander Dalgarno.

  5. Molecular thermometry of energetic materials

    SciTech Connect

    Fishbine, B.H.; Lippert, T.; Dick, J.J.

    1997-07-01

    When a solid object with a velocity <1 km/s strikes a solid high explosive, the increase in the bulk temperature of the explosive is usually too low to thermally initiate it. It is believed, however, that the energy in the stress or shock wave created by the impact can heat individual microscopic regions that ignite and cause detonation. Although many mechanisms have been suggested for how the impact energy creates these hot spots, there has been no real-time observation of their growth at early times because of their small dimensions (estimated to be 0.1--10 {micro}m), the short times required for their growth (estimated to be 0.5 {micro}s--1 ms), and because their temperatures are too low (estimated to be <2,000 K) for them to radiate much energy in the visible. One possible way to observe early hot-spot growth is to measure temperature-dependent changes in the optical properties--absorbance, diffuse reflection, Raman spectra--of either the components of the explosive or of molecules attached to them. This temperature measurement technique is called molecular thermometry. Molecular thermometers can respond to heating within a few picoseconds with spatial resolution that can, in principle, approach the diameter of a single molecule. Temperatures as high as 900 C have been measured by molecular thermometers in laser-pulse-heated polymers. The authors discuss the literature pertaining to molecular thermometry, the effect of stress on the optical properties of some molecules that may be used as thermometers, and experiments that have used molecular thermometry to probe, on the picosecond time scale, shock excitation of the vibrational modes of molecules of energetic material. The authors also suggest ways to use molecular thermometers to observe hot-spot formation in PBX9501, a plastic-bonded explosive, subjected to impact.

  6. Molecular outflows in starburst nuclei

    NASA Astrophysics Data System (ADS)

    Roy, Arpita; Nath, Biman B.; Sharma, Prateek; Shchekinov, Yuri

    2016-08-01

    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 NOB ≥ 105 (corresponding to a star formation rate (SFR)≥1 M⊙ yr-1 in the nuclear region), in a stratified disk with mid-plane density n0 ˜ 200-1000 cm-3 and scale height z0 ≥ 200(n0/102 cm-3)-3/5 pc, can form molecules in a cool dense and expanding shell. The associated molecular mass is ≥107 M⊙ 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 ≤ ΣSFR ≤ 50 M⊙ yr-1 kpc-2 favours the production of molecular outflows, consistent with observed values.

  7. 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

    SciTech Connect

    Lopes, J.; LeGuern, E.; Gouider, R.; Tardieu, S.; Abbas, N.

    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.

  8. Progress in molecular SIMS

    SciTech Connect

    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.

  9. Molecular-specific urokinase antibodies

    NASA Technical Reports Server (NTRS)

    Atassi, M. Zouhair (Inventor); Morrison, Dennis R. (Inventor)

    2009-01-01

    Antibodies have been developed against the different molecular forms of urokinase using synthetic peptides as immunogens. The peptides were synthesized specifically to represent those regions of the urokinase molecules which are exposed in the three-dimensional configuration of the molecule and are uniquely homologous to urokinase. Antibodies are directed against the lysine 158-isoleucine 159 peptide bond which is cleaved during activation from the single-chain (ScuPA) form to the bioactive double chain (54 KDa and 33 KDa) forms of urokinase and against the lysine 135 lysine 136 bond that is cleaved in the process of removing the alpha-chain from the 54 KDa form to produce the 33 KDa form of urokinase. These antibodies enable the direct measurement of the different molecular forms of urokinase from small samples of conditioned medium harvested from cell cultures.

  10. Molecular electronics: Observation of molecular rectification

    SciTech Connect

    Waldeck, D.H.; Beratan, D.N. )

    1993-07-30

    The authors review some experiments in molecular rectification and their implication for commercial uses of molecular electronic devices. Two of the cases involve rectification by single molecules which consist of an electron donor on one side, an electron acceptor on the other side, and a bridge in between, coupled to electrodes. The third case involves rectification at a graphite electrode derivatized with a Cu phthalocyanine derivative, and probed with a Pt/Ir scanning tunneling microscope tip. Some potential applications of molecular devices are in high-density memory storage of holographic memory devices, neural networks, cellular automata, and chemical and biochemical sensors.

  11. Molecular Research in Aquaculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular research and biotechnology have long been fields of study with applications useful to aquaculture and other animal sciences. Molecular Research in Aquaculture looks to provide an understanding of molecular research and its applications to the aquaculture industry in a format that allows in...

  12. Molecular Graphics and Chemistry.

    ERIC Educational Resources Information Center

    Weber, Jacques; And Others

    1992-01-01

    Explains molecular graphics, i.e., the application of computer graphics techniques to investigate molecular structure, function, and interaction. Structural models and molecular surfaces are discussed, and a theoretical model that can be used for the evaluation of intermolecular interaction energies for organometallics is described. (45…

  13. NGC 3503 and its molecular environment

    NASA Astrophysics Data System (ADS)

    Duronea, N. U.; Vasquez, J.; Cappa, C. E.; Corti, M.; Arnal, E. M.

    2012-01-01

    Aims: 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. Methods: We based our study on 12CO(1-0) observations of a region of ~0.6° 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. Results: 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 yields (7.6 ± 2.1) × 103M⊙ and density yields 400 ± 240 cm-3. The radio continuum data confirm the existence of an electron density gradient in NGC 3503. The IR emission shows a PDR bordering the higher density regions of the nebula. The spatial distribution of the CO emission shows that the nebula coincides with a molecular clump, and the strongest CO emission peak is located close to the higher electron density region. The more negative velocities of the molecular gas (about -27 km s-1), are coincident with NGC 3503. Candidate young stellar objects (YSOs) were detected toward the Hii region, suggesting that embedded star formation may be occurring in the neighborhood of the nebula. The clear electron density gradient, along with the spatial distribution of the molecular gas and PAHs in the region indicates that NGC 3503 is a blister-type Hii region that has probably undergone a champagne phase.

  14. The Object CLN 138 - a Double Star-Formation Region

    NASA Astrophysics Data System (ADS)

    Gyulbudaghian, A. L.

    2016-09-01

    A double star formation region associated with the biconical cometary nebula CLN 138 is studied. 12CO(1-0) observations of a molecular cloud associated with this object reveal the existence of several molecular clouds in this region, as well as the existence of red and blue molecular outflows. Several new Herbig-Haro objects are found, two of which have undergone a luminosity increase of at least 8m. The first star formation region is basically embedded in the molecular cloud; most of the stars in it are infrared stars and many have dust envelopes. The second star formation region has already left the molecular cloud; it has no IR stars and few of its stars have dust clouds.

  15. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect

    Reid, David M.; Collins, Michael A.

    2013-11-14

    A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

  16. Engineering molecular machines

    NASA Astrophysics Data System (ADS)

    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.

  17. Gravitational infall onto molecular filaments

    SciTech Connect

    Heitsch, Fabian

    2013-06-01

    Two aspects of filamentary molecular cloud evolution are addressed: (1) exploring analytically the role of the environment for the evolution of filaments demonstrates that considering them in isolation (i.e., just addressing the fragmentation stability) will result in unphysical conclusions about the filament's properties. Accretion can also explain the observed decorrelation between FWHM and peak column density. (2) Free-fall accretion onto finite filaments can lead to the characteristic 'fans' of infrared-dark clouds around star-forming regions. The fans may form due to tidal forces mostly arising at the ends of the filaments, consistent with numerical models and earlier analytical studies.

  18. Collisional excitation of formaldehyde in 'hot' interstellar molecular regions

    NASA Technical Reports Server (NTRS)

    Green, Sheldon

    1991-01-01

    Earlier calculations for rotational excitation of formaldehyde by collisions with He atoms are extended to include the lowest 81 rotational levels and kinetic temperatures to 300 K. Calculations are generally based on Green et al. (1978) but coupled differential equations are solved via a modified log-derivative propagator at low energies (Manolopoulos, 1986) and an R-matrix propagator at higher energies (Stechel, Walker, and Light, 1978). Consideration is given to the expected accuracy of the rates for excitation of formaldehyde by collisions with He atoms which are calculated in the present paper and to the expected differences between these rates and those for excitation by H2 molecules which comprise a larger fraction of the interstellar gas. The comparisons performed indicate that, for excitation by He, calculated state-to-state rates are likely to be 50 percent accurate, and total excitation rates, better than 20 percent. For excitation by H2, the rates should be increased by a factor of 2.2.

  19. Cellular and molecular basis of cerebellar development

    PubMed Central

    Martinez, Salvador; Andreu, Abraham; Mecklenburg, Nora; Echevarria, Diego

    2013-01-01

    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. PMID:23805080

  20. Molecular clouds in Orion and Monoceros

    NASA Technical Reports Server (NTRS)

    Morris, M.; Montani, J.; Thaddeus, P.

    1980-01-01

    A 1.2-m millimeter-wave telescope has been used to survey CO in the constellations of Orion and Monoceros. Many new molecular clouds have been found. The distribution of molecular material shows two striking characteristics: (1) Most of the molecular clouds in this region appear to be connected by continuous extensions and filaments. To judge from continuity in radial velocity, most of these connections appear to be real, and are not merely the result of projection along the line of sight; (2) There are at least two slender filamentary features longer than 10 deg in angular extent. These filaments may connect the molecular clouds lying well out of the Galactic plane to clouds lying in the plane. Their shape and orientation suggest that magnetic fields may play a role in their evolution. The observed velocity gradients may be explained by accelerated gas flow along the filament.

  1. Molecular biodiversity of Red Sea demosponges.

    PubMed

    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. PMID:26776057

  2. Finding Distant Galactic HII Regions

    NASA Astrophysics Data System (ADS)

    Anderson, L. D.; Armentrout, W. P.; Johnstone, B. M.; Bania, T. M.; Balser, Dana S.; Wenger, Trey V.; Cunningham, V.

    2015-12-01

    The WISE Catalog of Galactic H ii Regions contains ˜2000 H ii region candidates lacking ionized gas spectroscopic observations. All candidates have the characteristic H ii region mid-infrared morphology of WISE 12 μ {{m}} emission surrounding 22 μ {{m}} emission, and additionally have detected radio continuum emission. We here report Green Bank Telescope hydrogen radio recombination line and radio continuum detections in the X-band (9 GHz; 3 cm) of 302 WISE H ii region candidates (out of 324 targets observed) in the zone 225^\\circ ≥slant {\\ell }≥slant -20^\\circ , | {\\text{}}b| ≤slant 6^\\circ . Here we extend the sky coverage of our H ii region Discovery Survey, which now contains nearly 800 H ii 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, 5 have ({\\ell },{\\text{}}b,v) coordinates consistent with the Outer Scutum-Centaurus Arm (OSC), the most distant molecular spiral arm of the Milky Way. Due to the Galactic warp, these nebulae are found at Galactic latitudes >1° in the first Galactic quadrant, and therefore were missed in previous surveys of the Galactic plane. One additional region has a longitude and velocity consistent with the OSC but lies at a negative Galactic latitude (G039.183-01.422 -54.9 {km} {{{s}}}-1). With Heliocentric distances >22 kpc and Galactocentric distances >16 kpc, the OSC H ii regions are the most distant known in the Galaxy. We detect an additional three H ii regions near {\\ell }≃ 150^\\circ whose LSR velocities place them at Galactocentric radii >19 kpc. If their distances are correct, these nebulae may represent the limit to Galactic massive star formation.

  3. Returning "Region" to World Regional Geography

    ERIC Educational Resources Information Center

    Rees, Peter W.; Legates, Margaret

    2013-01-01

    World regional geography textbooks rarely focus on the process of region formation, despite frequent calls to reincorporate a regional approach to teaching global geography. An instructional strategy using problem-based learning in a small honors section of a large world regional geography course is described. Using a hypothetical scenario…

  4. Ionospheric research. [E region, F region, D region

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Progress is reported in the following areas: D-region theory; E and F-region; wave propagation; mass spectrometer measurements; and atmospheric reactions. Various supporting operations are included: design and construction of instrumentation; and programming.

  5. Standardized molecular typing.

    PubMed

    Müller, F M; Lischewski, A; Harmsen, D; Hacker, J

    1999-01-01

    Molecular typing methods are useful tools in molecular mycology. The results of these biotyping procedures may help to identify pathogenic strains in order to detect sources of nosocomial infection and for the investigation of epidemiological relationships. With respect to the facultative pathogen, Candida albicans, various methods such as pulse-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), DNA fingerprinting methods and hybridization with repetitive DNA elements have been described as useful tools in molecular epidemiology. The previously described hybridization method with the Candida albicans specific CARE-2 probe and subsequent rehybridization with a molecular size marker is a standardized reproducible typing method for comparison of results obtained in different laboratories. In a larger epidemiological study conducted at the University Hospital of Würzburg analysing clinical C. albicans isolates, we were able to describe relationships between sequential patient isolates. These findings demonstrate that standardized molecular typing methods are a powerful tool in molecular mycology studies. PMID:10865907

  6. W3 North: Far-infrared and radio molecular observations

    NASA Technical Reports Server (NTRS)

    Thronson, H. A., Jr.; Schwartz, P. R.; Smith, H. A.; Lada, C. J.; Glaccum, W.; Harper, D. A.

    1984-01-01

    The W3 North (G133.8 + 1.4) source is the northernmost member of a string of active star forming regions that marks the western boundary of the giant HII region W4. Far infrared and radio observations of molecular CO were made of the W3 star forming region. The W3 North object shows extended dust and gas emission which suggests a fairly advanced disruption of a molecular cloud. An estimate of the age of the embedded HII region is given, and emission maps of the W3 object are presented. The W3 North source may be the oldest object among the W3 complex of sources.

  7. Atomic and molecular supernovae

    SciTech Connect

    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.

  8. Atomic and molecular supernovae

    NASA Technical Reports Server (NTRS)

    Liu, Weihong

    1997-01-01

    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.

  9. Dense circumnuclear molecular gas in starburst galaxies

    NASA Astrophysics Data System (ADS)

    Green, C.-E.; Cunningham, M. R.; Green, J. A.; Dawson, J. R.; Jones, P. A.; López-Sánchez, Á. R.; Verdes-Montenegro, L.; Henkel, C.; Baan, W. A.; Martín, S.

    2016-04-01

    We present results from a study of the dense circumnuclear molecular gas of starburst galaxies. The study aims to investigate the interplay between starbursts, active galactic nuclei and molecular gas. We characterize the dense gas traced by HCN, HCO+ and HNC and examine its kinematics in the circumnuclear regions of nine starburst galaxies observed with the Australia Telescope Compact Array. We detect HCN (1-0) and HCO+ (1-0) in seven of the nine galaxies and HNC (1-0) in four. Approximately 7 arcsec resolution maps of the circumnuclear molecular gas are presented. The velocity-integrated intensity ratios, HCO+ (1-0)/HCN (1-0) and HNC (1-0)/HCN (1-0), are calculated. Using these integrated intensity ratios and spatial intensity ratio maps, we identify photon-dominated regions (PDRs) in NGC 1097, NGC 1365 and NGC 1808. We find no galaxy which shows the PDR signature in only one part of the observed nuclear region. We also observe unusually strong HNC emission in NGC 5236, but it is not strong enough to be consistent with X-ray-dominated region chemistry. Rotation curves are derived for five of the galaxies and dynamical mass estimates of the inner regions of three of the galaxies are made.

  10. Exercises in Molecular Computing

    PubMed Central

    2014-01-01

    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

  11. HIV Molecular Immunology 2014

    SciTech Connect

    Yusim, Karina; Korber, Bette Tina Marie; Barouch, Dan; Koup, Richard; de Boer, Rob; Moore, John P.; Brander, Christian; Haynes, Barton F.; Walker, Bruce D.

    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.

  12. The effects of HII regions

    NASA Astrophysics Data System (ADS)

    Dale, J. E.

    2016-05-01

    Recent work on the effects of HII regions on giant molecular clouds (GMCs) and their embedded clusters is discussed. Although the dispersive effects of ionising radiation on clouds, particularly massive ones with high escape velocities, is rather modest, it is argued that it is still a vitally important process in the evolution of GMCs and clusters. It is able to drive turbulence on GMC scales, to set the optical emergence timescales of at last ˜ 103 M⊙ clusters, and has a strong influence on the large-scale energy and momentum input of supernovae by determining their detonation environments.

  13. Molecular Typing and Differentiation

    EPA Science Inventory

    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...

  14. Molecular Beacons in Diagnostics

    PubMed Central

    Kramer, Fred Russell

    2012-01-01

    Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies. PMID:22619695

  15. Molecular biology of development

    SciTech Connect

    Davidson, E.H.; Firtel, R.A.

    1984-01-01

    This book is a compilation of papers presented at a symposium on the molecular biology of development. Topics discussed include: cytoplasmic localizations and pattern formations, gene expression during oogenesis and early development, developmental expression of gene families molecular aspects of plant development and transformation in whole organisms and cells.

  16. Magnetic Splitting of Molecular Lines in Sunspot

    NASA Astrophysics Data System (ADS)

    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. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  18. EDITORIAL: Molecular Imaging Technology

    NASA Astrophysics Data System (ADS)

    Asai, Keisuke; Okamoto, Koji

    2006-06-01

    'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

  19. Fragment oriented molecular shapes.

    PubMed

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  20. Magnetomotive Molecular Nanoprobes

    PubMed Central

    John, Renu; Boppart, Stephen A.

    2012-01-01

    Tremendous developments in the field of biomedical imaging in the past two decades have resulted in the transformation of anatomical imaging to molecular-specific imaging. The main approaches towards imaging at a molecular level are the development of high resolution imaging modalities with high penetration depths and increased sensitivity, and the development of molecular probes with high specificity. The development of novel molecular contrast agents and their success in molecular optical imaging modalities have lead to the emergence of molecular optical imaging as a more versatile and capable technique for providing morphological, spatial, and functional information at the molecular level with high sensitivity and precision, compared to other imaging modalities. In this review, we discuss a new class of dynamic contrast agents called magnetomotive molecular nanoprobes for molecular-specific imaging. Magnetomotive agents are superparamagnetic nanoparticles, typically iron-oxide, that are physically displaced by the application of a small modulating external magnetic field. Dynamic phase-sensitive position measurements are performed using any high resolution imaging modality, including optical coherence tomography (OCT), ultrasonography, or magnetic resonance imaging (MRI). The dynamics of the magnetomotive agents can be used to extract the biomechanical tissue properties in which the nanoparticles are bound, and the agents can be used to deliver therapy via magnetomotive displacements to modulate or disrupt cell function, or hyperthermia to kill cells. These agents can be targeted via conjugation to antibodies, and in vivo targeted imaging has been shown in a carcinogen-induced rat mammary tumor model. The iron-oxide nanoparticles also exhibit negative T2 contrast in MRI, and modulations can produce ultrasound imaging contrast for multimodal imaging applications. PMID:21517766

  1. Potential molecular wires and molecular alligator clips

    NASA Astrophysics Data System (ADS)

    Schumm, Jeffry S.; Pearson, Darren L.; Jones, LeRoy, II; Hara, Ryuichiro; Tour, James M.

    1996-12-01

    The synthesis of oligo(2-ethylphenylene-ethynylene)s, oligo(2-(0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s, and oligo(3-ethylthiophene-ethynylene)s is described via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, octamer and 16-mer of the oligo(3-ethylthiophene-ethynylene)s and oligo(2-0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s. The 16-mers are 100 Å and 128 Å long, respectively. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers versus the random coils of polystyrene. These differences become quite apparent at the octamer stage. The preparation of thiol-protected end groups is described. These may serve as molecular alligator clips for adhesion to gold surfaces. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

  2. Accelerated molecular dynamics methods

    SciTech Connect

    Perez, Danny

    2011-01-04

    The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

  3. Molecularly Imprinted Membranes

    PubMed Central

    Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

    2012-01-01

    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. PMID:24958291

  4. Molecular clumps in the W51 giant molecular cloud

    NASA Astrophysics Data System (ADS)

    Parsons, H.; Thompson, M. A.; Clark, J. S.; Chrysostomou, A.

    2012-08-01

    In this paper, we present a catalogue of dense molecular clumps located within the W51 giant molecular cloud (GMC). This work is based on Heterodyne Array Receiver Programme 13CO J = 3-2 observations of the W51 GMC and uses the automated CLUMPFIND algorithm to decompose the region into a total of 1575 clumps of which 1130 are associated with the W51 GMC. We clearly see the distinct structures of the W51 complex and the high-velocity stream previously reported. We find the clumps have characteristic diameters of 1.4 pc, excitation temperatures of 12 K, densities of 5.6 × 1021 cm-2, surface densities 0.02 g cm-2 and masses of 90 M⊙. We find a total mass of dense clumps within the GMC of 1.5 × 105 M⊙, with only 1 per cent of the clumps detected by number and 4 per cent by mass found to be supercritical. We find a clump-forming efficiency of 14 ± 1 per cent for the W51 GMC and a supercritical clump-forming efficiency of 0.5-0.5+2.3 per cent. Looking at the clump mass distribution, we find it is described by a single power law with a slope of α=2.4-0.1+0.2 above ˜100 M⊙. By comparing locations of supercritical clumps and young clusters, we see that any future star formation is likely to be located away from the currently active W51A region.

  5. [Molecular diagnosis of mycobacteria].

    PubMed

    Kessler, Harald H

    2003-01-01

    Tuberculosis is one of the leading infectious diseases in the world. Using conventional methods, the isolation, identification, and drug susceptibility testing of Mycobacterium tuberculosis and other clinically important mycobacteria can take several weeks. During the past several years, molecular methods have been developed for direct detection, species identification, and drug susceptibility testing of mycobacteria. These methods can potentially reduce the diagnostic time from weeks to hours. For direct detection of Mycobacterium tuberculosis from clinical specimens, several molecular assays are commercially available today. They have been shown useful for the routine diagnostic laboratory. DNA probes and polymerase chain reaction-based sequencing have been widely used to identify mycobacterial species. Molecular methods have also been applied for the detection of mutations that confer drug resistance in mycobacteria. All in all, the future of clinical mycobacteriology appears to be heading toward direct detection, species identification and drug resistance determination using molecular methods. PMID:13677254

  6. Nonequilibrium molecular dynamics

    SciTech Connect

    Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )

    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.

  7. Molecular photoionization dynamics

    SciTech Connect

    Dehmer, Joseph L.

    1982-05-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)

  8. Appendix II. Molecular Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The study of crop evolution, origins, and conservation entails the assessment of genetic variability with and between populations and species at different genetic, evolutionary, and taxonomic hierarchical levels. Molecular biology has greatly increased the amount of data and computational intensity...

  9. Are there molecular signatures?

    SciTech Connect

    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.

  10. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    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)

  11. Ontologies for molecular biology.

    PubMed

    Schulze-Kremer, S

    1998-01-01

    Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning. A prominent example is the concept "gene" which is used with different semantics by major international genomic databases. Ontologies are one means to provide a semantic repository to systematically order relevant concepts in molecular biology and to bridge the different notions in various databases by explicitly specifying the meaning of and relation between the fundamental concepts in an application domain. Here, the upper level and a database branch of a prospective ontology for molecular biology (OMB) is presented and compared to other ontologies with respect to suitability for molecular biology (http:/(/)igd.rz-berlin.mpg.de/approximately www/oe/mbo.html). PMID:9697223

  12. Atomic & Molecular Interactions

    SciTech Connect

    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.

  13. Regional Sustainable Environmental Management

    EPA Science Inventory

    Regional sustainable environmental management is an interdisciplinary effort to develop a sufficient understanding of the interactions between ecosystems, the economy, law, and technology to formulate effective long-term management strategies on a regional scale. Regional sustai...

  14. Atomic and Molecular Collisions at Liquid Surfaces.

    PubMed

    Tesa-Serrate, Maria A; Smoll, Eric J; Minton, Timothy K; McKendrick, Kenneth G

    2016-05-27

    The gas-liquid interface remains one of the least explored, but nevertheless most practically important, environments in which molecular collisions take place. These molecular-level processes underlie many bulk phenomena of fundamental and applied interest, spanning evaporation, respiration, multiphase catalysis, and atmospheric chemistry. We review here the research that has, during the past decade or so, been unraveling the molecular-level mechanisms of inelastic and reactive collisions at the gas-liquid interface. Armed with the knowledge that such collisions with the outer layers of the interfacial region can be unambiguously distinguished, we show that the scattering of gas-phase projectiles is a promising new tool for the interrogation of liquid surfaces with extreme surface sensitivity. Especially for reactive scattering, this method also offers absolute chemical selectivity for the groups that react to produce a specific observed product. PMID:27090845

  15. Atomic and Molecular Collisions at Liquid Surfaces

    NASA Astrophysics Data System (ADS)

    Tesa-Serrate, Maria A.; Smoll, Eric J.; Minton, Timothy K.; McKendrick, Kenneth G.

    2016-05-01

    The gas-liquid interface remains one of the least explored, but nevertheless most practically important, environments in which molecular collisions take place. These molecular-level processes underlie many bulk phenomena of fundamental and applied interest, spanning evaporation, respiration, multiphase catalysis, and atmospheric chemistry. We review here the research that has, during the past decade or so, been unraveling the molecular-level mechanisms of inelastic and reactive collisions at the gas-liquid interface. Armed with the knowledge that such collisions with the outer layers of the interfacial region can be unambiguously distinguished, we show that the scattering of gas-phase projectiles is a promising new tool for the interrogation of liquid surfaces with extreme surface sensitivity. Especially for reactive scattering, this method also offers absolute chemical selectivity for the groups that react to produce a specific observed product.

  16. Visible-Light-Activated Molecular Switches.

    PubMed

    Bléger, David; Hecht, Stefan

    2015-09-21

    The ability to influence key properties of molecular systems by using light holds much promise for the fields of materials science and life sciences. The cornerstone of such systems is molecules that are able to reversibly photoisomerize between two states, commonly referred to as photoswitches. One serious restriction to the development of functional photodynamic systems is the necessity to trigger switching in at least one direction by UV light, which is often damaging and penetrates only partially through most media. This review provides a summary of the different conceptual strategies for addressing molecular switches in the visible and near-infrared regions of the optical spectrum. Such visible-light-activated molecular switches tremendously extend the scope of photoswitchable systems for future applications and technologies. PMID:26096635

  17. Unusual Conductance in Cumulene Molecular Wires

    NASA Astrophysics Data System (ADS)

    Prasongkit, Jariyanee; Grigoriev, Anton; Wendin, Göran; Ahuja, Rajeev

    2009-03-01

    We report current-voltage curves and conductance of cumulene molecular wire suspended between Au(111) surfaces via thiolate bonds with full self-consistent ab initio calculation under external bias. The conductance of cumulene wires shows oscillatory behavior depending on the number of carbon atoms. Among all conjugated oligomers, we find that odd-number cumulene wires yield the highest conductance and present ballistic-like transport behavior. The reason has been traced to two factors: high density of state at the Fermi level, and the alignment of molecular orbital closed to Fermi level. Since the conductance depends weakly on applied bias, and the current voltage characteristic is linear under bias region -0.9 to 0.9 V, odd-number cumulene wire is a possible candidate as a near- perfect, ballistic one-dimensional molecular wire.

  18. I-VLBI of molecular masers

    NASA Astrophysics Data System (ADS)

    Moscadelli, L.; Porceddu, I.

    Intense maser emissions of several molecular species (OH, CH3OH, H2O, SiO) are widely observed toward both star-formation regions and late-type stars. VLBI observations of molecular masers offer an unique opportunity to study the kinematics of the circumstellar gas in both the earliest and latest evolution phases of a star. The forthcoming Sardinia Radio Telescope (SRT) together with the other two Italian antennae of Medicina and Noto, will in the near future constitute a three-element VLBI array of sufficiently high sensitivity and angular resolution to allow one to map the strongest maser lines of CH3OH (at 6.7 GHz), H2O (at 22.2 GHz) and SiO (at 43 GHz). The Italian VLBI network (I-VLBI) can be competitive in the observation of molecular masers provided that time flexibility and frequency agility will be granted.

  19. A dimension map for molecular aggregates.

    PubMed

    Jian, Cuiying; Tang, Tian; Bhattacharjee, Subir

    2015-05-01

    A pair of gyradius ratios, defined from the principal radii of gyration, are used to generate a dimension map that describes the geometry of molecular aggregates in water and in organic solvents. Molecular dynamics simulations were performed on the aggregation of representative biomolecules and polyaromatic compounds to demonstrate application of the dimension map. It was shown that molecular aggregate data on the dimension map were bounded by two boundary curves, and that the map could be separated into three regions representing three groups of structures: one-dimensional rod-like structures; two-dimensional planar structures or short-cylinder-like structures; and three-dimensional sphere-like structures. Examining the location of the aggregates on the dimension map and how the location changes with solvent type and solute material parameter provides a simple yet effective way to infer the aggregation manner and to study solubility and mechanism of aggregation. PMID:25768393

  20. Molecular Electronic Shift Registers

    NASA Technical Reports Server (NTRS)

    Beratan, David N.; Onuchic, Jose N.

    1990-01-01

    Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

  1. Introductory molecular genetics

    SciTech Connect

    Edwards-Moulds, J.

    1986-01-01

    This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.

  2. New approaches to molecular diagnosis.

    PubMed

    Korf, Bruce R; Rehm, Heidi L

    2013-04-10

    Advances in understanding the molecular basis of rare and common disorders, as well as in the technology of DNA analysis, are rapidly changing the landscape of molecular genetic and genomic testing. High-resolution molecular cytogenetic analysis can now detect deletions or duplications of DNA of a few hundred thousand nucleotides, well below the resolution of the light microscope. Diagnostic testing for "single-gene" disorders can be done by targeted analysis for specific mutations, by sequencing a specific gene to scan for mutations, or by analyzing multiple genes in which mutation may lead to a similar phenotype. The advent of massively parallel next-generation sequencing facilitates the analysis of multiple genes and now is being used to sequence the coding regions of the genome (the exome) for clinical testing. Exome sequencing requires bioinformatic analysis of the thousands of variants that are identified to find one that is contributing to the pathology; there is also a possibility of incidental identification of other medically significant variants, which may complicate genetic counseling. DNA testing can also be used to identify variants that influence drug metabolism or interaction of a drug with its cellular target, allowing customization of choice of drug and dosage. Exome and genome sequencing are being applied to identify specific gene changes in cancer cells to guide therapy, to identify inherited cancer risk, and to estimate prognosis. Genomic testing may be used to identify risk factors for common disorders, although the clinical utility of such testing is unclear. Genetic and genomic tests may raise new ethical, legal, and social issues, some of which may be addressed by existing genetic nondiscrimination legislation, but which also must be addressed in the course of genetic counseling. The purpose of this article is to assist physicians in recognizing where new approaches to genetic and genomic testing may be applied clinically and in being aware

  3. Workshop on Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Cummings, Michael P.

    2004-01-01

    Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

  4. Molecular classification of gliomas.

    PubMed

    Masui, Kenta; Mischel, Paul S; Reifenberger, Guido

    2016-01-01

    The identification of distinct genetic and epigenetic profiles in different types of gliomas has revealed novel diagnostic, prognostic, and predictive molecular biomarkers for refinement of glioma classification and improved prediction of therapy response and outcome. Therefore, the new (2016) World Health Organization (WHO) classification of tumors of the central nervous system breaks with the traditional principle of diagnosis based on histologic criteria only and incorporates molecular markers. This will involve a multilayered approach combining histologic features and molecular information in an "integrated diagnosis". We review the current state of diagnostic molecular markers for gliomas, focusing on isocitrate dehydrogenase 1 or 2 (IDH1/IDH2) gene mutation, α-thalassemia/mental retardation syndrome X-linked (ATRX) gene mutation, 1p/19q co-deletion and telomerase reverse transcriptase (TERT) promoter mutation in adult tumors, as well as v-raf murine sarcoma viral oncogene homolog B1 (BRAF) and H3 histone family 3A (H3F3A) aberrations in pediatric gliomas. We also outline prognostic and predictive molecular markers, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, and discuss the potential clinical relevance of biologic glioblastoma subtypes defined by integration of multiomics data. Commonly used methods for individual marker detection as well as novel large-scale DNA methylation profiling and next-generation sequencing approaches are discussed. Finally, we illustrate how advances in molecular diagnostics affect novel strategies of targeted therapy, thereby raising new challenges and identifying new leads for personalized treatment of glioma patients. PMID:26948350

  5. ASTROCHEMICAL CORRELATIONS IN MOLECULAR CLOUDS

    SciTech Connect

    Gaches, Brandt A. L.; Offner, Stella S. R.; Rosolowsky, Erik W.; Bisbas, Thomas G. E-mail: soffner@astro.umass.edu E-mail: tb@star.ucl.ac.uk

    2015-02-01

    We investigate the spectral correlations between different species used to observe molecular clouds. We use hydrodynamic simulations and a full chemical network to study the abundances of over 150 species in typical Milky Way molecular clouds. We perform synthetic observations in order to produce emission maps of a subset of these tracers. We study the effects of different lines of sight and spatial resolution on the emission distribution and perform a robust quantitative comparison of the species to each other. We use the Spectral Correlation Function (SCF), which quantifies the root mean squared difference between spectra separated by some length scale, to characterize the structure of the simulated cloud in position-position-velocity (PPV) space. We predict the observed SCF for a broad range of observational tracers, and thus identify homologous species. In particular, we show that the pairs C and CO, C{sup +} and CN, and NH{sub 3} and H{sub 2}CS have very similar SCFs. We measure the SCF slope variation as a function of beam size for all species and demonstrate that the beam size has a distinct effect on different species emission. However, for beams of up to 10'', placing the cloud at 1 kpc, the change is not large enough to move the SCF slopes into different regions of parameter space. The results from this study provide observational guidance for choosing the best tracer to probe various cloud length scales.

  6. Multisurface Adiabatic Reactive Molecular Dynamics.

    PubMed

    Nagy, Tibor; Yosa Reyes, Juvenal; Meuwly, Markus

    2014-04-01

    Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations. PMID:26580356

  7. Molecular physiology of rhodopsin: Computer simulation

    NASA Astrophysics Data System (ADS)

    Fel'Dman, T. B.; Kholmurodov, Kh. T.; Ostrovsky, M. A.

    2008-03-01

    Computer simulation is used for comparative investigation of the molecular dynamics of rhodopsin containing the chromophore group (11- cis-retinal) and free opsin. Molecular dynamics is traced within a time interval of 3000 ps; 3 × 106 discrete conformational states of rhodopsin and opsin are obtained and analyzed. It is demonstrated that the presence of the chromophore group in the chromophore center of opsin influences considerably the nearest protein environment of 11- cis-retinal both in the region of the β-ionone ring and in the region of the protonated Schiff base bond. Based on simulation results, a possible intramolecular mechanism of keeping rhodopsin as a G-protein-coupled receptor in the inactive state, i.e., the chromophore function as an efficient ligand antagonist, is discussed.

  8. Nanotechnology Review: Molecular Electronics to Molecular Motors

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  9. Molecular hydrogen jets from the Orion nebula

    NASA Astrophysics Data System (ADS)

    Taylor, K. N. R.; Storey, J. W. V.; Sandell, G.; Williams, P. M.; Zealey, W. J.

    1984-09-01

    In an attempt to understand the relationship of the recently discovered complex of Herbig Haro objects in Orion to the IR sources in this region, the authors have carried out a survey of the molecular hydrogen S(1) line distribution. These observations have led to the discovery of a previously unsuspected structure of finger-like filaments of H2 emission extending radially outwards from a common centre at IRC9.

  10. F 3 - molecular ions in fluoride crystals

    NASA Astrophysics Data System (ADS)

    Radzhabov, E. A.

    2016-02-01

    The UV absorption spectra of F 3 - molecular ions in LaF3, SrF2, CaF2, and BaF2 crystals doped with rare-earth elements are studied. Comparison of radiation-colored and additively colored crystals reveals the absorption bands of F 3 - hole centers in the region near 6 eV. Nonempirical calculations of optical transitions agree well with experimental results.

  11. Artificial Molecular Machines.

    PubMed

    Balzani; Credi; Raymo; Stoddart

    2000-10-01

    The miniaturization of components used in the construction of working devices is being pursued currently by the large-downward (top-down) fabrication. This approach, however, which obliges solid-state physicists and electronic engineers to manipulate progressively smaller and smaller pieces of matter, has its intrinsic limitations. An alternative approach is a small-upward (bottom-up) one, starting from the smallest compositions of matter that have distinct shapes and unique properties-namely molecules. In the context of this particular challenge, chemists have been extending the concept of a macroscopic machine to the molecular level. A molecular-level machine can be defined as an assembly of a distinct number of molecular components that are designed to perform machinelike movements (output) as a result of an appropriate external stimulation (input). In common with their macroscopic counterparts, a molecular machine is characterized by 1) the kind of energy input supplied to make it work, 2) the nature of the movements of its component parts, 3) the way in which its operation can be monitored and controlled, 4) the ability to make it repeat its operation in a cyclic fashion, 5) the timescale needed to complete a full cycle of movements, and 6) the purpose of its operation. Undoubtedly, the best energy inputs to make molecular machines work are photons or electrons. Indeed, with appropriately chosen photochemically and electrochemically driven reactions, it is possible to design and synthesize molecular machines that do work. Moreover, the dramatic increase in our fundamental understanding of self-assembly and self-organizational processes in chemical synthesis has aided and abetted the construction of artificial molecular machines through the development of new methods of noncovalent synthesis and the emergence of supramolecular assistance to covalent synthesis as a uniquely powerful synthetic tool. The aim of this review is to present a unified view of the field

  12. Comments on Regional Geography.

    ERIC Educational Resources Information Center

    Taaffe, Edward J.

    1985-01-01

    Reasons why regional geography should play a vital role in the development of U.S. geography are discussed. In addition, problems facing regional geographers are examined. A revival of regional geography can be significantly strengthened if there is more effective communication between regional and scientific geographers. (RM)

  13. Giant Molecular Magnetocapacitance

    SciTech Connect

    Wu, Yuning; Zhang, Xiaoguang; Cheng, Hai-Ping

    2013-01-01

    Capacitance of a nanoscale system is usually thought of having two contributions, a classical electrostatic contribution and a quantum contribution dependent on the density of states and/or molecular orbitals close to the Fermi energy. In this letter we demonstrate that in molecular nano-magnets and other magnetic nanoscale systems, the quantum part of the capacitance becomes spin-dependent, and is tunable by an external magnetic field. This molecular magnetocapacitance can be realized using single molecule nano-magnets and/or other nano-structures that have antiferromagnetic ground states. As a proof of principle, first-principles calculation of the nano-magnet [Mn3O(sao)3(O2CMe)(H2O)(py)3] shows that the charging energy of the high-spin state is 260 meV lower than that of the low-spin state, yielding a 6% difference in capacitance. A magnetic field of ~40T can switch the spin state, thus changing the molecular capacitance. A smaller switching field may be achieved using nanostructures with a larger moment. Molecular magnetocapacitance may lead to revolutionary device designs, e.g., by exploiting the Coulomb blockade magnetoresistance whereby a small change in capacitance can lead to a huge change in resistance.

  14. Applications of Molecular Imaging

    PubMed Central

    Galbán, Craig; Galbán, Stefanie; Van Dort, Marcian; Luker, Gary D.; Bhojani, Mahaveer S.; Rehemtualla, Alnawaz; Ross, Brian D.

    2015-01-01

    Today molecular imaging technologies play a central role in clinical oncology. The use of imaging techniques in early cancer detection, treatment response and new therapy development is steadily growing and has already significantly impacted clinical management of cancer. In this chapter we will overview three different molecular imaging technologies used for the understanding of disease biomarkers, drug development, or monitoring therapeutic outcome. They are (1) optical imaging (bioluminescence and fluorescence imaging) (2) magnetic resonance imaging (MRI), and (3) nuclear imaging (e.g, single photon emission computed tomography (SPECT) and positron emission tomography (PET)). We will review the use of molecular reporters of biological processes (e.g. apoptosis and protein kinase activity) for high throughput drug screening and new cancer therapies, diffusion MRI as a biomarker for early treatment response and PET and SPECT radioligands in oncology. PMID:21075334

  15. Stueckelberg and Molecular Physics

    NASA Astrophysics Data System (ADS)

    Lacki, Jan

    The first period of E. C. G. Stueckelberg's scientific career was marked by important contributions he made to molecular physics.1 After publishing his thesis in 1927 in Basel [1] Stueckelberg joined the prestigious Palmer Physical Laboratory in Princeton where he worked under the guidance of Karl Taylor Compton, brother of Arthur Holly Compton. Stueckelberg owed this position devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3 to a recommendation by A. Sommerfeld.2 In this stimulating environment, he devoted several papers to problems of molecular physics. Stueckelberg had the benefit at Princeton of exchanges with other gifted members of the Palmer Physical Laboratory, Philip M. Morse and E. U. Condon among others.3

  16. Primate molecular divergence dates.

    PubMed

    Steiper, Michael E; Young, Nathan M

    2006-11-01

    With genomic data, alignments can be assembled that greatly increase the number of informative sites for analysis of molecular divergence dates. Here, we present an estimate of the molecular divergence dates for all of the major primate groups. These date estimates are based on a Bayesian analysis of approximately 59.8 kbp of genomic data from 13 primates and 6 mammalian outgroups, using a range of paleontologically supported calibration estimates. Results support a Cretaceous last common ancestor of extant primates (approximately 77 mya), an Eocene divergence between platyrrhine and catarrhine primates (approximately 43 mya), an Oligocene origin of apes and Old World monkeys (approximately 31 mya), and an early Miocene (approximately 18 mya) divergence of Asian and African great apes. These dates are examined in the context of other molecular clock studies. PMID:16815047

  17. Molecular psychiatry of zebrafish.

    PubMed

    Stewart, A M; Ullmann, J F P; Norton, W H J; Parker, M O; Brennan, C H; Gerlai, R; Kalueff, A V

    2015-02-01

    Due to their well-characterized neural development and high genetic homology to mammals, zebrafish (Danio rerio) have emerged as a powerful model organism in the field of biological psychiatry. Here, we discuss the molecular psychiatry of zebrafish, and its implications for translational neuroscience research and modeling central nervous system (CNS) disorders. In particular, we outline recent genetic and technological developments allowing for in vivo examinations, high-throughput screening and whole-brain analyses in larval and adult zebrafish. We also summarize the application of these molecular techniques to the understanding of neuropsychiatric disease, outlining the potential of zebrafish for modeling complex brain disorders, including attention-deficit/hyperactivity disorder (ADHD), aggression, post-traumatic stress and substance abuse. Critically evaluating the advantages and limitations of larval and adult fish tests, we suggest that zebrafish models become a rapidly emerging new field in modern molecular psychiatry research. PMID:25349164

  18. Porous Organic Molecular Materials

    SciTech Connect

    Tian, Jian; Thallapally, Praveen K.; McGrail, B. Peter

    2012-01-01

    Most nanoporous materials with molecular-scale pores are extended frameworks composed of directional covalent or coordination bonding, such as porous metal-organic frameworks and organic network polymers. By contrast, nanoporous materials comprised of discrete organic molecules, between which there are only weak non-covalent interactions, are seldom encountered. Indeed, most organic molecules pack efficiently in the solid state to minimize the void volume, leading to non-porous materials. In recent years, a significant number of nanoporous organic molecular materials, which may be either crystalline or amorphous, have been confirmed by the studies of gas adsorption and they are surveyed in this Highlight. In addition, the possible advantages of porous organic molecular materials over porous networks are discussed.

  19. Molecular Rotors as Switches

    PubMed Central

    Xue, Mei; Wang, Kang L.

    2012-01-01

    The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene) monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V) revealed a temperature-dependent negative differential resistance (NDR) associated with the device. The analysis of the device I–V characteristics suggests the source of the

  20. Molecular subgroups of medulloblastoma

    PubMed Central

    Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

    2014-01-01

    Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

  1. Molecular Umbrella Transport

    PubMed Central

    Mehiri, Mohamed; Chen, Wen-Hua; Janout, Vaclav; Regen, Steven L.

    2009-01-01

    The ability of a series of molecular umbrellas, derived from cholic acid, L-lysine, spermidine and Cascade Blue, to cross fluid liposomal membranes made from 1-palmitoyl-2-oleyol-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) (95/5, mol/mol) has been determined. In sharp contrast to the clasic “size/lipophilicity” rule of membrane transport, those molecular umbrellas that were larger in size and less lipophilic crossed these liposomal membranes more readily. The likely origin for this unusual behavior is briefly discussed. PMID:19140686

  2. Synthetic mechanochemical molecular swimmer.

    PubMed

    Golestanian, Ramin

    2010-07-01

    A minimal design for a molecular swimmer is proposed that is based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net charges through catalyzed chemical reactions involving ionic components. The mechanochemical cycle is designed such that the resulting conformational changes would be sufficient for achieving low Reynolds number propulsion. The system is analyzed within the recently developed framework of stochastic swimmers to take account of the noisy environment at the molecular scale. The swimming velocity of the device is found to depend on the concentration of the fuel molecule according to the Michaelis-Menten rule in enzymatic reactions. PMID:20867483

  3. Molecular Pathology Informatics.

    PubMed

    Roy, Somak

    2015-06-01

    Molecular informatics (MI) is an evolving discipline that will support the dynamic landscape of molecular pathology and personalized medicine. MI provides a fertile ground for development of clinical solutions to bridge the gap between clinical informatics and bioinformatics. Rapid adoption of next generation sequencing (NGS) in the clinical arena has triggered major endeavors in MI that are expected to bring a paradigm shift in the practice of pathology. This brief review presents a broad overview of various aspects of MI, particularly in the context of NGS based testing. PMID:26065793

  4. Substructured multibody molecular dynamics.

    SciTech Connect

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  5. Molecular Engineering of DNA: Molecular Beacons

    PubMed Central

    Tang, Zhiwen; Yang, Chaoyong James; Kim, Youngmi; Fang, Xiaohong; Li, Wei; Wu, Yanrong; Medley, Colin D.; Cao, Zehui; Li, Jun; Colon, Patrick; Lin, Hui

    2009-01-01

    Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein–DNA interaction studies, and protein recognition. PMID:19065690

  6. Chemistry of star-forming regions.

    PubMed

    Herbst, Eric

    2005-05-12

    The space between stars is not empty but contains gas-phase and particulate matter under varying conditions. Neutral matter is found mainly in large regions of the interstellar medium known as "clouds", the largest of which, termed "giant molecular clouds", are essentially molecular in nature. Stars and planetary systems form inside these giant clouds when portions collapse and heat up. The details of the collapse can be followed by observation of the chemical changes in the molecular composition of the gas and dust particles. Moreover, an understanding of the chemical processes yields much information on the time scales and histories of the assorted stages. Among the most recent additions to our chemical knowledge of star formation are a deeper understanding of isotopic fractionation, especially involving deuterium, and a realization that the role of neutral-neutral reactions is more salient than once thought possible. PMID:16833724

  7. Casting polymer nets to optimize noisy molecular codes

    PubMed Central

    Tlusty, Tsvi

    2008-01-01

    Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be understood from the statistics of a two-dimensional network made of polymers. The noisy code is defined by partitioning the space of symbols into regions according to their meanings. The “polymers” are the boundaries between these regions, and their statistics define the cost and the quality of the noisy code. When the parameters that control the cost–quality balance are varied, the polymer network undergoes a transition, where the number of encoded meanings rises discontinuously. Effects of population dynamics on the evolution of molecular codes are discussed. PMID:18550822

  8. Molecular chemistry and the missing mass problem in planetary nebulae

    NASA Astrophysics Data System (ADS)

    Kimura, R. K.; Gruenwald, R.; Aleman, I.

    2012-05-01

    Context. 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. Aims: 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. Methods: 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. Results: Our models show that the inclusion of an incident flux of X-rays is required to explain the molecular composition derived for planetary nebulae. We also obtain a more accurate relation for the N(CO)/N(H2) ratio in these objects. Molecular masses obtained by previous works in the literature were then recalculated, showing that these masses can be underestimated by up to three orders of magnitude. We conclude that the problem of the missing mass in planetary nebulae can be solved by a more accurate calculation of the molecular mass.

  9. Dust in a few southern H II regions

    NASA Technical Reports Server (NTRS)

    Ghosh, Swarna Kanti; Iyengar, K. V. K.; Rengarajan, T. N.; Tandon, S. N.; Verma, R. P.; Daniel, R. R.

    1989-01-01

    The property of dust in four southern H II region/molecular cloud complexes (RCW 108, RCW 57, RCW 122, and G351.6-1.3) was discussed. These regions were observed at an effective wavelength of 150 micron using TIFR balloon borne 1 m telescope and deconvolved maps with a resolution of 1 min were obtained. The data were combined with other available data to derive the properties of the infrared emitting dust in these regions.

  10. Biophysics of molecular gastronomy.

    PubMed

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. PMID:25815978

  11. [Ortho-molecular nutrition].

    PubMed

    Martínez Bradshaw, Alejandro

    2005-03-01

    Ortho-molecular nutrition contemplates the deficiency of certain nutrients, not their deprivation, as the generator of short-term and long-term pathologies. By means of supplying these nutrients, an organism recovers. This method consists in building up an organism's functions by following the guides and indications provided by the organism itself. PMID:15871343

  12. Molecular Adsorber Coating

    NASA Technical Reports Server (NTRS)

    Straka, Sharon; Peters, Wanda; Hasegawa, Mark; Hedgeland, Randy; Petro, John; Novo-Gradac, Kevin; Wong, Alfred; Triolo, Jack; Miller, Cory

    2011-01-01

    A document discusses a zeolite-based sprayable molecular adsorber coating that has been developed to alleviate the size and weight issues of current ceramic puck-based technology, while providing a configuration that more projects can use to protect against degradation from outgassed materials within a spacecraft, particularly contamination-sensitive instruments. This coating system demonstrates five times the adsorption capacity of previously developed adsorber coating slurries. The molecular adsorber formulation was developed and refined, and a procedure for spray application was developed. Samples were spray-coated and tested for capacity, thermal optical/radiative properties, coating adhesion, and thermal cycling. Work performed during this study indicates that the molecular adsorber formulation can be applied to aluminum, stainless steel, or other metal substrates that can accept silicate-based coatings. The coating can also function as a thermal- control coating. This adsorber will dramatically reduce the mass and volume restrictions, and is less expensive than the currently used molecular adsorber puck design.

  13. Atomic and Molecular Physics

    NASA Technical Reports Server (NTRS)

    Bhatia, Anand K.

    2005-01-01

    A symposium on atomic and molecular physics was held on November 18, 2005 at Goddard Space Flight Center. There were a number of talks through the day on various topics such as threshold law of ionization, scattering of electrons from atoms and molecules, muonic physics, positron physics, Rydberg states etc. The conference was attended by a number of physicists from all over the world.

  14. Molecular Detection of Sarcocystis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When people eat undercooked beef or pork containing viable Sarcocystis hominis or Sarcocystis suihominis, they can contract acute gastro-intestinal infections that culminate, about two weeks later, with the excretion of parasites infectious for cattle or swine, respectively. Molecular methods can p...

  15. Molecular contributions to conservation

    USGS Publications Warehouse

    Haig, Susan M.

    1998-01-01

    Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

  16. Caroviologens: Towards molecular wires

    NASA Astrophysics Data System (ADS)

    Blanchard-Desce, M.; Arrhenius, T. S.; Dvolaïtzky, M.; Kugimiya, S.-I.; Lazrak, T.; Lehn, J.-M.

    1992-07-01

    Bispyridinium conjugated polyenes of different lengths and charges have been synthesized. Since they combine the features of carotenoids and of viologens, they have been termed caroviologens. Such molecules, possessing an extended conjugated chain fitted with polar electroactive endgroups, and having a length sufficient to span a lipid membrane could function as transmembrane electron channels, i.e., as molecular wires.

  17. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  18. Making Molecular Borromean Rings

    ERIC Educational Resources Information Center

    Pentecost, Cari D.; Tangchaivang, Nichol; Cantrill, Stuart J.; Chichak, Kelly S.; Peters, Andrea J.; Stoddart, Fraser J.

    2007-01-01

    A procedure that requires seven 4-hour blocks of time to allow undergraduate students to prepare the molecular Borromean rings (BRs) on a gram-scale in 90% yield is described. The experiment would serve as a nice capstone project to culminate any comprehensive organic laboratory course and expose students to fundamental concepts, symmetry point…

  19. Gymnastics of molecular chaperones.

    PubMed

    Mayer, Matthias P

    2010-08-13

    Molecular chaperones assist folding processes and conformational changes in many proteins. In order to do so, they progress through complex conformational cycles themselves. In this review, I discuss the diverse conformational dynamics of the ATP-dependent chaperones of the Hsp60, Hsp70, Hsp90, and Hsp100 families. PMID:20705236

  20. Molecular Stiffness of Selectins*

    PubMed Central

    Sarangapani, Krishna K.; Marshall, Bryan T.; McEver, Rodger P.; Zhu, Cheng

    2011-01-01

    During inflammation, selectin-ligand interactions provide forces for circulating leukocytes to adhere to vascular surfaces, which stretch the interacting molecules, suggesting that mechanical properties may be pertinent to their biological function. From mechanical measurements with atomic force microscopy, we analyzed the molecular characteristics of selectins complexed with ligands and antibodies. Respective stiffness of L-, E-, and P-selectins (4.2, 1.4, and 0.85 piconewton/nm) correlated inversely with the number (2, 6, and 9) of consensus repeats in the selectin structures that acted as springs in series to dominate their compliance. After reconstitution into a lipid bilayer, purified membrane P-selectin remained a dimer, capable of forming dimeric bonds with P-selectin glycoprotein ligand (PSGL)-1, endoglycan-Ig, and a dimeric form of a glycosulfopeptide modeled after the N terminus of PSGL-1. By comparison, purified membrane L- and E-selectin formed only monomeric bonds under identical conditions. Ligands and antibodies were much less stretchable than selectins. The length of endoglycan-Ig was found to be 51 ± 12 nm. These results provide a comprehensive characterization of the molecular stiffness of selectins and illustrate how mechanical measurements can be utilized for molecular analysis, e.g. evaluating the multimericity of selectins and determining the molecular length of endoglycan. PMID:21216951

  1. Soybean Molecular Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A history of the various DNA marker types used in the assessment of molecular genetic diversity in soybean [Glycine max (L.) Merr.] is followed by a description of a number of studies on the assessment of genetic diversity. These studies include a review of reports on 1) the quantification and comp...

  2. Reading the Molecular Clock.

    ERIC Educational Resources Information Center

    McKean, Kevin

    1983-01-01

    Suggesting that the evolutionary record may be written in proteins and genes, discusses research in which species are compared by immunology, DNA, and radioimmunoassay. Molecular studies show that DNA from humans and chimps is 98 percent identical, a degree of similarity usually occurring only among animals of the same genus. (JN)

  3. Targeted Molecular Imaging in Oncology: Focus on Radiation Therapy

    PubMed Central

    Nimmagadda, Sridhar; Ford, Eric C.; Wong, John W.; Pomper, Martin G.

    2008-01-01

    Anatomically based technologies (CT, MR, etc.) are in routine use in radiotherapy for planning and assessment purposes. Even with improvements in imaging, however, radiotherapy is still limited in efficacy and toxicity in certain applications. Further advances may be provided by technologies that image the molecular activities of tumors and normal tissues. Possible uses for molecular imaging include better localization of tumor regions and early assay for the radiation response of tumors and normal tissues. Critical to the success of this approach is the identification and validation of molecular probes that are suitable in the radiotherapy context. Recent developments in molecular imaging probes and integration of functional imaging with radiotherapy are promising. This review focuses on recent advances in molecular imaging strategies and probes that may aid in improving the efficacy of radiotherapy. PMID:18314068

  4. Complex regional pain syndrome

    MedlinePlus

    Complex regional pain syndrome (CRPS) is a chronic pain condition that can affect any area of the ... Bailey A, Audette JF. Complex regional pain syndrome. In: Frontera ... of Physical Medicine and Rehabilitation. 2nd ed. Philadelphia, ...

  5. Utah: Salt Lake Region

    Atmospheric Science Data Center

    2014-05-15

    article title:  Winter and Summer Views of the Salt Lake Region     View Larger Image Magnificent views of the region surrounding Salt Lake City, Utah are captured in these winter and summer images from the ...

  6. Serrated colorectal cancer: Molecular classification, prognosis, and response to chemotherapy

    PubMed Central

    Murcia, Oscar; Juárez, Miriam; Hernández-Illán, Eva; Egoavil, Cecilia; Giner-Calabuig, Mar; Rodríguez-Soler, María; Jover, Rodrigo

    2016-01-01

    Molecular advances support the existence of an alternative pathway of colorectal carcinogenesis that is based on the hypermethylation of specific DNA regions that silences tumor suppressor genes. This alternative pathway has been called the serrated pathway due to the serrated appearance of tumors in histological analysis. New classifications for colorectal cancer (CRC) were proposed recently based on genetic profiles that show four types of molecular alterations: BRAF gene mutations, KRAS gene mutations, microsatellite instability, and hypermethylation of CpG islands. This review summarizes what is known about the serrated pathway of CRC, including CRC molecular and clinical features, prognosis, and response to chemotherapy. PMID:27053844

  7. Serrated colorectal cancer: Molecular classification, prognosis, and response to chemotherapy.

    PubMed

    Murcia, Oscar; Juárez, Miriam; Hernández-Illán, Eva; Egoavil, Cecilia; Giner-Calabuig, Mar; Rodríguez-Soler, María; Jover, Rodrigo

    2016-04-01

    Molecular advances support the existence of an alternative pathway of colorectal carcinogenesis that is based on the hypermethylation of specific DNA regions that silences tumor suppressor genes. This alternative pathway has been called the serrated pathway due to the serrated appearance of tumors in histological analysis. New classifications for colorectal cancer (CRC) were proposed recently based on genetic profiles that show four types of molecular alterations: BRAF gene mutations, KRAS gene mutations, microsatellite instability, and hypermethylation of CpG islands. This review summarizes what is known about the serrated pathway of CRC, including CRC molecular and clinical features, prognosis, and response to chemotherapy. PMID:27053844

  8. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  9. Unbound molecular complexes in M33

    NASA Astrophysics Data System (ADS)

    Wilson, Christine D.

    1990-07-01

    The HI content of the nearby spiral galaxy M33 (d approx. 0.8 Mpc) has been the subject of many detailed studies (most recently Deul and van der Hulst 1987), but similar data on the molecular gas component has been lacking. This galaxy is currently undergoing vigorous high-mass star formation, as evidenced by the many OB associations and HII regions, and so is expected to possess at least some molecular gas. Interferometric studies have detected molecular clouds similar to Galactic Giant Molecular Clouds (GMCs) (Boulanger et al. 1988; Wilson et al. 1988). Researchers have recently mapped the nuclear region of M33 in the CO J=1-0 line with a 12 m telescope (half power beam width 55 inches approx. 210 pc) out to a radius of 3.5 minutes in order to trace the detailed distribution of the molecular gas. The resulting map reveals six large complexes with diameters of 200 to 400 pc. Interferometer observations of these regions have resolved them into individual molecular clouds similar to Galactic GMCs (Wilson et al. 1988). The complexes shown are much larger than individual Galactic GMCs (Sanders, Scoville, and Solomon 1985), but are somewhat smaller on average than the large associations seen in the grand-design spiral galaxy M51 (Rand and Kulkarni 1989). If we extend the velocity-diameter relation observed for Galactic GMCs to these larger structures, the predicted velocity widths are a factor of 1.5 to 3 times greater than the observed full-width half-maximum velocities (13 to 29 km (s-1). The peak brightness temperatures are approx. 0.2 K, at least a factor of 10 lower than what is observed for Galactic GMCs. If these large structures are made up of objects similar to Galactic GMCs, the area filling factor of the small clouds is roughly 10 percent. These results suggest that these complexes are not very large GMCs, but rather are associations of many individual GMCs or GMCs embedded in a diffuse gas component.

  10. 2009 Regional Reports

    ERIC Educational Resources Information Center

    Zitzow, Larry; Barbush, Jim; Riese, Gail; Quirk, Robert John; Morris, John P.; Hargrave, Heather

    2010-01-01

    APPA's six regions serve member institutions across the United States and Canada. They function independently from international APPA and offer their own educational programs, annual meetings, publications, and other benefits. Each region also maintains its own set of officers, committees, and activities. Participating in regions and state and…

  11. Learning Regions in Germany

    ERIC Educational Resources Information Center

    Thinesse-Demel, Jutta

    2010-01-01

    In 2000, the German Federal Ministry of Education and Research (BMBF) launched the programme "Learning Regions--Providing Support for Networks'" in cooperation with the Lander. It was co-financed by the European Social Fund (ESF). Some 90 regions were selected and financially supported. After one year, 71 regions continued to build-up their…

  12. Molecular clouds in Orion and Monoceros

    SciTech Connect

    Maddalena, R.J.

    1986-01-01

    About one-eighth of a well-sampled 850 deg/sup 2/ region of Orion and Monoceros, extending from the Taurus dark cloud complex to the CMa OB 1 association, shows emission at the frequency of the J = 1 ..-->.. 0 transition of CO coming from either local clouds (d < 1 kpc) lying as much as 25/sup 8/ from the galactic plane or from more distant objects located within a few degrees of the plane and well outside the solar circle. Local giant molecular clouds associated with Orion A and B have enhanced temperatures and densities near their western edges possibly due to compression of molecular gas by a high pressure region created by the cumulative effects of approx.10 supernovae that occurred in the Orion OB association. Another giant molecular cloud found to be associated with Mon R2 may be related to the Orion clouds. Two filamentary clouds (one possible 200 pc long but only 3-10 pc wide) were found that may represent a new class of object; magnetic fields probably play a role in confining these filaments. An expanding ring of clouds concentric with the H II region S 264 and its ionizing 08 star lambda Ori was also investigated, and a possible evolutionary sequence for the ring is given in detail: the clouds probably constitute fragments of the original cloud from which lambda Ori formed, the gas pressure of the H II region and the rocket effect having disrupted the cloud and accelerated the fragments to their present velocities.

  13. Molecular gas in spiral galaxies

    NASA Astrophysics Data System (ADS)

    Casoli, F.; Sauty, S.; Gerin, M.; Boselli, A.; Fouque, P.; Braine, J.; Gavazzi, G.; Lequeux, J.; Dickey, J.

    1998-03-01

    molecular to atomic gas ratio shows a constant value from Sa to Sbc's, and a factor of 10 decrease for late-types, beginning at Sc's. This effect can be attributed to the low CO emission of late-type, low-mass galaxies; we find no such decrease for objects with a dynamical mass larger than 10(11) Mo . These high-mass objects actually show an increase of their normalized atomic and molecular gas content towards late-types, while for low-mass objects, this is seen on HI only. Several authors have tried to search for galaxies deficient in HH in the core of clusters such as Virgo or Coma, but these studies were hampered by the lack of a suitable reference sample (Kenney & Young 1989, Casoli et al. 1991, Horellou et al. 1995b). Using isolated galaxies and galaxies in the outer regions of clusters as a reference sample, we give a predictor for the normalized HH mass of a galaxy Mi /D25 (2) , which depends upon its normalized far-infrared emission LFIR /D25 (2) and its morphological type. This predictor allows us to define a ``CO deficiency factor'', CODEF, analogous to what has been defined for the HI emission. We find that there is no significant CO deficiency of galaxies in the cores of rich clusters.

  14. Some Stereochemical Principles from Polymers: Molecular Symmetry and Molecular Flexibility

    ERIC Educational Resources Information Center

    Price, Charles C.

    1973-01-01

    Discusses the use of the properties of polyethylene, polypropylene, polyisobutylene, and their three epoxides to illustrate the relationships of entropy to molecular properties and the concepts of molecular chirality, geometry, and flexibility. (CC)

  15. Little Massive Substructure in CMZ Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Kauffmann, J.; Pillai, T.; Zhang, Q.; Menten, K. M.; Goldsmith, P. F.; Lu, X.; Guzman, A. E.

    2016-05-01

    The Central Molecular Zone (CMZ; inner ˜100pc) hosts some of the most dense and massive molecular clouds of the Milky Way. Studying these clouds can potentially lead to a better understanding of the dense clouds seen in the central starburst regions in nearby galaxies or in the early universe. The clouds share an unusual feature: they form stars at an unusually slow rate compared to other Milky Way clouds of similar mass and density. Here we use interferometer data from ALMA and the SMA to show that this reduced star formation rate is a consequence of the cloud density structure: CMZ clouds have unusually flat density slopes. The clouds do, for example, exceed the average density of the Orion A molecular cloud by an order of magnitude on spatial scales ˜5 pc, but the cores of CMZ clouds with ˜0.1 pc radius often have masses and densities lower than what is found in the Orion KL region. This relative absence of highest-density gas probably explains the suppression of star formation. The clouds are relatively turbulent, and ALMA observations of H2CO and SiO indicate that the turbulence is induced by high-velocity shocks. We speculate that these shocks might prevent the formation of high-mass cores.

  16. Functionalized gold nanorods for molecular optoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Eghtedari, Mohammad; Oraevsky, Alexander; Conjusteau, Andre; Copland, John A.; Kotov, Nicholas A.; Motamedi, Massoud

    2007-02-01

    The development of gold nanoparticles for molecular optoacoustic imaging is a very promising area of research and development. Enhancement of optoacoustic imaging for molecular detection of tumors requires the engineering of nanoparticles with geometrical and molecular features that can enhance selective targeting of malignant cells while optimizing the sensitivity of optoacoustic detection. In this article, cylindrical gold nanoparticles (i.e. gold nanorods) were fabricated with a plasmon resonance frequency in the near infra-red region of the spectrum, where deep irradiation of tissue is possible using an Alexandrite laser. Gold nanorods (Au-NRs) were functionalized by covalent attachment of Poly(ethylene glycol) to enhance their biocompatibility. These particles were further functionalized with the aim of targeting breast cancer cells using monoclonal antibodies that binds to Her2/neu receptors, which are over expressed on the surface of breast cancer cells. A custom Laser Optoacoustic Imaging System (LOIS) was designed and employed to image nanoparticle-targeted cancer cells in a phantom and PEGylated Au-NRs that were injected subcutaneously into a nude mouse. The results of our experiments show that functionalized Au-NRs with a plasmon resonance frequency at near infra-red region of the spectrum can be detected and imaged in vivo using laser optoacoustic imaging system.

  17. Molecular scale simulation of homopolymer wall slip.

    PubMed

    Dorgan, John R; Rorrer, Nicholas A

    2013-04-26

    The first molecular scale simulation of highly entangled polydisperse homopolymers that is capable of capturing all three regions--no slip, weak slip, and strong slip--of the hydrodynamic boundary condition is presented. An on-lattice dynamic Monte Carlo technique capable of correctly capturing both unentangled and entangled polymer dynamics is used to study the molecular details of wall slip phenomena for homopolymers and energetically neutral walls. For unentangled chains (those exhibiting Rouse dynamics) weak slip is not present but evidence of strong slip is manifest at very high shear rates. For entangled chains (of sufficient length to exhibit reptation dynamics), both weak and strong slip are observed. Consistent with numerous experimental studies, disentanglement and cohesive failure occur at high shear rates. Disentanglement is clearly evidenced in a nonlinear velocity profile that exhibits shear banding, in an excess of chain ends at the slip plane, and perhaps most importantly in a nonmonotonic stress versus shear rate response. The chain end density exhibits a pretransitional periodicity prior to disentanglement. Unentangled Rouse chains do not show this pretransitional response or a bifurcation in their stress versus shear rate response. Finally, it is shown that when polydispersity is introduced, slip phenomena are severely reduced and the inherent constitutive bifurcation is limited to a small region. Predictions are in post facto agreement with many experiments, are distinct from existing results obtained using molecular dynamics simulation techniques, and shed light on fundamental mechanisms of polymer wall slip. PMID:23679746

  18. Regional flood frequency analysis

    SciTech Connect

    Singh, V.P.

    1987-01-01

    This book, the fourth of a four volume set, contains five sections encompassing major aspects of regional flood frequency analysis. Each section starts usually with an invited state-of-the-art paper followed by contributed papers. The first section provides an assessment of regional flood frequency analysis. Methods for performing regional frequency analysis for ungaged watersheds are presented in Section 2. More discussion on regional frequency analysis is provided in Section 3. Selection and comparison of regional frequency methods are dealt with in Secti