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Sample records for global molecular characterization

  1. Contributing to Tumor Molecular Characterization Projects with a Global Impact | Office of Cancer Genomics

    Cancer.gov

    My name is Nicholas Griner and I am the Scientific Program Manager for the Cancer Genome Characterization Initiative (CGCI) in the Office of Cancer Genomics (OCG). Until recently, I spent most of my scientific career working in a cancer research laboratory. In my postdoctoral training, my research focused on identifying novel pathways that contribute to both prostate and breast cancers and studying proteins within these pathways that may be targeted with cancer drugs.

  2. Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences.

    PubMed

    Lin, Y-H; Abad, J A; Maroon-Lango, C J; Perry, K L; Pappu, H R

    2014-08-01

    Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVS(O)) or Andean (PVS(A)) strains. Five isolates - 41956, Cosimar, Galaxy, ND2492-2R, and Q1 - were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa, whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVS(O). PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVS(O), while Q3 and Q5 clustered with known PVS(A) strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVS(A) and PVS(O) strains, a higher π value was found for PVS(A). Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVS(O), whereas a balancing selection pressure was found on PVS(A).

  3. Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling

    PubMed Central

    Dinh, Trinh V; Bienvenut, Willy V; Linster, Eric; Feldman-Salit, Anna; Jung, Vincent A; Meinnel, Thierry; Hell, Rüdiger; Giglione, Carmela; Wirtz, Markus

    2015-01-01

    Protein Nα-terminal acetylation represents one of the most abundant protein modifications of higher eukaryotes. In humans, six Nα-acetyltransferases (Nats) are responsible for the acetylation of approximately 80% of the cytosolic proteins. N-terminal protein acetylation has not been evidenced in organelles of metazoans, but in higher plants is a widespread modification not only in the cytosol but also in the chloroplast. In this study, we identify and characterize the first organellar-localized Nat in eukaryotes. A primary sequence-based search in Arabidopsis thaliana revealed seven putatively plastid-localized Nats of which AT2G39000 (AtNAA70) showed the highest conservation of the acetyl-CoA binding pocket. The chloroplastic localization of AtNAA70 was demonstrated by transient expression of AtNAA70:YFP in Arabidopsis mesophyll protoplasts. Homology modeling uncovered a significant conservation of tertiary structural elements between human HsNAA50 and AtNAA70. The in vivo acetylation activity of AtNAA70 was demonstrated on a number of distinct protein Nα-termini with a newly established global acetylome profiling test after expression of AtNAA70 in E. coli. AtNAA70 predominately acetylated proteins starting with M, A, S and T, providing an explanation for most protein N-termini acetylation events found in chloroplasts. Like HsNAA50, AtNAA70 displays Nε-acetyltransferase activity on three internal lysine residues. All MS data have been deposited in the ProteomeXchange with identifier PXD001947 (http://proteomecentral.proteomexchange.org/dataset/PXD001947). PMID:25951519

  4. Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling.

    PubMed

    Dinh, Trinh V; Bienvenut, Willy V; Linster, Eric; Feldman-Salit, Anna; Jung, Vincent A; Meinnel, Thierry; Hell, Rüdiger; Giglione, Carmela; Wirtz, Markus

    2015-07-01

    Protein N(α) -terminal acetylation represents one of the most abundant protein modifications of higher eukaryotes. In humans, six N(α) -acetyltransferases (Nats) are responsible for the acetylation of approximately 80% of the cytosolic proteins. N-terminal protein acetylation has not been evidenced in organelles of metazoans, but in higher plants is a widespread modification not only in the cytosol but also in the chloroplast. In this study, we identify and characterize the first organellar-localized Nat in eukaryotes. A primary sequence-based search in Arabidopsis thaliana revealed seven putatively plastid-localized Nats of which AT2G39000 (AtNAA70) showed the highest conservation of the acetyl-CoA binding pocket. The chloroplastic localization of AtNAA70 was demonstrated by transient expression of AtNAA70:YFP in Arabidopsis mesophyll protoplasts. Homology modeling uncovered a significant conservation of tertiary structural elements between human HsNAA50 and AtNAA70. The in vivo acetylation activity of AtNAA70 was demonstrated on a number of distinct protein N(α) -termini with a newly established global acetylome profiling test after expression of AtNAA70 in E. coli. AtNAA70 predominately acetylated proteins starting with M, A, S and T, providing an explanation for most protein N-termini acetylation events found in chloroplasts. Like HsNAA50, AtNAA70 displays N(ε) -acetyltransferase activity on three internal lysine residues. All MS data have been deposited in the ProteomeXchange with identifier PXD001947 (http://proteomecentral.proteomexchange.org/dataset/PXD001947).

  5. Molecular Characterization of Arylsulfatase G

    PubMed Central

    Kowalewski, Björn; Lübke, Torben; Kollmann, Katrin; Braulke, Thomas; Reinheckel, Thomas; Dierks, Thomas; Damme, Markus

    2014-01-01

    Arylsulfatase G (ARSG) is a recently identified lysosomal sulfatase that was shown to be responsible for the degradation of 3-O-sulfated N-sulfoglucosamine residues of heparan sulfate glycosaminoglycans. Deficiency of ARSG leads to a new type of mucopolysaccharidosis, as described in a mouse model. Here, we provide a detailed molecular characterization of the endogenous murine enzyme. ARSG is expressed and proteolytically processed in a tissue-specific manner. The 63-kDa single-chain precursor protein localizes to pre-lysosomal compartments and tightly associates with organelle membranes, most likely the endoplasmic reticulum. In contrast, proteolytically processed ARSG fragments of 34-, 18-, and 10-kDa were found in lysosomal fractions and lost their membrane association. The processing sites and a disulfide bridge between the 18- and 10-kDa chains could be roughly mapped. Proteases participating in the processing were identified as cathepsins B and L. Proteolytic processing is dispensable for hydrolytic sulfatase activity in vitro. Lysosomal transport of ARSG in the liver is independent of mannose 6-phosphate, sortilin, and Limp2. However, mutation of glycosylation site N-497 abrogates transport of ARSG to lysosomes in human fibrosarcoma cells, due to impaired mannose 6-phosphate modification. PMID:25135642

  6. Molecular characterization of Rhodnius prolixus' embryonic cuticle.

    PubMed

    Souza-Ferreira, Paula S; Moreira, Mônica F; Atella, Geórgia C; Oliveira-Carvalho, Ana Lúcia; Eizemberg, Roberto; Majerowicz, David; Melo, Ana C A; Zingali, Russolina B; Masuda, Hatisaburo

    2014-08-01

    The embryonic cuticle (EC) of Rhodnius prolixus envelopes the entire body of the embryo during hatching and provides physical protection, allowing the embryo to pass through a narrow chorionic border. Most of the knowledge about the EC of insects is derived from studies on ultrastructure and secretion processes during embryonic development, and little is known about the molecular composition of this structure. We performed a comprehensive molecular characterization of the major components extracted from the EC of R. prolixus, and we discuss the role of the different molecules that were identified during the eclosion process. The results showed that, similar to the post-embryonic cuticles of insects, the EC of R. prolixus is primarily composed of carbohydrates (57%), lipids (19%), and proteins (8%). Considering only the carbohydrates, chitin is by far the major component (approximately 70%), and it is found primarily along the body of the EC. It is scarce or absent in its prolongations, which are composed of glycosaminoglycans. In addition to chitin, we also identified amino (15%), neutral (12%) and acidic (3%) carbohydrates in the EC of R. prolixus. In addition carbohydrates, we also identified neutral lipids (64.12%) and phospholipids (35.88%). Proteomic analysis detected 68 proteins (55 were identified and 13 are hypothetical proteins) using the sequences in the R. prolixus genome (http://www.vectorbase.org). Among these proteins, 8 out of 15 are associated with cuticle metabolism. These proteins are unequivocally cuticle proteins, and they have been described in other insects. Approximately 35% of the total proteins identified were classified as having a structural function. Chitin-binding protein, amino peptidase, amino acid oxidase, oxidoreductase, catalase and peroxidase are all proteins associated with cuticle metabolism. Proteins known to be cuticle constituents may be related to the function of the EC in assisting the insect during eclosion. To our

  7. Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology.

    PubMed

    Dilly, G F; Gaitán-Espitia, J D; Hofmann, G E

    2015-03-01

    This is the first de novo transcriptome and complete mitochondrial genome of an Antarctic sea urchin species sequenced to date. Sterechinus neumayeri is an Antarctic sea urchin and a model species for ecology, development, physiology and global change biology. To identify transcripts important to ocean acidification (OA) and thermal stress, this transcriptome was created pooling, and 13 larval samples representing developmental stages on day 11 (late gastrula), 19 (early pluteus) and 30 (mid pluteus) maintained at three CO2 levels (421, 652, and 1071 μatm) as well as four additional heat-shocked samples. The normalized cDNA pool was sequenced using emulsion PCR (pyrosequencing) resulting in 1.34M reads with an average read length of 492 base pairs. 40,994 isotigs were identified, averaging 1188 bp with a median coverage of 11×. Additional primer design and gap sequencing were required to complete the mitochondrial genome. The mitogenome of S. neumayeri is a circular DNA molecule with a length of 15 684 bp that contains all 37 genes normally found in metazoans. We detail the main features of the transcriptome and the mitogenome architecture and investigate the phylogenetic relationships of S. neumayeri within Echinoidea. In addition, we provide comparative analyses of S. neumayeri with its closest relative, Strongylocentrotus purpuratus, including a list of potential OA gene targets. The resources described here will support a variety of quantitative (genomic, proteomic, multistress and comparative) studies to interrogate physiological responses to OA and other stressors in this important Antarctic calcifier.

  8. Global smoothing and continuation for large-scale molecular optimization

    SciTech Connect

    More, J.J.; Wu, Zhijun

    1995-10-01

    We discuss the formulation of optimization problems that arise in the study of distance geometry, ionic systems, and molecular clusters. We show that continuation techniques based on global smoothing are applicable to these molecular optimization problems, and we outline the issues that must be resolved in the solution of large-scale molecular optimization problems.

  9. Identifying the Molecular Origin of Global Warming

    NASA Technical Reports Server (NTRS)

    Bera, Partha P.; Francisco, Joseph S.; Lee, Timothy J.

    2009-01-01

    We have investigated the physical characteristics of greenhouse gases (GHGs) to assess which properties are most important in determining the efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), nitrogen fluorides, and various other known atmospheric trace molecules have been included in this study. Compounds containing the halogens F or Cl have in common very polar X-F or X-Cl bonds, particularly the X-F bonds. It is shown that as more F atoms bond to the same central atom, the bond dipoles become larger as a result of the central atom becoming more positive. This leads to a linear increase in the total or integrated XF bond dipole derivatives for the molecule, which leads to a non-linear (quadratic) increase in infrared (IR) intensity. Moreover, virtually all of the X-F bond stretches occur in the atmospheric IR window as opposed to X-H stretches, which do not occur in the atmospheric window. It is concluded that molecules possessing several F atoms will always have a large radiative forcing parameter in the calculation of their global warming potential. Some of the implications for global warming and climate change are discussed.

  10. Molecular characterization of hepatocarcinogenesis using mouse models

    PubMed Central

    Teoh, Wei Wei; Xie, Min; Vijayaraghavan, Aadhitthya; Yaligar, Jadegoud; Tong, Wei Min; Goh, Liang Kee; Sabapathy, Kanaga

    2015-01-01

    ABSTRACT Hepatocellular carcinoma (HCC) is a deadly disease, often unnoticed until the late stages, when treatment options become limited. Thus, there is a crucial need to identify biomarkers for early detection of developing HCC, as well as molecular pathways that would be amenable to therapeutic intervention. Although analysis of human HCC tissues and serum components may serve these purposes, inability of early detection also precludes possibilities of identification of biomarkers or pathways that are sequentially perturbed at earlier phases of disease progression. We have therefore explored the option of utilizing mouse models to understand in a systematic and longitudinal manner the molecular pathways that are progressively deregulated by various etiological factors in contributing to HCC formation, and we report the initial findings in characterizing their validity. Hepatitis B surface antigen transgenic mice, which had been exposed to aflatoxin B1 at various stages in life, were used as a hepatitis model. Our findings confirm a synergistic effect of both these etiological factors, with a gender bias towards males for HCC predisposition. Time-based aflatoxin B1 treatment also demonstrated the requirement of non-quiescent liver for effective transformation. Tumors from these models with various etiologies resemble human HCCs histologically and at the molecular level. Extensive molecular characterization revealed the presence of an 11-gene HCC-expression signature that was able to discern transformed human hepatocytes from primary cells, regardless of etiology, and from other cancer types. Moreover, distinct molecular pathways appear to be deregulated by various etiological agents en route to formation of HCCs, in which common pathways converge, highlighting the existence of etiology-specific as well as common HCC-specific molecular perturbations. This study therefore highlights the utility of these mouse models, which provide a rich resource for the

  11. Molecular and immunological characterization of shellfish allergens.

    PubMed

    Leung, P S; Chu, K H

    1998-03-15

    Shellfish (crustaceans and mollusks) have long been known as a common cause of allergic reactions to food. Like other food allergies, the allergic reactions to shellfish involve IgE-mediated Type I hypersensitivity. Biochemical and molecular studies have documented the major shrimp allergen is the muscle protein tropomyosin. Subsequent molecular cloning studies on lobsters and crabs have characterized this protein as the common allergen in crustaceans. There has also been strong immunological evidence that tropomyosin is a cross-reactive allergen among crustaceans and mollusks. This is further confirmed by recent studies on the identification of allergens in squid and abalone. The advances in the characterization of shellfish allergens will not only enhance our understanding on the physiological basis of shellfish allergy but also lay the groundwork for the development of diagnostic and therapeutic design in food allergies.

  12. Meteorological Characterization of Global Dust Sources

    NASA Technical Reports Server (NTRS)

    Ginoux, Paul; Prospero, Joe; Torres, Omar; Einaudi, Franco (Technical Monitor)

    2000-01-01

    The global distribution of absorbing aerosols index (AI) derived from Nimbus 7 Total Ozone Mapping Spectrometer (TOMS) measurements has been used to identify the major sources of atmospheric dust particles [Prospero, et al., 2000]. In this presentation, we will show that the TOMS aerosol index can also be used to the meteorological characterization of the source areas. We found a huge "dust belt" with a strong correlation between the TOMS index and the sea-level pressure wrapping all the major dust sources. To handle the difficulty of using quantitatively the TOMS Al and its strong dependency on the aerosol layer altitude, the Al has been correlated to the planetary boundary layer depth (PBL) and the surface wind speed. The strongest correlation is obtained with the product of these two variables and at the precise location of the dust sources identified by Prospero et al. The relation between the TOMS Al and the product of the PBL height and the surface wind speed has been used to study the interannual variability of the North-Africa dust sources in relation with the North Atlantic Oscillation (NAO). Finally, we will show that even on a short time base the variability of the TOMS Al can be related to the surface wind speed and PBL height.

  13. Low-molecular-weight heparins: differential characterization/physical characterization.

    PubMed

    Guerrini, Marco; Bisio, Antonella

    2012-01-01

    Low-molecular-weight heparins (LMWHs), derived from unfractionated heparin (UFH) through different depolymerization processes, have advantages with respect to the parent heparin in terms of pharmacokinetics, convenience of administration, and reduced side effects. Each LMWH can be considered as an independent drug with its own activity profile, placing significance on their biophysical characterization, which will also enable a better understanding of their structure-function relationship. Several chemical and physical methods, some involving sample modification, are now available and are reviewed.

  14. Molecular characterization of bromeliads from northeast Brazil.

    PubMed

    Vieira, S D; Rabbani, A R C; Santos, F; Silva-Mann, R; Arrigoni-Blank, M F; Prata, A P N; Resende, L V; Pasqual, M; Blank, A F

    2014-01-01

    Bromeliaceae is an important botany family that includes many species with economic value; demand for members of this family is increasing. However, illegal collection frequently occurs, drastically reducing the species populations; thus, it is necessary to collect and store Bromeliaceae genetic material. In this study, we identified and quantified genetic variability of the Bromeliad family using dominant markers to create the first Germplasm Bank in the northeast region of Brazil. Molecular tools were used to characterize the collected accessions. The combination of 11 inter-simple sequence repeats and 13 random amplified polymorphic DNA markers were used to detect the genetic variability of wild bromeliad accessions. PMID:25501194

  15. Diversity in global maize germplasm: characterization and utilization.

    PubMed

    Prasanna, B M

    2012-11-01

    Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. 'Seeds of Discovery' (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is

  16. Molecular diagnostic and surveillance tools for global malaria control.

    PubMed

    Erdman, Laura K; Kain, Kevin C

    2008-01-01

    Malaria is the most devastating parasitic infection in the world, annually causing over 1 million deaths and extensive morbidity. The global burden of malaria has increased over the last several decades, as have rates of imported malaria into non-endemic regions. Rapid and accurate diagnostics are a crucial component of malaria control strategies, and epidemiological surveillance is required to monitor trends in malaria prevalence and antimalarial drug resistance. Conventional malaria diagnostic and surveillance tools can be cumbersome and slow with limitations in both sensitivity and specificity. New molecular techniques have been developed in an attempt to overcome these restrictions. These molecular techniques are discussed with regard to their technical advantages and disadvantages, with an emphasis on the practicality of implementation in malaria-endemic and non-endemic regions.

  17. Molecular Characterization of Pancreatic Serous Microcystic Adenomas

    PubMed Central

    Moore, Patrick S.; Zamboni, Giuseppe; Brighenti, Antonietta; Lissandrini, Daniele; Antonello, Davide; Capelli, Paola; Rigaud, Gildas; Falconi, Massimo; Scarpa, Aldo

    2001-01-01

    Pancreatic serous microcystic adenomas (SCAs) are rare, benign tumors with a striking female preference. Virtually no information is available about chromosomal or genetic anomalies in this disease. We performed extensive molecular characterization of 21 cases of formalin-fixed, paraffin-embedded sporadic SCAs consisting in genome-wide allelic loss analysis with 79 microsatellite markers covering all 22 autosomes, assessment of microsatellite instability, and mutational analysis of the VHL, K-ras, and p53 genes in nine cases for which frozen tissue was available. Although no case showed microsatellite instability of the type seen in mismatch repair-deficient tumors, a relatively low fractional allelic loss of 0.08 was found. Losses on chromosome 10q were the most frequent event in SCAs (50% of cases), followed by allelic losses on chromosome 3p (40% of cases). Moderately frequent losses (>25% of cases) were found on chromosomes 1q, 2q, and 7q. The VHL gene, located on chromosome 3p, had somatic inactivating mutations in two of nine cases (22%), whereas no mutations were found in either K-ras or p53, in agreement with the finding that all 21 cases stained negative for p53 by immunohistochemistry. Our study indicates that the involvement of chromosomal arms 10q and 3p is characteristic of SCAs and that the VHL gene is involved in a subset of sporadic cases. PMID:11141506

  18. Microbial ureases: significance, regulation, and molecular characterization.

    PubMed Central

    Mobley, H L; Hausinger, R P

    1989-01-01

    Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not conclusive. In contrast, ureases from gram-negative bacteria studied thus far clearly possess three distinct subunits with Mrs of 65,000 to 73,000 (alpha), 10,000 to 12,000 (beta), and 8,000 to 10,000 (gamma). Tightly bound nickel is present in all ureases and appears to participate in catalysis. Urease genes have been cloned from several species, and nickel-containing recombinant ureases have been characterized. Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha. In addition to these genes, several other peptides are encoded in the urease operon of some species. The roles for these other genes are not firmly established, but may involve regulation, urea transport, nickel transport, or nickel processing. PMID:2651866

  19. Microbial ureases: significance, regulation, and molecular characterization.

    PubMed

    Mobley, H L; Hausinger, R P

    1989-03-01

    Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not conclusive. In contrast, ureases from gram-negative bacteria studied thus far clearly possess three distinct subunits with Mrs of 65,000 to 73,000 (alpha), 10,000 to 12,000 (beta), and 8,000 to 10,000 (gamma). Tightly bound nickel is present in all ureases and appears to participate in catalysis. Urease genes have been cloned from several species, and nickel-containing recombinant ureases have been characterized. Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha. In addition to these genes, several other peptides are encoded in the urease operon of some species. The roles for these other genes are not firmly established, but may involve regulation, urea transport, nickel transport, or nickel processing. PMID:2651866

  20. Supernova feedback in molecular clouds: global evolution and dynamics

    NASA Astrophysics Data System (ADS)

    Körtgen, Bastian; Seifried, Daniel; Banerjee, Robi; Vázquez-Semadeni, Enrique; Zamora-Avilés, Manuel

    2016-07-01

    We use magnetohydrodynamical simulations of converging warm neutral medium flows to analyse the formation and global evolution of magnetized and turbulent molecular clouds subject to supernova feedback from massive stars. We show that supernova feedback alone fails to disrupt entire, gravitationally bound, molecular clouds, but is able to disperse small-sized (˜10 pc) regions on time-scales of less than 1 Myr. Efficient radiative cooling of the supernova remnant as well as strong compression of the surrounding gas result in non-persistent energy and momentum input from the supernovae. However, if the time between subsequent supernovae is short and they are clustered, large hot bubbles form that disperse larger regions of the parental cloud. On longer time-scales, supernova feedback increases the amount of gas with moderate temperatures (T ≈ 300-3000 K). Despite its inability to disrupt molecular clouds, supernova feedback leaves a strong imprint on the star formation process. We find an overall reduction of the star formation efficiency by a factor of 2 and of the star formation rate by roughly factors of 2-4.

  1. Next generation of global land cover characterization, mapping, and monitoring

    NASA Astrophysics Data System (ADS)

    Giri, C.; Pengra, B.; Long, J.; Loveland, T. R.

    2013-12-01

    Land cover change is increasingly affecting the biophysics, biogeochemistry, and biogeography of the Earth's surface and the atmosphere, with far-reaching consequences to human well-being. However, our scientific understanding of the distribution and dynamics of land cover and land cover change (LCLCC) is limited. Previous global land cover assessments performed using coarse spatial resolution (300 m-1 km) satellite data did not provide enough thematic detail or change information for global change studies and for resource management. High resolution (˜30 m) land cover characterization and monitoring is needed that permits detection of land change at the scale of most human activity and offers the increased flexibility of environmental model parameterization needed for global change studies. However, there are a number of challenges to overcome before producing such data sets including unavailability of consistent global coverage of satellite data, sheer volume of data, unavailability of timely and accurate training and validation data, difficulties in preparing image mosaics, and high performance computing requirements. Integration of remote sensing and information technology is needed for process automation and high-performance computing needs. Recent developments in these areas have created an opportunity for operational high resolution land cover mapping, and monitoring of the world. Here, we report and discuss these advancements and opportunities in producing the next generations of global land cover characterization, mapping, and monitoring at 30-m spatial resolution primarily in the context of United States, Group on Earth Observations Global 30 m land cover initiative (UGLC).

  2. Molecular Characterization of Bacterial Respiration on Minerals

    SciTech Connect

    Blake, Robert C.

    2013-04-26

    The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength

  3. Global Molecular Characterization of the Chromate Stress Response in Shewanella oneidensis MR-1: Identification of a Putative DNA-Binding Response Regulator and Azoreductase Involved in Cr(VI) Detoxification

    SciTech Connect

    Chourey, Karuna; Thompson, Melissa R.; Brown, Steven D.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Thompson, Dorothea K.

    2006-04-05

    Shewanella oneidensis MR-1 is a model environmental organism that possesses diverse respiratory capacities, including the ability to reduce soluble Cr(VI) to sparingly soluble, less toxic Cr(III). Effective bioremediation of Cr-contaminated sites requires knowledge of the molecular mechanisms and regulation of heavy metal resistance and biotransformation by dissimilatory metal-reducing bacteria. Towards this goal, our ERSP-funded work is focused on the identification and functional analysis of genes/proteins comprising the response pathways for chromate detoxification and/or reduction. Previous transcriptomic profiling and whole-cell proteomic analyses implicated the involvement of a functionally undefined DNA-binding response regulator (SO2426) and a putative azoreductase (SO3585) in the chromate stress response of MR-1. Here we describe a detailed functional analysis of SO2426 and SO3585 in order to begin to understand the role of these proteins in the cellular response to chromate. The protein products encoded by genes so2426 and so3585 were expressed and detected only in chromate-shocked samples as determined by multidimensional high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Both genes were also highly induced (>46-fold) in MR-1 cells actively reducing chromate based on whole-genome microarray analysis. We have created in-frame deletions of the so2426 and so3585 loci in the MR-1 chromosome and have characterized the phenotype of the resulting mutants in the presence of varying concentrations of Cr, Cu, Co, Sr, and H{sub 2}O{sub 2} under aerobic respiratory conditions. Growth studies indicated that the so2426 deletion mutant was more sensitive to heavy metals compared to the WT reference, and chromate reduction by the so2426 mutant was impaired significantly. The growth response of the mutant to H{sub 2}O{sub 2} was similar to that of MR-1. To gain insight into the regulon of this response regulator, MR-1 microarrays were used to

  4. CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS

    SciTech Connect

    Swanson, Jessica

    2011-08-31

    This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.

  5. Global Latitudinal Differences of Molecular Absorption on Jupiter

    NASA Astrophysics Data System (ADS)

    Tejfel, V. G.

    2002-09-01

    In the future planetary monitoring from the groundbased observatories or space telescopes the selection of a number of planetary state indices will be necessary to obtain homogeneous temporal series of numerical planetary characteristics. In 1999 special observations of latitude-longitudinal distribution of absorption in the methane bands on Jupiter were carried out. CCD-spectra of the central meridian of Jupiter were recorded in each 3 minutes that corresponded a turning of Jupiter by 1.8 degrees. All the longitudes of the planet were twice covered and full number of spectrograms was 388. A comparison of the latitudinal dependence of absorption in the different absorption bands has revealed some noticeable global, longitudinally independent differences in the character of latitudinal variations of absorption. So, equatorial depression of absorption is well expressed in the bands at 725 and 887 nm, but it is absent in the band at 619 nm. It is interesting that for the band 798 nm, which is a combination of the methane and ammonia absorption, the similar depression is displaced significantly northward from the equator (minimum of the absorption take place at the latitude about +15 deg) in contrast with the depression observed for the band CH4 887 nm. Very small northward displacement is noticeable also for the CH4 725 nm equatorial depression. There is no determined relationship between the value of molecular absorption and visible albedo of the cloud belts. Standard deviations calculated at the longitudinally averaging of the central meridian profiles of the band central depths R are small and no more than 1-2 per cent of mean value. Thus the latitudinal differences are more clearly expressed than longitudinal variations and the global, longitudinally averaged N-S profiles of the absorption variations may be considered as one of characteristics of the current state of Jupiter (as well as of Saturn). There may be not significant mistake if the individual profiles R

  6. Comprehensive molecular characterization of gastric adenocarcinoma

    PubMed Central

    Bass, Adam J.; Thorsson, Vesteinn; Shmulevich, Ilya; Reynolds, Sheila M.; Miller, Michael; Bernard, Brady; Hinoue, Toshinori; Laird, Peter W.; Curtis, Christina; Shen, Hui; Weisenberger, Daniel J.; Schultz, Nikolaus; Shen, Ronglai; Weinhold, Nils; Kelsen, David P.; Bowlby, Reanne; Chu, Andy; Kasaian, Katayoon; Mungall, Andrew J.; Robertson, A. Gordon; Sipahimalani, Payal; Cherniack, Andrew; Getz, Gad; Liu, Yingchun; Noble, Michael S.; Pedamallu, Chandra; Sougnez, Carrie; Taylor-Weiner, Amaro; Akbani, Rehan; Lee, Ju-Seog; Liu, Wenbin; Mills, Gordon B.; Yang, Da; Zhang, Wei; Pantazi, Angeliki; Parfenov, Michael; Gulley, Margaret; Piazuelo, M. Blanca; Schneider, Barbara G.; Kim, Jihun; Boussioutas, Alex; Sheth, Margi; Demchok, John A.; Rabkin, Charles S.; Willis, Joseph E.; Ng, Sam; Garman, Katherine; Beer, David G.; Pennathur, Arjun; Raphael, Benjamin J.; Wu, Hsin-Ta; Odze, Robert; Kim, Hark K.; Bowen, Jay; Leraas, Kristen M.; Lichtenberg, Tara M.; Weaver, Stephanie; McLellan, Michael; Wiznerowicz, Maciej; Sakai, Ryo; Getz, Gad; Sougnez, Carrie; Lawrence, Michael S.; Cibulskis, Kristian; Lichtenstein, Lee; Fisher, Sheila; Gabriel, Stacey B.; Lander, Eric S.; Ding, Li; Niu, Beifang; Ally, Adrian; Balasundaram, Miruna; Birol, Inanc; Bowlby, Reanne; Brooks, Denise; Butterfield, Yaron S. N.; Carlsen, Rebecca; Chu, Andy; Chu, Justin; Chuah, Eric; Chun, Hye-Jung E.; Clarke, Amanda; Dhalla, Noreen; Guin, Ranabir; Holt, Robert A.; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Li, Haiyan A.; Lim, Emilia; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen L.; Nip, Ka Ming; Robertson, A. Gordon; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Beroukhim, Rameen; Carter, Scott L.; Cherniack, Andrew D.; Cho, Juok; Cibulskis, Kristian; DiCara, Daniel; Frazer, Scott; Fisher, Sheila; Gabriel, Stacey B.; Gehlenborg, Nils; Heiman, David I.; Jung, Joonil; Kim, Jaegil; Lander, Eric S.; Lawrence, Michael S.; Lichtenstein, Lee; Lin, Pei; Meyerson, Matthew; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Saksena, Gordon; Schumacher, Steven E.; Sougnez, Carrie; Stojanov, Petar; Tabak, Barbara; Taylor-Weiner, Amaro; Voet, Doug; Rosenberg, Mara; Zack, Travis I.; Zhang, Hailei; Zou, Lihua; Protopopov, Alexei; Santoso, Netty; Parfenov, Michael; Lee, Semin; Zhang, Jianhua; Mahadeshwar, Harshad S.; Tang, Jiabin; Ren, Xiaojia; Seth, Sahil; Yang, Lixing; Xu, Andrew W.; Song, Xingzhi; Pantazi, Angeliki; Xi, Ruibin; Bristow, Christopher A.; Hadjipanayis, Angela; Seidman, Jonathan; Chin, Lynda; Park, Peter J.; Kucherlapati, Raju; Akbani, Rehan; Ling, Shiyun; Liu, Wenbin; Rao, Arvind; Weinstein, John N.; Kim, Sang-Bae; Lee, Ju-Seog; Lu, Yiling; Mills, Gordon; Laird, Peter W.; Hinoue, Toshinori; Weisenberger, Daniel J.; Bootwalla, Moiz S.; Lai, Phillip H.; Shen, Hui; Triche, Timothy; Van Den Berg, David J.; Baylin, Stephen B.; Herman, James G.; Getz, Gad; Chin, Lynda; Liu, Yingchun; Murray, Bradley A.; Noble, Michael S.; Askoy, B. Arman; Ciriello, Giovanni; Dresdner, Gideon; Gao, Jianjiong; Gross, Benjamin; Jacobsen, Anders; Lee, William; Ramirez, Ricardo; Sander, Chris; Schultz, Nikolaus; Senbabaoglu, Yasin; Sinha, Rileen; Sumer, S. Onur; Sun, Yichao; Weinhold, Nils; Thorsson, Vésteinn; Bernard, Brady; Iype, Lisa; Kramer, Roger W.; Kreisberg, Richard; Miller, Michael; Reynolds, Sheila M.; Rovira, Hector; Tasman, Natalie; Shmulevich, Ilya; Ng, Santa Cruz Sam; Haussler, David; Stuart, Josh M.; Akbani, Rehan; Ling, Shiyun; Liu, Wenbin; Rao, Arvind; Weinstein, John N.; Verhaak, Roeland G.W.; Mills, Gordon B.; Leiserson, Mark D. M.; Raphael, Benjamin J.; Wu, Hsin-Ta; Taylor, Barry S.; Black, Aaron D.; Bowen, Jay; Carney, Julie Ann; Gastier-Foster, Julie M.; Helsel, Carmen; Leraas, Kristen M.; Lichtenberg, Tara M.; McAllister, Cynthia; Ramirez, Nilsa C.; Tabler, Teresa R.; Wise, Lisa; Zmuda, Erik; Penny, Robert; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Curely, Erin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Shelton, Troy; Shelton, Candace; Sherman, Mark; Benz, Christopher; Lee, Jae-Hyuk; Fedosenko, Konstantin; Manikhas, Georgy; Potapova, Olga; Voronina, Olga; Belyaev, Smitry; Dolzhansky, Oleg; Rathmell, W. Kimryn; Brzezinski, Jakub; Ibbs, Matthew; Korski, Konstanty; Kycler, Witold; ŁaŸniak, Radoslaw; Leporowska, Ewa; Mackiewicz, Andrzej; Murawa, Dawid; Murawa, Pawel; Spychała, Arkadiusz; Suchorska, Wiktoria M.; Tatka, Honorata; Teresiak, Marek; Wiznerowicz, Maciej; Abdel-Misih, Raafat; Bennett, Joseph; Brown, Jennifer; Iacocca, Mary; Rabeno, Brenda; Kwon, Sun-Young

    2014-01-01

    Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies. PMID:25079317

  7. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...

  8. Computational molecular characterization of the flavonoid rutin.

    PubMed

    Payán-Gómez, Sergio A; Flores-Holguín, Norma; Pérez-Hernández, Antonino; Piñón-Miramontes, Manuel; Glossman-Mitnik, Daniel

    2010-06-22

    In this work, we make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Rutin, as well as to predict the infrared (IR) and ultraviolet (UV-Vis) spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for this molecule as a means of validation of the used model chemistry.

  9. Computational molecular characterization of the flavonoid rutin

    PubMed Central

    2010-01-01

    In this work, we make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Rutin, as well as to predict the infrared (IR) and ultraviolet (UV-Vis) spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for this molecule as a means of validation of the used model chemistry. PMID:20569488

  10. Mendel's genes: toward a full molecular characterization.

    PubMed

    Reid, James B; Ross, John J

    2011-09-01

    The discipline of classical genetics is founded on the hereditary behavior of the seven genes studied by Gregor Mendel. The advent of molecular techniques has unveiled much about the identity of these genes. To date, four genes have been sequenced: A (flower color), LE (stem length), I (cotyledon color), and R (seed shape). Two of the other three genes, GP (pod color) and FA (fasciation), are amenable to candidate gene approaches on the basis of their function, linkage relationships, and synteny between the pea and Medicago genomes. However, even the gene (locus) identity is not known for certain for the seventh character, the pod form, although it is probably V. While the nature of the mutations used by Mendel cannot be determined with certainty, on the basis of the varieties available in Europe in the 1850s, we can speculate on their nature. It turns out that these mutations are attributable to a range of causes-from simple base substitutions and changes to splice sites to the insertion of a transposon-like element. These findings provide a fascinating connection between Mendelian genetics and molecular biology that can be used very effectively in teaching new generations of geneticists. Mendel's characters also provide novel insights into the nature of the genes responsible for characteristics of agronomic and consumer importance.

  11. Comprehensive Molecular Characterization of Urothelial Bladder Carcinoma

    PubMed Central

    2014-01-01

    Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. To date, no molecularly targeted agents have been approved for the disease. As part of The Cancer Genome Atlas project, we report here an integrated analysis of 131 urothelial carcinomas to provide a comprehensive landscape of molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved in cell cycle regulation, chromatin regulation, and kinase signaling pathways, as well as 9 genes not previously reported as significantly mutated in any cancer. RNA sequencing revealed four expression subtypes, two of which (papillary-like and basal/squamous-like) were also evident in miRNA sequencing and protein data. Whole-genome and RNA sequencing identified recurrent in-frame activating FGFR3-TACC3 fusions and expression or integration of several viruses (including HPV16) that are associated with gene inactivation. Our analyses identified potential therapeutic targets in 69% of the tumours, including 42% with targets in the PI3K/AKT/mTOR pathway and 45% with targets (including ERBB2) in the RTK/MAPK pathway. Chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any common cancer studied to date, suggesting the future possibility of targeted therapy for chromatin abnormalities. PMID:24476821

  12. Cancer Research from Molecular Discovery to Global Health

    Cancer.gov

    A science writers' seminar to discuss the latest research in cancer genetics and global health efforts, including talks from leaders of NCI’s new centers of cancer genomics and global health will be held Dec. 13, 2011, at NCI.

  13. Molecular characterization of patchouli (Pogostemon spp) germplasm.

    PubMed

    Sandes, S S; Zucchi, M I; Pinheiro, J B; Bajay, M M; Batista, C E A; Brito, F A; Arrigoni-Blank, M F; Alvares-Carvalho, S V; Silva-Mann, R; Blank, A F

    2016-01-01

    Patchouli [Pogostemon cablin (Blanco) Benth.] is an aromatic, herbaceous plant belonging to the Lamiaceae family native to Southeast Asia. Its leaves produce an essential oil regularly used by the perfume and cosmetics industries. However, since patchouli from the Philippines and India were described and named Pogostemon patchouli, there has been a divergence in the identity of these species. The objective of the current study was to study the genetic diversity of patchouli accessions in the Active Germplasm Bank of Universidade Federal de Sergipe using microsatellite and inter simple sequence repeat markers. The results of both types of molecular markers showed that there are two well-defined clusters of accessions that harbor exclusive alleles. It was observed that these two clusters are genetically distant, suggesting that they belong to two different species. Based on the results, two accessions were classified as Pogostemon heyneanus and the remaining accessions were classified as P. cablin.

  14. Molecular characterization of patchouli (Pogostemon spp) germplasm.

    PubMed

    Sandes, S S; Zucchi, M I; Pinheiro, J B; Bajay, M M; Batista, C E A; Brito, F A; Arrigoni-Blank, M F; Alvares-Carvalho, S V; Silva-Mann, R; Blank, A F

    2016-01-01

    Patchouli [Pogostemon cablin (Blanco) Benth.] is an aromatic, herbaceous plant belonging to the Lamiaceae family native to Southeast Asia. Its leaves produce an essential oil regularly used by the perfume and cosmetics industries. However, since patchouli from the Philippines and India were described and named Pogostemon patchouli, there has been a divergence in the identity of these species. The objective of the current study was to study the genetic diversity of patchouli accessions in the Active Germplasm Bank of Universidade Federal de Sergipe using microsatellite and inter simple sequence repeat markers. The results of both types of molecular markers showed that there are two well-defined clusters of accessions that harbor exclusive alleles. It was observed that these two clusters are genetically distant, suggesting that they belong to two different species. Based on the results, two accessions were classified as Pogostemon heyneanus and the remaining accessions were classified as P. cablin. PMID:26909987

  15. Characterizing the LANDSAT Global Long-Term Data Record

    NASA Technical Reports Server (NTRS)

    Arvidson, T.; Goward, S. N.; Williams, D. L.

    2006-01-01

    The effects of global climate change are fast becoming politically, sociologically, and personally important: increasing storm frequency and intensity, lengthening cycles of drought and flood, expanding desertification and soil salinization. A vital asset in the analysis of climate change on a global basis is the 34-year record of Landsat imagery. In recognition of its increasing importance, a detailed analysis of the Landsat observation coverage within the US archive was commissioned. Results to date indicate some unexpected gaps in the US-held archive. Fortunately, throughout the Landsat program, data have been downlinked routinely to International Cooperator (IC) ground stations for archival, processing, and distribution. These IC data could be combined with the current US holdings to build a nearly global, annual observation record over this 34-year period. Today, we have inadequate information as to which scenes are available from which IC archives. Our best estimate is that there are over four million digital scenes in the IC archives, compared with the nearly two million scenes held in the US archive. This vast pool of Landsat observations needs to be accurately documented, via metadata, to determine the existence of complementary scenes and to characterize the potential scope of the global Landsat observation record. Of course, knowing the extent and completeness of the data record is but the first step. It will be necessary to assure that the data record is easy to use, internally consistent in terms of calibration and data format, and fully accessible in order to fully realize its potential.

  16. Molecular characterization of Eimeria species in macropods.

    PubMed

    Yang, Rongchang; Fenwick, Stan; Potter, Abbey; Elliot, Aileen; Power, Michelle; Beveridge, Ian; Ryan, Una

    2012-10-01

    A total of 597 faecal samples were collected from western grey kangaroos (Macropus fuliginosus), Euros (M. robustus), red kangaroos (M. rufus) in Western Australia and Eastern Grey Kangaroos (M. giganteus) from Victoria and screened for the presence of Eimeria by PCR at the 18S ribosomal RNA (rRNA) locus. The overall prevalence was 24.3% (145/597). At the 18S rRNA locus, sequences were obtained for 25 of the 145 positives. Phylogenetic analysis indicated that all the macropod-derived Eimeria species grouped in a separate marsupial clade that included Eimeria trichosuri from brushtail possums. At least 6 different clades were identified within the marsupial isolates and many of the genotypes identified are likely to be valid species, however morphological and biological data need to be collected to match sequences to previously characterized Eimeria species or identify if they are new species.

  17. First molecular characterization of Cryptosporidium in Yemen.

    PubMed

    Alyousefi, N A; Mahdy, M A K; Lim, Y A L; Xiao, L; Mahmud, R

    2013-05-01

    Cryptosporidium is a protozoan parasite of humans and animals and has a worldwide distribution. The parasite has a unique epidemiology in Middle Eastern countries where the IId subtype family of Cryptosporidium parvum dominates. However, there has been no information on Cryptosporidium species in Yemen. Thus, this study was conducted in Yemen to examine the distribution of Cryptosporidium species and subtype families. Fecal samples were collected from 335 patients who attended hospitals in Sana'a city. Cryptosporidium species were determined by PCR and sequence analysis of the 18 s rRNA gene. Cryptosporidium parvum and C. hominis subtypes were identified based on sequence analysis of the 60 kDa glycoprotein (gp60) gene. Out of 335 samples, 33 (9.9%) were positive for Cryptosporidium. Of them, 97% were identified as C. parvum whilst 1 case (3%) was caused by C. hominis. All 7 C. parvum isolates subtyped belonged to the IIaA15G2R1 subtype. The common occurrence of the zoonotic IIa subtype family of C. parvum highlights the potential occurrence of zoonotic transmission of cryptosporidiosis in Yemen. However, this postulation needs confirmation with future molecular epidemiological studies of cryptosporidiosis in both humans and animals in Yemen.

  18. Molecular characterization of Korean rabies virus isolates

    PubMed Central

    Park, Young-Nam; Hong, Gyeong-Soo; Kang, Hee-Kyung; Oh, Yoon-I; Cho, Soo-Dong; Song, Jae-Young

    2011-01-01

    The nucleoprotein (N) and glycoprotein (G) of 11 Korean rabies virus (RABV) isolates collected from animals diagnosed with rabies between 2008 and 2009 were subjected to molecular and phylogenetic analyses. Six isolates originated from domestic animals (cattle and dogs) and five were obtained from wild free-ranging raccoon dogs. The similarities in the nucleotide sequences of the N gene among all Korean isolates ranged from 98.1 to 99.8%, while those of the G gene ranged from 97.9 to 99.3%. Based on the nucleotide analysis of the N and G genes, the Korean RABV isolates were confirmed as genotype I of Lyssavirus and classified into four distinct subgroups with high similarity. Phylogenetic analysis showed that the Korean isolates were most closely related to the non-Korean NeiMeng1025B and 857r strains, which were isolated from rabid raccoon dogs in Eastern China and Russia, respectively. These findings suggest that the Korean RABV isolates originated from a rabid raccoon dog in Northeastern Asia. Genetic analysis of the Korean RABV isolates revealed no substitutions at several antigenic sites, indicating that the isolates circulating in Korea may be pathogenic in several hosts. PMID:21368564

  19. Molecular characterization of Cryptosporidium isolates from humans in Equatorial Guinea.

    PubMed

    Blanco, María Alejandra; Iborra, Asunción; Vargas, Antonio; Nsie, Eugenia; Mbá, Luciano; Fuentes, Isabel

    2009-12-01

    The aim of the study was to perform a molecular characterization of clinical isolates of Cryptosporidium species from Equatorial Guinea. Standard laboratory methods were used to identify 35 cryptosporidiosis cases among 185 patients. PCR-RFLP successfully identified 34 Cryptosporidium species from these 35 cases, comprising C. parvum (52.9%), C. hominis (44.1%) and C. meleagridis (2.9%); over 90% of the species were isolated from HIV-positive patients. This is the first report of the molecular characterization of Cryptosporidium species isolated from humans in Equatorial Guinea and shows that zoonotic and anthroponotic transmission is present in this country.

  20. Optical Characterization of Molecular Contaminant Films

    NASA Technical Reports Server (NTRS)

    Visentine, James T.

    2007-01-01

    A semi-empirical method of optical characterization of thin contaminant films on surfaces of optical components has been conceived. The method was originally intended for application to films that become photochemically deposited on such optical components as science windows, lenses, prisms, thinfilm radiators, and glass solar-cell covers aboard spacecraft and satellites in orbit. The method should also be applicable, with suitable modifications, to thin optical films (whether deposited deliberately or formed as contaminants) on optical components used on Earth in the computer microchip laser communications and thin-film industries. The method is expected to satisfy the need for a means of understanding and predicting the reductions in spectral transmittance caused by contaminant films and the consequent deterioration of performances of sensitive optical systems. After further development, this method could become part of the basis of a method of designing optical systems to minimize or compensate for the deleterious effects of contaminant films. In the original outer-space application, these deleterious effects are especially pronounced because after photochemical deposition, the films become darkened by further exposure to solar vacuum ultraviolet (VUV) radiation. In this method, thin contaminant films are theoretically modeled as thin optical films, characterized by known or assumed values of thickness, index of refraction, and absorption coefficient, that form on the outer surfaces of the original antireflection coating on affected optical components. The assumed values are adjusted as needed to make actual spectral transmittance values approximate observed ones as closely as possible and to correlate these values with amounts of VUV radiation to which the optical components have been exposed. In an initial study, the method was applied in correlating measured changes in transmittance of high-purity fused silica photochemically coated with silicone films of

  1. Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update.

    PubMed

    Thomson, Michael M; Nájera, Rafael

    2005-01-01

    The picture of HIV-1 genetic diversity in the global pandemic continues to evolve. Identification of new variants, including circulating and unique recombinant forms, recognition of new outbreaks and of changes in established epidemics, and characterization of growing numbers of full-length genomes provide a view of high dynamism and increasing complexity. The pervasive role of recombination as a major driving force in the generation of diversity in the HIV-1 pandemic is becoming evident, and is particularly visible in areas in which different genetic forms meet, referred to as "geographic recombination hotspots". The importance of superinfection and its impact on HIV-1 diversification and propagation is surfacing, although restrictions to superinfection are also apparent. Genetic diversity within subtypes is increasing over time and new geographically localized lineages deriving from point introductions are being recognized. Characterization of such variants may be of relevance to vaccine development and may allow the detection of intrasubtype recombination and superinfection. Recent studies supporting the correlation of HIV-1 clades to immune responses and to drug resistance-associated mutations lend increasing relevance to the role of molecular epidemiology as an essential tool in combating the AIDS pandemic. However, knowledge on the global HIV-1 genetic diversity and its implications is still far from adequate and a major scaling up of efforts is needed. PMID:16425961

  2. Elucidating diversity of exosomes: biophysical and molecular characterization methods.

    PubMed

    Khatun, Zamila; Bhat, Anjali; Sharma, Shivani; Sharma, Aman

    2016-09-01

    Exosomes are cell-secreted nanovesicles present in biological fluids in normal and diseased conditions. Owing to their seminal role in cell-cell communication, emerging evidences suggest that exosomes are fundamental regulators of various diseases. Due to their potential usefulness in disease diagnosis, robust isolation and characterization of exosomes is critical in developing exosome-based assays. In the last few years, different exosome characterization methods, both biophysical and molecular, have been developed to characterize these tiny vesicles. Here, in this review we summarize: first, biophysical techniques based on spectroscopy (e.g., Raman spectroscopy, dynamic light scattering) and other principles, for example, scanning electron microscopy, atomic force microscopy; second, antibody-based molecular techniques including flow cytometry, transmission electron microscopy and third, nanotechnology-dependent exosome characterization methodologies. PMID:27488053

  3. Molecular characterization of two lipoxygenases from barley.

    PubMed

    van Mechelen, J R; Schuurink, R C; Smits, M; Graner, A; Douma, A C; Sedee, N J; Schmitt, N F; Valk, B E

    1999-04-01

    Two full-length lipoxygenase cDNA sequences (LoxB and LoxC) from barley (Hordeum distichum cv. L. Triumph) are described. The cDNAs share high homology with the barley LoxA cDNA. Southern blotting experiments indicate single copy numbers of the three lipoxygenase genes. RFLP mapping revealed the presence of single lipoxygenase loci. LoxA and LoxB map on chromosome 4 and LoxC on chromosome 7. Two isoenzymes, LOX1 and LOX2, have been purified previously from germinating barley and characterized. LOX1 is encoded by LoxA, while LOX2 is encoded by LoxC. The product related to the third cDNA (loxB) has not been identified so far, suggesting a low protein abundance for the corresponding isoform in barley. Transcripts corresponding with these LOX genes are predominantly observed in grain and in seedling, whereas transcripts corresponding to LoxB and LoxC are also observed in mature vegetative tissue. No lipoxygenase mRNA could be detected in aleurone layer of germinating grain. No significant differences in lipoxygenase mRNA levels were observed in developing grains grown under dormant or non-dormant conditions, suggesting that LOX is not directly involved in induction of grain dormancy.

  4. From puffs to global Ca2+ signals: how molecular properties shape global signals.

    PubMed

    Skupin, Alexander; Falcke, Martin

    2009-09-01

    The universality of Ca(2+) as second messenger in living cells is achieved by a rich spectrum of spatiotemporal cellular concentration dynamics. Ca(2+) release from internal storage compartments plays a key role in shaping cytosolic Ca(2+) signals. Deciphering this signaling mechanism is essential for a deeper understanding of its physiological function and general concepts of cell signaling. Here, we review recent experimental findings demonstrating the stochasticity of Ca(2+) oscillations and its relevance for modeling Ca(2+) dynamics. The stochasticity arises by the hierarchical signal structure that carries molecular fluctuations of single channels onto the level of the cell leading to a stochastic medium as theoretically predicted. The result contradicts the current opinion of Ca(2+) being a cellular oscillator. We demonstrate that cells use array enhanced coherence resonance to form rather regular spiking signals and that the "oscillations" carry information despite the involved stochasticity. The knowledge on the underlying mechanism also allows for determination of intrinsic properties from global observations. In the second part of the paper, we briefly survey different modeling approaches with regard to the experimental results. We focus on the dependence of the standard deviation on the mean period of the oscillations. It shows that limit cycle oscillations cannot describe the experimental data and that generic models have to include the spatial aspects of Ca(2+) signaling.

  5. Molecular characterization of Ethiopian indigenous goat populations.

    PubMed

    Hassen, Halima; Lababidi, Samer; Rischkowsky, Barbara; Baum, Michael; Tibbo, Markos

    2012-08-01

    Six Ethiopian indigenous goat populations viz. Gumuz, Agew, Begia-Medir, Bati, Abergelle, and Central Abergelle were genotyped for 15 microsatellite markers recommended by Food and Agriculture Organization of the United Nations and International Society for Animal Genetics. A total of 158 individual goats were tested to assess genetic variations within and between the goat populations in the Amhara Region of Ethiopia. The markers revealed 100% polymorphism across six goat populations indicating the presence of genetic diversity, which is an important variable to measure genetic variability within and between populations. The mean observed and expected heterozygosity values ranged from 0.56 (Central Abergelle) to 0.68 (Bati) and 0.59 (Abergelle) to 0.69 (Agew goat), respectively. The lowest genetic distance was observed between Begia-Medir and Central Abergelle (0.039), and the largest distances between Agew and Abergelle (0.140) and Gumuz and Abergelle (0.169). Neighbor-joining and the unweighted pair group method with arithmetic mean methods with bootstrap value of 1,000 was used which grouped the six goat populations into two major groups viz. the Abergelle goat cluster as one group and the Agew, Gumuz, Bati, Begia-Medir, and Central Abergelle goats as the second group. In our study, the obtained higher total variation within the goat populations (95%) confirms a close relatedness of the studied goat ecotypes, which might have happened due to the existence of uncontrolled animal breeding strategies resulting from uncontrolled movement of animals through various market routes and agricultural extension systems. The study contributed to the genetic characterization of Ethiopian indigenous goat populations and demonstrated the usefulness of the 15 microsatellite makers for biodiversity studies in goats.

  6. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

    PubMed

    Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V; Sanchez, Laura M; Garg, Neha; Peng, Yao; Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; Boya P, Cristopher A; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J N; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M C; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard Ø; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

    2016-08-01

    The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

  7. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

    PubMed

    Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V; Sanchez, Laura M; Garg, Neha; Peng, Yao; Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; Boya P, Cristopher A; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J N; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M C; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard Ø; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

    2016-08-01

    The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data. PMID:27504778

  8. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    PubMed

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions. PMID:26908260

  9. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach

    PubMed Central

    Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P.

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions. PMID:26908260

  10. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    PubMed

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  11. Selenium Characterization in the Global Rice Supply Chain

    SciTech Connect

    Williams, Paul N.; Lombi, Enzo; Sun, Guo-Xin; Scheckel, Kirk; Zhu, Yong-Guan; Feng, Xinbin; Zhu, Jianming; Carey, Anne-Marie; Adomako, Eureka; Lawgali, Youseff; Deacon, Claire; Meharg, Andrew A.

    2009-08-13

    For up to 1 billion people worldwide, insufficient dietary intake of selenium (Se) is a serious health constraint. Cereals are the dominant Se source for those on low protein diets, as typified by the global malnourished population. With crop Se content constrained largely by underlying geology, regional soil Se variations are often mirrored by their locally grown staples. Despite this, the Se concentrations of much of the world's rice, the mainstay of so many, is poorly characterized, for both total Se content and Se speciation. In this study, 1092 samples of market sourced polished rice were obtained. The sampled rice encompassed dominant rice producing and exporting countries. Rice from the U.S. and India were found to be the most enriched, while mean average levels were lowest in Egyptian rice: {approx}32-fold less than their North American equivalents. By weighting country averages by contribution to either global production or export, modeled baseline values for both were produced. Based on a daily rice consumption of 300 g day{sup -1}, around 75% of the grains from the production and export pools would fail to provide 70% of daily recommended Se intakes. Furthermore, Se localization and speciation characterization using X-ray fluorescence ({mu}-XRF) and X-ray absorption near edge structure ({mu}-XANES) techniques were investigated in a Se-rich sample. The results revealed that the large majority of Se in the endosperm was present in organic forms.

  12. Cytological and molecular characterization of three gametoclones of citrus clementina

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidizat...

  13. Complete characterization of molecular vibration using frequency resolved gating.

    PubMed

    Xu, Xiaoji G; Konorov, Stanislav O; Zhdanovich, Sergey; Hepburn, John W; Milner, Valery

    2007-03-01

    The authors propose a new approach to vibration spectroscopy based on the coherent anti-Stokes Raman scattering of broadband ultrashort laser pulses. The proposed method reveals both the amplitude and the phase of molecular vibrations by utilizing the cross-correlation frequency resolved optical gating (XFROG) technique. The spectrum of the anti-Stokes pulse is measured as a function of the time delay between the laser-induced molecular vibrations and a well characterized broadband femtosecond probe pulse. The iterative XFROG algorithm provides a simultaneous complete characterization of molecular vibrations both in frequency and time domains with high resolution. They demonstrate experimentally the feasibility of the proposed method and show one of its potential applications in disentangling the time behavior of a mixture of vibrationally excited molecules. The technique of femtosecond pulse shaping is used for further improvement of accuracy and stability against noise.

  14. Tessera terrain on Venus: Global characterization from Magellan data

    NASA Technical Reports Server (NTRS)

    Ivanov, Mikhail; Head, James W.

    1993-01-01

    Tessera terrain is characterized by relatively high elevations and complex tectonic patterns; analysis of Venera 15/16 data showed that large (up to thousands of km across) and small (up to hundreds of km across) occurrences of tesserae are widespread and non-randomly distributed and make up about 10-15 percent of the surface of Venus north of approximately 30 deg N. In a previous analysis, we used the Magellan Cycle 1 and 2 data to map the global distribution of tesserae on the basis of the following: (1) complex deformational patterns (two or more trends); (2) relatively high radar backscatter; and (3) relatively high elevation. Here we report on the quantitative aspects of tesserae areal, size, and shape distribution and on the characteristics and distribution of tesserae boundaries. Experiments on volcanic flooding of tessera and implications for tessera presence beneath the plains and analysis of the distribution of impact craters on tesserae and the plains are reported elsewhere.

  15. Cheese Classification, Characterization, and Categorization: A Global Perspective.

    PubMed

    Almena-Aliste, Montserrat; Mietton, Bernard

    2014-02-01

    Cheese is one of the most fascinating, complex, and diverse foods enjoyed today. Three elements constitute the cheese ecosystem: ripening agents, consisting of enzymes and microorganisms; the composition of the fresh cheese; and the environmental conditions during aging. These factors determine and define not only the sensory quality of the final cheese product but also the vast diversity of cheeses produced worldwide. How we define and categorize cheese is a complicated matter. There are various approaches to cheese classification, and a global approach for classification and characterization is needed. We review current cheese classification schemes and the limitations inherent in each of the schemes described. While some classification schemes are based on microbiological criteria, others rely on descriptions of the technologies used for cheese production. The goal of this review is to present an overview of comprehensive and practical integrative classification models in order to better describe cheese diversity and the fundamental differences within cheeses, as well as to connect fundamental technological, microbiological, chemical, and sensory characteristics to contribute to an overall characterization of the main families of cheese, including the expanding world of American artisanal cheeses. PMID:26082106

  16. Cheese Classification, Characterization, and Categorization: A Global Perspective.

    PubMed

    Almena-Aliste, Montserrat; Mietton, Bernard

    2014-02-01

    Cheese is one of the most fascinating, complex, and diverse foods enjoyed today. Three elements constitute the cheese ecosystem: ripening agents, consisting of enzymes and microorganisms; the composition of the fresh cheese; and the environmental conditions during aging. These factors determine and define not only the sensory quality of the final cheese product but also the vast diversity of cheeses produced worldwide. How we define and categorize cheese is a complicated matter. There are various approaches to cheese classification, and a global approach for classification and characterization is needed. We review current cheese classification schemes and the limitations inherent in each of the schemes described. While some classification schemes are based on microbiological criteria, others rely on descriptions of the technologies used for cheese production. The goal of this review is to present an overview of comprehensive and practical integrative classification models in order to better describe cheese diversity and the fundamental differences within cheeses, as well as to connect fundamental technological, microbiological, chemical, and sensory characteristics to contribute to an overall characterization of the main families of cheese, including the expanding world of American artisanal cheeses.

  17. Characterization of Capsicum species using anatomical and molecular data.

    PubMed

    Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

    2013-02-28

    Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

  18. Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses

    PubMed Central

    Chen, Haifeng; Hu, Yuan

    2016-01-01

    Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses. PMID:27335620

  19. Molecular Characterization of Actinide Oxocations from Protactinium to Plutonium

    SciTech Connect

    Den Auwer, C.; Guilbaud, P.; Guillaumont, D.; Moisy, P.; Hennig, C.; Scheinost, A.; Conradson, S. D.

    2007-02-02

    This presentation addresses the structural characterization by EXAFS of actinide cations at oxidation states (V) and (VI) as one walks across the periodic table from Z = 91 (protactinium) to Z = 94 (plutonium). A structural comparison between Pa, U, Np and Pu oxocations in aqueous solution at formal oxidation states (V) and (VI) is carried out. These results are corroborated by quantum chemical and molecular dynamics calculations.

  20. Molecular systematics and global phylogeography of angel sharks (genus Squatina).

    PubMed

    Stelbrink, Björn; von Rintelen, Thomas; Cliff, Geremy; Kriwet, Jürgen

    2010-02-01

    Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events. PMID:19647086

  1. Recent discoveries in molecular characterization of acute myeloid leukemia.

    PubMed

    Khasawneh, Mohamad K; Abdel-Wahab, Omar

    2014-06-01

    Acute myeloid leukemia (AML) is a clinically heterogeneous disease, yet it is one of the most molecularly well-characterized cancers. Risk stratification of patients currently involves determination of the presence of cytogenetic abnormalities in combination with molecular genetic testing in a few genes. Several new recurrent genetic molecular abnormalities have recently been identified, including TET2, ASXL1, IDH1, IDH2, DNMT3A, and PHF6. Mutational analyses have identified that patients with DNMT3A or NPM1 mutations or MLL translocation have improved overall survival with high-dose chemotherapy. Mutational profiling can refine prognostication, particularly for patients in the intermediate-risk group or with a normal karyotype. CD25 expression status improves prognostic risk classification in AML independent of established biomarkers. Biomarkers such as 2- hydroxyglutarate in IDH1/2-mutant AML patients predict patient responses and minimal residual disease. These recent discoveries are being incorporated into our existing molecular risk stratification as well as the exploration of new therapeutics directed to these molecular targets.

  2. Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment

    PubMed Central

    Wang, Haixing; Qian, Wei-Jun; Chin, Mark H.; Petyuk, Vladislav A.; Barry, Richard C.; Liu, Tao; Gritsenko, Marina A.; Mottaz, Heather M.; Moore, Ronald J.; Camp, David G.; Khan, Arshad H.; Smith, Desmond J.; Smith, Richard D.

    2007-01-01

    Given the growing interest in applying genomic and proteomic approaches for studying the mammalian brain using mouse models, we hereby present a global proteomic approach for analyzing brain tissue and for the first time a comprehensive characterization of the whole mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 non-redundant proteins (∼34% of the predicted mouse proteome). 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models. The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases. PMID:16457602

  3. Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma

    PubMed Central

    Linehan, W. Marston; Spellman, Paul T.; Ricketts, Christopher J.; Creighton, Chad J.; Fei, Suzanne S.; Davis, Caleb; Wheeler, David A.; Murray, Bradley A.; Schmidt, Laura; Vocke, Cathy D.; Peto, Myron; Al Mamun, Abu Amar M.; Shinbrot, Eve; Sethi, Anurag; Brooks, Samira; Rathmell, W. Kimryn; Brooks, Angela N.; Hoadley, Katherine A.; Robertson, A. Gordon; Brooks, Denise; Bowlby, Reanne; Sadeghi, Sara; Shen, Hui; Weisenberger, Daniel J.; Bootwalla, Moiz; Baylin, Stephen B.; Laird, Peter W.; Cherniack, Andrew D.; Saksena, Gordon; Haake, Scott; Li, Jun; Liang, Han; Lu, Yiling; Mills, Gordon B.; Akbani, Rehan; Leiserson, Mark D.M.; Raphael, Benjamin J.; Anur, Pavana; Bottaro, Donald; Albiges, Laurence; Barnabas, Nandita; Choueiri, Toni K.; Czerniak, Bogdan; Godwin, Andrew K.; Hakimi, A. Ari; Ho, Thai; Hsieh, James; Ittmann, Michael; Kim, William Y.; Krishnan, Bhavani; Merino, Maria J.; Mills Shaw, Kenna R.; Reuter, Victor E.; Reznik, Ed; Shelley, Carl Simon; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Tickoo, Satish; Burnett, Kenneth; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph D.; Penny, Robert J.; Shelton, Candace; Shelton, W. Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Avedon, Melissa T.; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Santos, Tracie; Wise, Lisa; Zmuda, Erik; Demchok, John A.; Felau, Ina; Hutter, Carolyn M.; Sheth, Margi; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Ayala, Brenda; Baboud, Julien; Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Ally, Adrian; Balasundaram, Miruna; Balu, Saianand; Beroukhim, Rameen; Bodenheimer, Tom; Buhay, Christian; Butterfield, Yaron S.N.; Carlsen, Rebecca; Carter, Scott L.; Chao, Hsu; Chuah, Eric; Clarke, Amanda; Covington, Kyle R.; Dahdouli, Mahmoud; Dewal, Ninad; Dhalla, Noreen; Doddapaneni, HarshaVardhan; Drummond, Jennifer; Gabriel, Stacey B.; Gibbs, Richard A.; Guin, Ranabir; Hale, Walker; Hawes, Alicia; Hayes, D. Neil; Holt, Robert A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Steven J.M.; Jones, Corbin D.; Kalra, Divya; Kovar, Christie; Lewis, Lora; Li, Jie; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Meng, Shaowu; Meyerson, Matthew; Mieczkowski, Piotr A.; Moore, Richard A.; Morton, Donna; Mose, Lisle E.; Mungall, Andrew J.; Muzny, Donna; Parker, Joel S.; Perou, Charles M.; Roach, Jeffrey; Schein, Jacqueline E.; Schumacher, Steven E.; Shi, Yan; Simons, Janae V.; Sipahimalani, Payal; Skelly, Tara; Soloway, Matthew G.; Sougnez, Carrie; Tam, Angela; Tan, Donghui; Thiessen, Nina; Veluvolu, Umadevi; Wang, Min; Wilkerson, Matthew D.; Wong, Tina; Wu, Junyuan; Xi, Liu; Zhou, Jane; Bedford, Jason; Chen, Fengju; Fu, Yao; Gerstein, Mark; Haussler, David; Kasaian, Katayoon; Lai, Phillip; Ling, Shiyun; Radenbaugh, Amie; Van Den Berg, David; Weinstein, John N.; Zhu, Jingchun; Albert, Monique; Alexopoulou, Iakovina; Andersen, Jeremiah J; Auman, J. Todd; Bartlett, John; Bastacky, Sheldon; Bergsten, Julie; Blute, Michael L.; Boice, Lori; Bollag, Roni J.; Boyd, Jeff; Castle, Erik; Chen, Ying-Bei; Cheville, John C.; Curley, Erin; Davies, Benjamin; DeVolk, April; Dhir, Rajiv; Dike, Laura; Eckman, John; Engel, Jay; Harr, Jodi; Hrebinko, Ronald; Huang, Mei; Huelsenbeck-Dill, Lori; Iacocca, Mary; Jacobs, Bruce; Lobis, Michael; Maranchie, Jodi K.; McMeekin, Scott; Myers, Jerome; Nelson, Joel; Parfitt, Jeremy; Parwani, Anil; Petrelli, Nicholas; Rabeno, Brenda; Roy, Somak; Salner, Andrew L.; Slaton, Joel; Stanton, Melissa; Thompson, R. Houston; Thorne, Leigh; Tucker, Kelinda; Weinberger, Paul M.; Winemiller, Cythnia; Zach, Leigh Anne; Zuna, Rosemary

    2016-01-01

    Background Papillary renal cell carcinoma, accounting for 15% of renal cell carcinoma, is a heterogeneous disease consisting of different types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal cell carcinoma; no effective forms of therapy for advanced disease exist. Methods We performed comprehensive molecular characterization utilizing whole-exome sequencing, copy number, mRNA, microRNA, methylation and proteomic analyses of 161 primary papillary renal cell carcinomas. Results Type 1 and Type 2 papillary renal cell carcinomas were found to be different types of renal cancer characterized by specific genetic alterations, with Type 2 further classified into three individual subgroups based on molecular differences that influenced patient survival. MET alterations were associated with Type 1 tumors, whereas Type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-ARE pathway. A CpG island methylator phenotype (CIMP) was found in a distinct subset of Type 2 papillary renal cell carcinoma characterized by poor survival and mutation of the fumarate hydratase (FH) gene. Conclusions Type 1 and Type 2 papillary renal cell carcinomas are clinically and biologically distinct. Alterations in the MET pathway are associated with Type 1 and activation of the NRF2-ARE pathway with Type 2; CDKN2A loss and CIMP in Type 2 convey a poor prognosis. Furthermore, Type 2 papillary renal cell carcinoma consists of at least 3 subtypes based upon molecular and phenotypic features. PMID:26536169

  4. A two-locus molecular characterization of Paramecium calkinsi.

    PubMed

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

    2012-03-01

    Paramecium calkinsi (Ciliophora, Protozoa) is a euryhaline species which was first identified in freshwater habitats, but subsequently several strains were also collected from brackish water. It is characterized by clockwise spiral swimming movement and the general morphology of the "bursaria type." The present paper is the first molecular characterization of P. calkinsi strains recently collected in distant regions in Russia using ITS1-5.8S- ITS2-5'LSU rDNA (1100bp) and COI (620bp) mtDNA sequenced gene fragments. For comparison, our molecular analysis includes P. bursaria, exhibiting a similar "bursaria morphotype" as well as species representing the "aurelia type," i.e., P. caudatum, P. multimicronucleatum, P. jenningsi, and P. schewiakoffi, and some species of the P. aurelia species complex (P. primaurelia, P. tetraurelia, P. sexaurelia, and P. tredecaurelia). We also use data from GenBank concerning other species in the genus Paramecium and Tetrahymena (which used as an outgroup). The division of the genus Paramecium into four subgenera (proposed by Fokin et al. 2004) is clearly presented by the trees. There is a clear separation between P. calkinsi strains collected from different regions (races). Consequently, given the molecular distances between them, it seems that these races may represent different syngens within the species.

  5. MoCha: Molecular Characterization of Unknown Pathways.

    PubMed

    Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

    2016-04-01

    Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

  6. MoCha: Molecular Characterization of Unknown Pathways.

    PubMed

    Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

    2016-04-01

    Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license. PMID:26950055

  7. Molecular Characterization of First Human Bartonella Strain Isolated in Italy

    PubMed Central

    Ciervo, Alessandra; Petrucca, Andrea; Ciarrocchi, Simonetta; Pinto, Antonella; Bonazzi, Lucio; Fabio, Anna; Farnetti, Enrico; Chomel, Bruno B.; Ciceroni, Lorenzo

    2001-01-01

    The aim of this study was to characterize a Bartonella strain (BA-1) isolated from a blood culture of an Italian, human immunodeficiency virus-positive patient with bacillary angiomatosis. We analyzed the isolate using molecular biology methods such as whole-cell fatty acid analysis, PCR-restriction fragment length polymorphism analysis, type-specific 16S rRNA PCRs, sequence analysis of the 16S rRNA, pulsed-field gel electrophoresis, and arbitrarily primed PCR. The BA-1 isolate turned out to be a Bartonella quintana strain, similar but not identical to B. quintana Oklahoma, which was used as a control strain. PMID:11724882

  8. SEDPHAT – a platform for global ITC analysis and global multi-method analysis of molecular interactions

    PubMed Central

    Zhao, Huaying; Piszczek, Grzegorz; Schuck, Peter

    2014-01-01

    Isothermal titration calorimetry experiments can provide significantly more detailed information about molecular interactions when combined in global analysis. For example, global analysis can improve the precision of binding affinity and enthalpy, and of possible linkage parameters, even for simple bimolecular interactions, and greatly facilitate the study of multi-site and multi-component systems with competition or cooperativity. A pre-requisite for global analysis is the departure from the traditional binding model, including an ‘n’-value describing unphysical, non-integral numbers of sites. Instead, concentration correction factors can be introduced to account for either errors in the concentration determination or for the presence of inactive fractions of material. SEDPHAT is a computer program that embeds these ideas and provides a graphical user interface for the seamless combination of biophysical experiments to be globally modeled with a large number of different binding models. It offers statistical tools for the rigorous determination of parameter errors, correlations, as well as advanced statistical functions for global ITC (gITC) and global multi-method analysis (GMMA). SEDPHAT will also take full advantage of error bars of individual titration data points determined with the unbiased integration software NITPIC. The present communication reviews principles and strategies of global analysis for ITC and its extension to GMMA in SEDPHAT. We will also introduce a new graphical tool for aiding experimental design by surveying the concentration space and generating simulated data sets, which can be subsequently statistically examined for their information content. This procedure can replace the ‘c’-value as an experimental design parameter, which ceases to be helpful for multi-site systems and in the context of gITC. PMID:25477226

  9. SEDPHAT--a platform for global ITC analysis and global multi-method analysis of molecular interactions.

    PubMed

    Zhao, Huaying; Piszczek, Grzegorz; Schuck, Peter

    2015-04-01

    Isothermal titration calorimetry experiments can provide significantly more detailed information about molecular interactions when combined in global analysis. For example, global analysis can improve the precision of binding affinity and enthalpy, and of possible linkage parameters, even for simple bimolecular interactions, and greatly facilitate the study of multi-site and multi-component systems with competition or cooperativity. A pre-requisite for global analysis is the departure from the traditional binding model, including an 'n'-value describing unphysical, non-integral numbers of sites. Instead, concentration correction factors can be introduced to account for either errors in the concentration determination or for the presence of inactive fractions of material. SEDPHAT is a computer program that embeds these ideas and provides a graphical user interface for the seamless combination of biophysical experiments to be globally modeled with a large number of different binding models. It offers statistical tools for the rigorous determination of parameter errors, correlations, as well as advanced statistical functions for global ITC (gITC) and global multi-method analysis (GMMA). SEDPHAT will also take full advantage of error bars of individual titration data points determined with the unbiased integration software NITPIC. The present communication reviews principles and strategies of global analysis for ITC and its extension to GMMA in SEDPHAT. We will also introduce a new graphical tool for aiding experimental design by surveying the concentration space and generating simulated data sets, which can be subsequently statistically examined for their information content. This procedure can replace the 'c'-value as an experimental design parameter, which ceases to be helpful for multi-site systems and in the context of gITC.

  10. Walnut allergens: molecular characterization, detection and clinical relevance.

    PubMed

    Costa, J; Carrapatoso, I; Oliveira, M B P P; Mafra, I

    2014-03-01

    Food-induced allergies have been regarded as an emergent problem of public health. Classified as important allergenic ingredients, the presence of walnut and other nuts as hidden allergens in processed foods constitutes a risk for sensitized individuals, being a real problem of allergen management. Attending to the increasing importance dedicated to walnut allergy, this review intends to provide the relevant and up-to-date information on main issues such as the prevalence of walnut allergy, the clinical threshold levels, the molecular characterization of walnut allergens and their clinical relevance, as well as the methodologies for walnut allergen detection in foods. As the walnut used in human diet comes from Juglans regia and Juglans nigra, the molecular characterization of the allergens from both species included in the prolamins (Jug r 1, Jug n 1 and Jug r 3), cupins (Jug r 2, Jug n 2 and Jug r 4) and profilins (Jug r 5), together with respective clinical relevance, were compiled in this review. The most recent progresses on walnut allergen detection techniques (protein- and DNA-based) are described and critically compared, including the emergent multitarget approaches.

  11. Molecular characterization of Ephedra species found in Pakistan.

    PubMed

    Ghafoor, S; Shah, M M; Ahmad, H; Swati, Z A; Shah, S H; Pervez, A; Farooq, U

    2007-12-11

    Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency.

  12. Bovine Ephemeral Fever in Iran: Diagnosis, Isolation and Molecular Characterization

    PubMed Central

    Bakhshesh, Mehran; Abdollahi, Darab

    2015-01-01

    Background: Bovine ephemeral fever (BEFV) is an arthropod-borne disease of cattle and water buffaloes. BEFV occurs seasonally in tropical, subtropical and temperate regions of Africa, Asia and Australia. It has been known for the past decades in Iran based on clinical signs but lack of an accurate diagnosis has made the real feature of disease obscured. This is the first scientific report on isolation and identification of the agent in which molecular diagnosis of BEFV was also set up with high sensitivity and specificity. Methods: The viral agent was successfully isolated through serial passages in brain of suckling mice and cell culture. In addition, the circulating virus during the autumn 2012 in Iran was molecularly characterized based on partial G gene. Results: Alignment of 3 virus sequences from different parts of Iran revealed that they are identical suggesting that the circulating viruses were most likely the same in this period. Phylogenetic analysis of the Iranian sequences with 17 sequences in the GenBank from the world showed that it is identical to the virus circulated in Turkey during the same period suggesting that the virus was circulated in a large geographic region. Conclusion: These results offer primary information about BEFV in Iran. To better understanding the epidemiology of the virus, further studies based on seroepidemiology, molecular epidemiology, entomology and meteorology together with finding the model of animal transportation in the region are necessary. PMID:26623431

  13. Molecular characterization of Ehrlichia canis infecting dogs, Buenos Aires.

    PubMed

    Cicuttin, Gabriel L; De Salvo, María N; Gury Dohmen, Federico E

    2016-07-01

    Canine monocytic ehrlichiosis (CME) is a worldwide potentially fatal tick-borne rickettsial disease of dogs caused by Ehrlichia canis and transmitted by Rhipicephalus sanguineus sensu lato. CME diagnosis includes indirect (serology) and direct (e.g. blood smears and PCR) methods. PCR is more sensitive and specific than direct microscopic examination and positive PCR results confirm infection, whereas positive serologic test results only confirm exposure. The aim of the present study was to perform a molecular characterization of E. canis from canine samples of the Metropolitan Area of Buenos Aires. We studied 223 blood samples of dogs submitted to our institute for CME diagnoses. The samples were initially screened for Anaplasmataceae family by PCR, resulting in 30 positive dogs (13.4%). Subsequently, positive DNAs were analyzed by nested PCR 16S rRNA specific for E. canis or Anaplasma platys, resulting in 15 (6.7%) and 16 (7.2%) positive dogs, respectively. For molecular characterization, samples positive for E. canis were subjected to amplification of a fragment of the dsb and p28 genes. The nucleotide sequences obtained for the dsb fragment resulted in 100% identity with others E. canis found in dogs from different regions of worldwide. The nucleotide sequences obtained for p28 gene resulted in 100% of identity with each other and closely with E. canis str. Jaboticabal (Brazil). Identity with others sequences of E. canis ranged from 76.9 to 79.7%. The occurrence of canine cases molecularly confirmed in Metropolitan Area of Buenos Aires highlights the need for more studies in order to understand epidemiological factors associated with CME, especially the disease transmission dynamic in South America given the existence of two lineages of R. sanguineus sensu lato with different vectorial capacity for transmission of E. canis. PMID:27236582

  14. Molecular dynamics modeling and characterization of graphene/polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Rahman, Rezwanur

    The current work focuses on the characterization of graphene based nanocomposites using molecular dynamic simulation and multiscale modeling approaches. Both graphene-epoxy and graphene-cellulose nanocomposites were considered in this study. A hierarchical multiscale modeling approach has been proposed using peridynamics and molecular dynamics simulation. Firstly, the mechanical properties of crosslinked graphene/epoxy (G-Ep) nanocomposites were investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. The influence of graphene's weight concentration, aspect ratio and dispersion on stress-strain response and elastic properties were studied. The results show significant improvement in Young's modulus and shear modulus for the G-Ep system in comparison to the neat epoxy resin. It appears that the RDF, molecular energy and aspect ratios are influenced by both graphene concentrations and aspect ratios. The graphene concentrations in the range of 1-3% are seen to improve Young's modulus and shorter graphenes are observed to be more effective than larger ones. In addition, the dispersed graphene system is more promising in enhancing in-plane elastic modulus than the agglomerated graphene system. The cohesive and pullout forces versus displacements data were plotted under normal and shear modes in order to characterize interfacial properties. The cohesive force is significantly improved by attaching the graphene with a chemical bond at the graphene-epoxy interface. In the second part of the work, cellulose was considered to study the mechanical properties of graphene-cellulose bionanocomposite. Similar to graphene-epoxy systems, the effect of graphene dispersion and agglomeration were studied in the stress-strain plots of graphene-cellulose system. A pcff forcefield was used to define intermolecular and intramolecular interactions. The effect of graphene's aspect ratio and weight concentration on the structural property of each unitcell was

  15. Global foot-and-mouth disease research update and gap analysis: 7 - pathogenesis and molecular biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2014, the GFRA (Global Foot-and-mouth disease Research Alliance) conducted a gap analysis of FMD (Foot-and-Mouth Disease) research. This work has been updated and reported in a series of papers, in this article we report findings in the fields of 1) pathogenesis and 2) molecular biology. The arti...

  16. Molecular characterization of lactobacilli isolated from fermented idli batter

    PubMed Central

    Agaliya, Perumal Jayaprabha; Jeevaratnam, Kadirvelu

    2013-01-01

    Lactic acid bacteria are non pathogenic organism widely distributed in nature typically involved in a large number of spontaneous food fermentation. The purpose of this study was to characterize the bacteriocinogenic lactobacilli from fermented idli batter which can find application in biopreservation and biomedicine. Eight most promising lactobacilli were chosen from twenty two isolates based on their spectrum of activity against other lactic acid bacteria and pathogens. The eight lactobacilli were characterized based on the various classical phenotypic tests, physiological tests and biochemical tests including various carbohydrate utilization profiles. All isolates were homo fermentative, catalase, and gelatin negative. Molecular characterization was performed by RAPD, 16S rRNA analysis, 16S ARDRA, and Multiplex PCR for species identification. RAPD was carried out using the primer R2 and M13. Five different clusters were obtained based on RAPD indicating strain level variation. 16S rRNA analysis showed 99 to 100% homology towards Lactobacillus plantarum. The restriction digestion pattern was similar for all the isolates with the restriction enzyme AluI. The subspecies were identified by performing Multiplex PCR using species specific primer. Among the five clusters, three clusters were clearly identified as Lactobacillus plantarum subsp. plantarum, Lactobacillus pentosus, and Lactobacillus plantarum subsp. argentoratensis. PMID:24688512

  17. Photoelectrical characterization of a new low molecular weight compound

    NASA Astrophysics Data System (ADS)

    Siderov, V.; Dobrikov, G. H.; Zhivkov, I.; Dobrikov, G. M.; Georgiev, Y.; Yordanov, R.; Honova, J.; Weiter, M.

    2014-12-01

    Photoelectrical characterization of a newly synthesized low molecular weight compound was carried out. 1,8-naphtalimide (chemical formula C32H34N4O5S) was originally synthesized and analyzed by NMR spectroscopy. Thin films were deposited in vacuum on commercially pre-patterned ITO covered glass substrates and the samples were prepared in clean room environment. The films deposited were characterized by SEM. Photoelectrical characteristics of the samples prepared were estimated by dark current-voltage measurement, spectral dependence of the photoconductivity and measurement under exposure with light, produced by solar simulator. Finally electroluminescence measurements were performed. It was found that the samples exhibit diode behaviour. The low values characterizing photovoltaic parameters obtained could be connected with the relative higher series resistance (Rseries). The predominant influence of Rseries is assumed as the relative high photoluminescence, measured from solution should be related to a relatively strong charge carrier photogeneration. This result is supported by electroluminescent measurement. Another reason for the low values of the photovoltaic parameters measured could be the non-optimized film thickness leading to a non-optimal light absorption and increased charge carrier recombination. The assumption for the predominant influence of Rseries is supported by the electroluminescent measurements.

  18. Molecular characterization of lactobacilli isolated from fermented idli batter.

    PubMed

    Agaliya, Perumal Jayaprabha; Jeevaratnam, Kadirvelu

    2013-12-01

    Lactic acid bacteria are non pathogenic organism widely distributed in nature typically involved in a large number of spontaneous food fermentation. The purpose of this study was to characterize the bacteriocinogenic lactobacilli from fermented idli batter which can find application in biopreservation and biomedicine. Eight most promising lactobacilli were chosen from twenty two isolates based on their spectrum of activity against other lactic acid bacteria and pathogens. The eight lactobacilli were characterized based on the various classical phenotypic tests, physiological tests and biochemical tests including various carbohydrate utilization profiles. All isolates were homo fermentative, catalase, and gelatin negative. Molecular characterization was performed by RAPD, 16S rRNA analysis, 16S ARDRA, and Multiplex PCR for species identification. RAPD was carried out using the primer R2 and M13. Five different clusters were obtained based on RAPD indicating strain level variation. 16S rRNA analysis showed 99 to 100% homology towards Lactobacillus plantarum. The restriction digestion pattern was similar for all the isolates with the restriction enzyme AluI. The subspecies were identified by performing Multiplex PCR using species specific primer. Among the five clusters, three clusters were clearly identified as Lactobacillus plantarum subsp. plantarum, Lactobacillus pentosus, and Lactobacillus plantarum subsp. argentoratensis.

  19. Molecular characterization of lactobacilli isolated from fermented idli batter.

    PubMed

    Agaliya, Perumal Jayaprabha; Jeevaratnam, Kadirvelu

    2013-12-01

    Lactic acid bacteria are non pathogenic organism widely distributed in nature typically involved in a large number of spontaneous food fermentation. The purpose of this study was to characterize the bacteriocinogenic lactobacilli from fermented idli batter which can find application in biopreservation and biomedicine. Eight most promising lactobacilli were chosen from twenty two isolates based on their spectrum of activity against other lactic acid bacteria and pathogens. The eight lactobacilli were characterized based on the various classical phenotypic tests, physiological tests and biochemical tests including various carbohydrate utilization profiles. All isolates were homo fermentative, catalase, and gelatin negative. Molecular characterization was performed by RAPD, 16S rRNA analysis, 16S ARDRA, and Multiplex PCR for species identification. RAPD was carried out using the primer R2 and M13. Five different clusters were obtained based on RAPD indicating strain level variation. 16S rRNA analysis showed 99 to 100% homology towards Lactobacillus plantarum. The restriction digestion pattern was similar for all the isolates with the restriction enzyme AluI. The subspecies were identified by performing Multiplex PCR using species specific primer. Among the five clusters, three clusters were clearly identified as Lactobacillus plantarum subsp. plantarum, Lactobacillus pentosus, and Lactobacillus plantarum subsp. argentoratensis. PMID:24688512

  20. Molecular characterization of norovirus GII strains identified in Albania.

    PubMed

    Donia, Domenica; Cenko, Fabian; Divizia, Maurizio

    2013-04-01

    Noroviruses (NoVs) are considered as the leading cause of diarrheal diseases in all groups of age. In the last decade the number of NoV outbreaks worldwide is increasing. Data published by the systems of NoV surveillance show the GII.4 strain as the human predominant genotype circulating worldwide and new genetic variants of GII.4 were associated with epidemic events. In Albania the economy transformation has damaged significantly the environment and a large circulation of enteric viruses was reported in the past with the presence of NoV among the genotyped strains. This study aimed to characterize, by molecular analysis, the NoV GII strains detected in Albania during two time periods: in 2010 from the outbreak occurred in Ballsh and in 2002-2003 from sporadic cases of diarrhoea. A total of 21 Nov GII strains were characterized. The NoV GII.4 was genotyped more frequently and it was related closely to the pandemic variants recorded in GenBank. During 2002-2003, six NoV GII recombinant strains have been characterized.

  1. Integration of molecular pathology, epidemiology and social science for global precision medicine.

    PubMed

    Nishi, Akihiro; Milner, Danny A; Giovannucci, Edward L; Nishihara, Reiko; Tan, Andy S; Kawachi, Ichiro; Ogino, Shuji

    2016-01-01

    The precision medicine concept and the unique disease principle imply that each patient has unique pathogenic processes resulting from heterogeneous cellular genetic and epigenetic alterations and interactions between cells (including immune cells) and exposures, including dietary, environmental, microbial and lifestyle factors. As a core method field in population health science and medicine, epidemiology is a growing scientific discipline that can analyze disease risk factors and develop statistical methodologies to maximize utilization of big data on populations and disease pathology. The evolving transdisciplinary field of molecular pathological epidemiology (MPE) can advance biomedical and health research by linking exposures to molecular pathologic signatures, enhancing causal inference and identifying potential biomarkers for clinical impact. The MPE approach can be applied to any diseases, although it has been most commonly used in neoplastic diseases (including breast, lung and colorectal cancers) because of availability of various molecular diagnostic tests. However, use of state-of-the-art genomic, epigenomic and other omic technologies and expensive drugs in modern healthcare systems increases racial, ethnic and socioeconomic disparities. To address this, we propose to integrate molecular pathology, epidemiology and social science. Social epidemiology integrates the latter two fields. The integrative social MPE model can embrace sociology, economics and precision medicine, address global health disparities and inequalities, and elucidate biological effects of social environments, behaviors and networks. We foresee advancements of molecular medicine, including molecular diagnostics, biomedical imaging and targeted therapeutics, which should benefit individuals in a global population, by means of an interdisciplinary approach of integrative MPE and social health science.

  2. Nanoscale octahedral molecular sieves: Syntheses, characterization, and applications

    NASA Astrophysics Data System (ADS)

    Liu, Jia

    The major part of this research consists of studies on novel synthesis methods, characterization, and catalytic applications of nanoscale manganese oxide octahedral molecular sieves. The second part involves studies of new applications of bulk porous molecular sieve and layered materials (MSLM), zeolites, and inorganic powder materials for diminishing wound bleeding. Manganese oxide octahedral molecular sieves (OMS) are very important microporous materials. They have been used widely as bulk materials in catalysis, separations, chemical sensors, and batteries, due to their unique tunnel structures and useful properties. Novel methods have been developed to synthesize novel nanoscale octahedral molecular sieve manganese oxides (OMS) and metal-substituted OMS materials in order to modify their physical and chemical properties and to improve their catalytic applications. Different synthetic routes were investigated to find better, faster, and cheaper pathways to produce nanoscale or metal-substituted OMS materials. In the synthetic study of nanosize OMS materials, a combination of sol-gel synthesis and hydrothermal reaction was used to prepare pure crystalline nanofibrous todorokite-type (OMS-1) and cryptomelane-typed (OMS-2) manganese oxides using four alkali cations (Li+, K+, Na +, Rb+) and NH4+ cations. In the synthesis study of nanoscale and metal-substituted OMS materials, a combination of sol-gel synthesis and solid-state reaction was used to prepare transition metal-substituted OMS-2 nanorods, nanoneedles, and nanowires. Preparative parameters of syntheses, such as cation templates, heating temperature and time, were investigated in these syntheses of OMS-1 and OMS-2 materials. The catalytic activities of the novel synthetic nanoscale OMS materials has been evaluated on green oxidation of alcohols and toluene and were found to be much higher than their correspondent bulk materials. New applications of bulk manganese oxide molecular sieve and layered materials

  3. Molecular characterization of the human microbiome from a reproductive perspective.

    PubMed

    Mor, Amir; Driggers, Paul H; Segars, James H

    2015-12-01

    The process of reproduction inherently poses unique microbial challenges because it requires the transfer of gametes from one individual to the other, meanwhile preserving the integrity of the gametes and individuals from harmful microbes during the process. Advances in molecular biology techniques have expanded our understanding of the natural organisms living on and in our bodies, including those inhabiting the reproductive tract. Over the past two decades accumulating evidence has shown that the human microbiome is tightly related to health and disease states involving the different body systems, including the reproductive system. Here we introduce the science involved in the study of the human microbiome. We examine common methods currently used to characterize the human microbiome as an inseparable part of the reproductive system. Finally, we consider a few limitations, clinical implications, and the critical need for additional research in the field of human fertility.

  4. [Molecular characterization of breast cancer in clinical practice].

    PubMed

    Zemmouri, Y; De Croze, D; Vincent Salomon, A; Rouzier, R; Bonneau, C

    2016-05-01

    Breast cancer involves various types of tumors. The objective of this review was to provide a summary of the main methods currently available in clinical practice to characterize breast cancers at a molecular level and to discuss their prognostic and predictive values. Hormonal receptors expression and the HER2 status are prognostic markers and can also predict the response to targeted therapies. Their analysis through immunohistochemistry is systematical. Ki67 is an effective prognostic marker, but its reliability is debated because of its low reproducibility between laboratories and between pathologists. Commercial genomic signatures are all considered valid prognostic tools and may guide physicians to make therapeutic choices. These signatures are costly and should therefore be restricted to situations in which the use of chemotherapy remains equivocal. PMID:27150068

  5. Molecular characterization of maple syrup urine disease patients from Tunisia.

    PubMed

    Jaafar, N; Moleirinho, A; Kerkeni, E; Monastiri, K; Seboui, H; Amorim, A; Prata, M J; Quental, S

    2013-03-15

    Maple syrup urine disease (MSUD) is a rare disorder of branched-chain amino acids (BCAA) metabolism caused by the defective function of branched-chain α-ketoacid dehydrogenase complex (BCKD). The disease causal mutations can occur either in BCKDHA, BCKDHB or DBT genes encoding respectively the E1α, E1β and E2 subunits of the complex. In this study we report the molecular characterization of 3 Tunisian patients with the classic form of MSUD. Two novel putative mutations have been identified: the alteration c.716A>G (p.Glu239Gly) in BCKDHB and a small deletion (c.1333_1336delAATG; p.Asn445X) detected in DBT gene.

  6. Molecular based subtyping of feline mammary carcinomas and clinicopathological characterization.

    PubMed

    Soares, Maria; Madeira, Sara; Correia, Jorge; Peleteiro, Maria; Cardoso, Fátima; Ferreira, Fernando

    2016-06-01

    Molecular classification of feline mammary carcinomas (FMC) from which specific behavioral patterns may be estimated has potential applications in veterinary clinical practice and in comparative oncology. In this perspective, the main goal of this study was to characterize both the clinical and the pathological features of the different molecular phenotypes found in a population of FMC (n = 102), using the broadly accepted IHC-based classification established by St. Gallen International Expert Consensus panel. The luminal B/HER2-negative subtype was the most common (29.4%, 30/102) followed by luminal B/HER2-positive subtype (19.6%, 20/102), triple negative basal-like (16.7%, 17/102), luminal A (14.7%, 15/102), triple negative normal-like (12.7%, 13/102) and finally, HER2-positive subtype (6.9%, 7/102). Luminal A subtype was significantly associated with smaller tumors (p = 0.024) and with well differentiated ones (p < 0.001), contrasting with the triple negative basal-like subtype, that was associated with larger and poorly differentiated tumors (p < 0.001), and with the presence of necrotic areas in the tumoral lesion (p = 0.003). In the survival analysis, cats with Luminal A subtype presented the highest survival time (mean OS = 943.6 days) and animals with triple negative basal-like subtype exhibited the lowest survival time (OS mean = 368.9 days). Moreover, two thirds (64%, 32/50) of the queens with multiple primary tumors showed different molecular subtypes in each carcinoma, revealing that all independent lesions should be analyzed in order to improve the clinical management of animals. Finally, the similarities between the subtypes of feline mammary tumors and human breast cancer, reveal that feline can be a valuable model for comparative studies. PMID:27212699

  7. Full characterization of an intense pulsed hyperthermal molecular beam

    NASA Astrophysics Data System (ADS)

    Watanabe, D.; Che, D.-C.; Fukuyama, T.; Hashinokuchi, M.; Teraoka, Y.; Kasai, T.

    2005-05-01

    A molecular beam technique for generating an intense pulsed hyperthermal molecular beam (pulsed HTMB) was developed. The beam source consists of a pulse valve, a cooling-water bottle that protects the pulse valve from heat transfer of the high temperature nozzle, and a nozzle with a heater. The point was a pulse-valve operation with the high temperature nozzle which was 30-mm long and was made of pyrolytic boron nitride. The pulsed HTMB of HCl was practically generated. The total beam intensity of the pulsed HTMB was measured by a quadrupole mass spectrometer. It was determined that the beam intensity of the pulsed HTMB was two orders of magnitude larger than that obtained in continuous-HTMB conditions. The pulsed HTMB of HCl was fully characterized by means of (2+1) resonance-enhanced multiphoton ionization and ion time-of-flight techniques. We found that the velocity distribution of the pulsed HTMB was well expressed as supersonic molecular beams. At the highest nozzle temperature of 1400 K, the mean translational energy value of HCl molecules was 1.38 eV. The translational energy distribution of the pulsed HTMB covered a range from 0.8 to 1.6 eV. The fraction of higher translational energy molecules greater than 1.0 eV was 80% in the 1400 K nozzle. The rotational state distributions of HCl molecules in the pulsed HTMB were expressed as the Boltzmann distribution. While the rotational temperature decreased by an adiabatic expansion of the beam, the vibrational temperature, which was determined by the ratio of the ground-state population to the excited state one, almost equaled the nozzle temperature.

  8. Molecular characterization of Hepatozoon canis in dogs from Colombia.

    PubMed

    Vargas-Hernandez, Giovanni; André, Marcos R; Munhoz, Thiago D; Faria, Joice M L; Machado, Rosangela Z; Tinucci-Costa, Mirela

    2012-01-01

    Hepatozoonosis is a tick-borne disease whose transmission to dogs occurs by ingestion of oocysts infected ticks or feeding on preys infested by infected ticks. Until now, there is no previous report of molecular characterization of Hepatozoon sp. in dogs from Colombia. EDTA blood samples were collected from 91 dogs from central-western region of Colombia (Bogotá, Bucaramanga, and Villavicencio cities) and submitted to 18S rRNA Hepatozoon sp. PCR and blood smears confection. Phylogenetic analysis was used to access the identity of Hepatozoon species found in sampled dogs. From 91 sampled dogs, 29 (31.8%) were positive to Hepatozoon sp. (25 dogs were only positive in PCR, 1 was positive only in blood smears, and 3 were positive in both blood smears and PCR). After sequencing, the found Hepatozoon sp. DNA showed 100% of identity with Hepatozoon canis DNA isolates. The phylogenetic tree supported the identity of the found Hepatozoon sp. DNA, showing that the isolates from Colombia were placed in the same clade than other H. canis isolates from Venezuela, Spain, and Taiwan. This is the first molecular detection of H. canis in dogs from Colombia.

  9. Molecular methods for identification and characterization of novel papillomaviruses.

    PubMed

    Kocjan, B J; Bzhalava, D; Forslund, O; Dillner, J; Poljak, M

    2015-09-01

    Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and β-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.

  10. Characterizing entanglement with global and marginal entropic measures

    SciTech Connect

    Adesso, Gerardo; Illuminati, Fabrizio; De Siena, Silvio

    2003-12-01

    We qualify the entanglement of arbitrary mixed states of bipartite quantum systems by comparing global and marginal mixednesses quantified by different entropic measures. For systems of two qubits we discriminate the class of maximally entangled states with fixed marginal mixednesses, and determine an analytical upper bound relating the entanglement of formation to the marginal linear entropies. This result partially generalizes to mixed states the quantification of entanglement with marginal mixednesses holding for pure states. We identify a class of entangled states that, for fixed marginals, are globally more mixed than product states when measured by the linear entropy. Such states cannot be discriminated by the majorization criterion.

  11. Supported Molecular Catalysts: Synthesis, in-situ Characterization and Performance

    SciTech Connect

    Haw, James F

    2010-12-14

    The technological advantages of solid catalysts (robustness for operation at high temperatures, lack of corrosion, and ease of separation of products) can be combined with the advantages of soluble catalysts (e.g., selectivity) by synthesis of structurally discrete, nearly uniform catalysts on supports. Our goal is to synthesize, characterize, test, and model such catalysts and their reactions, thereby opening a door to unprecedented fundamental understanding of the properties of such materials. We employ molecular chemistry in nano-scale cages of zeolites and on surfaces of tailored porous solids for the precise synthesis of catalysts with discrete, uniform, well-defined sites, primarily mononuclear metal complexes, characterizing them (sometimes in the functioning state) with a broad range of complementary experimental techniques and using computational chemistry to interpret the results, map out reaction paths, provide bases for the design of new catalysts, improve methods of data analysis, and identify key experiments. The effort is directly in support of DOE's energy, environmental, and national security missions as well as the support of DOE's basic science mission to develop the tools and understanding needed for the success of the applied mission areas. The research is demonstrating progress in understanding, modeling, and controlling chemical reactivity at interfaces to develop a fundamental understanding of how to control catalytic reactions for a broad range of applications.

  12. Molecular characterization of beta-thalassemia in the Sardinian population

    SciTech Connect

    Rosatelli, M.C.; Faa, V.; Sardu, R.; Saba, L. Cao, A. ); Dozy, A.; Kan, Y.W. ); Meloni, A. )

    1992-02-01

    This study reports the molecular characterization of [beta]-thalassemia in the Sardinian population. Three thousand [beta]-thalassemia chromosomes from prospective parents presenting at the genetic service were initially analyzed by dot blot analysis with oligonucleotide probes complementary to the most common [beta]-thalassemia mutations in the Mediterranean at-risk populations. The mutation which remained uncharacterized by this approach were defined by denaturing gradient gel electrophoresis (DGGE) followed by direct sequence analysis on amplified DNA. The authors reconfirmed that the predominant mutation in the Sardinian population is the codon 39 nonsense mutation, which accounts for 95.7% of the [beta]-thalassemia chromosomes. The other two relatively common mutations are frameshifts at codon 6 (2.1%) and at codon 76 (0.7%), relatively uncommon in other Mediterranean-origin populations. In this study they have detected a novel [beta]-thalassemia mutation, i.e., a frameshift at codon 1, in three [beta]-thalassemia chromosomes. The DGGE procedure followed by direct sequencing on amplified DNA is a powerful approach for the characterization of unknown mutations in this genetic system.

  13. Almond allergens: molecular characterization, detection, and clinical relevance.

    PubMed

    Costa, Joana; Mafra, Isabel; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P

    2012-02-15

    Almond ( Prunus dulcis ) has been widely used in all sorts of food products (bakery, pastry, snacks), mostly due to its pleasant flavor and health benefits. However, it is also classified as a potential allergenic seed known to be responsible for triggering several mild to life-threatening immune reactions in sensitized and allergic individuals. Presently, eight groups of allergenic proteins have been identified and characterized in almond, namely, PR-10 (Pru du 1), TLP (Pru du 2), prolamins (Pru du 2S albumin, Pru du 3), profilins (Pru du 4), 60sRP (Pru du 5), and cupin (Pru du 6, Pru du γ-conglutin), although only a few of them have been tested for reactivity with almond-allergic sera. To protect sensitized individuals, labeling regulations have been implemented for foods containing potential allergenic ingredients, impelling the development of adequate analytical methods. This work aims to present an updated and critical overview of the molecular characterization and clinical relevance of almond allergens, as well as review the main methodologies used to detect and quantitate food allergens with special emphasis on almond. PMID:22260748

  14. Molecular characterization of Theileria orientalis from cattle in Ethiopia.

    PubMed

    Gebrekidan, Hagos; Gasser, Robin B; Baneth, Gad; Yasur-Landau, Daniel; Nachum-Biala, Yaarit; Hailu, Asrat; Jabbar, Abdul

    2016-07-01

    This study reports the first molecular characterization of Theileria orientalis in local breeds of cattle in Ethiopia. A conventional PCR utilizing major piroplasm surface protein (MPSP) gene and an established multiplexed tandem PCR (MT-PCR) were used to characterize T. orientalis and to assess the infection intensity, respectively. Of 232 blood samples tested, T. orientalis DNA was detected in only 2.2% of samples using conventional PCR; two genotypes buffeli (1.3%; 3/232) and type 5 (0.9%; 2/232) of T. orientalis were detected. Phylogenetic analysis revealed that the buffeli MPSP sequences from Ethiopia were closely related to those reported from Kenya, Sri Lanka and Myanmar, and type 5 sequences from Ethiopia grouped with those from Korea, Japan, Vietnam and Thailand. A higher number of samples (3.9%; 9/232) were test-positive by MT-PCR and four genotypes (buffeli, chitose, ikeda and type 5) of T. orientalis were detected. The average intensity of infections with genotypes buffeli (DNA copy numbers 11,056) and type 5 (7508) were significantly higher (P<0.0001) than the pathogenic genotype ikeda (61 DNA copies). This first insight into T. orientalis from cattle in Ethiopia using MPSP gene provides a basis for future studies of T. orientalis in various agroclimatic zones and of the impact of oriental theilerosis on cattle in this and other countries of Africa. PMID:27034193

  15. Almond allergens: molecular characterization, detection, and clinical relevance.

    PubMed

    Costa, Joana; Mafra, Isabel; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P

    2012-02-15

    Almond ( Prunus dulcis ) has been widely used in all sorts of food products (bakery, pastry, snacks), mostly due to its pleasant flavor and health benefits. However, it is also classified as a potential allergenic seed known to be responsible for triggering several mild to life-threatening immune reactions in sensitized and allergic individuals. Presently, eight groups of allergenic proteins have been identified and characterized in almond, namely, PR-10 (Pru du 1), TLP (Pru du 2), prolamins (Pru du 2S albumin, Pru du 3), profilins (Pru du 4), 60sRP (Pru du 5), and cupin (Pru du 6, Pru du γ-conglutin), although only a few of them have been tested for reactivity with almond-allergic sera. To protect sensitized individuals, labeling regulations have been implemented for foods containing potential allergenic ingredients, impelling the development of adequate analytical methods. This work aims to present an updated and critical overview of the molecular characterization and clinical relevance of almond allergens, as well as review the main methodologies used to detect and quantitate food allergens with special emphasis on almond.

  16. Selenium Characterization In The Global Rice Supply Chain

    EPA Science Inventory

    For up to 1 billion people worldwide, insufficient dietary intake of selenium (Se) is a serious health constraint. Cereals are the dominant Se source for those on low protein diets, as typified by the global malnourished population. With crop Se content constrained largely by u...

  17. Molecular characterization of soil organic matter: a historic overview

    NASA Astrophysics Data System (ADS)

    Kögel-Knabner, Ingrid; Rumpel, Cornelia

    2014-05-01

    The characterization of individual molecular components of soil organic matter started in the early 19th century, but proceeded slowly. The major focus at this time was on the isolation and differentiation of different humic and fulvic acid fractions, which were considered to have a defined chemical composition and structure. The isolation and structural anlysis of specific individual soil organic matter components became more popular in the early 20th century. In 1936 40 different individual compounds had been isolated and a specific chemical strucutre had been attributed. These structural attributions were confirmed later for some, but not all of these individual compounds. In the 1950 much more individual compounds could be isolated and characterized, using complicated and time consuming chromatography. It became obvious that soil also contains a number of compounds of microbial origin, such as e.g., amino sugars and lipids. With the improvement of chrmoatographic separation techniques and the use of gas chromatography in combination with thin layerchromatography in the 1960 hundreds of individual compounds have been isolated and identified, most of them after chemical degradation of humic or fulvic acids. The chemical degradative techniques were amended with analytical pyrolysis in the 1970s. More and more, bulk soil organic matter was analyzed with these techniques and the advent of solid-stae 13C NMR spectroscopy around the 1980s allowed for the characterization of the composition of bulk soil organic matter. The gas chromatographic separation of organic matter can nowadays be combined with specific detectors, such that specific attributes ofindividual molecules can be analyzed, e.g. the radiocarbon content or the stable isotope composition.

  18. A global indicator as a tool to follow airborne molecular contamination in a controlled environment.

    PubMed

    Cariou, Stéphane; Guillot, Jean-Michel; Pépin, Laurence; Kaluzny, Pascal; Faure, Louis-Paul

    2005-02-01

    The impact of pollutants on production quality in nanotechnology necessitates reduction of contaminant levels in cleanrooms. So, devising a global airborne-pollutant indicator (GAPI) for rapid determination of the level of pollution and its danger to the process is justified. This tool used relative impact weights of the different molecules to quantify the pollution. A calculation of impact weight is proposed in this paper. Impact weights could take into account several characteristics of the molecules (molecular volume, sticking coefficient, ...). They could also be combined to be as close as possible to reality. An example of calculations of the impact of molecular volumes on air quality is given.

  19. Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

    NASA Astrophysics Data System (ADS)

    Hasan, Nor'Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

    2016-02-01

    Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

  20. Clinical and molecular characterization of chikungunya virus in South Thailand.

    PubMed

    Theamboonlers, Apiradee; Rianthavorn, Pornpimol; Praianantathavorn, Kesmanee; Wuttirattanakowit, Norra; Poovorawan, Yong

    2009-07-01

    In 2008, an outbreak of chikungunya virus (CHIKV) occurred in Narathiwat province, south Thailand. To determine the clinical significance, molecular epidemiology and evolutionary origin of the CHIKV causing this outbreak, 47 patients who had been admitted to Narathiwatratchanakharin provincial hospital due to acute febrile illness were enrolled in this study. Sera were tested for IgM antibodies, and RT-PCR was performed for CHIKV and dengue virus. We diagnosed 10 patients with CHIKV infection and 5 with dengue virus infection. Joint pain is a significant symptom of chikungunya fever. Five strains of CHIKV were isolated. Their genome sequences were different from those isolated from the previous outbreaks in Thailand (1988, 1995-1996) but similar to the sequences isolated from the 2008 Singapore outbreak. We speculated that the outbreak was caused by a group of viruses different from the previous outbreaks. RT-PCR, serology to detect IgM antibodies or paired sera for IgG for CHIKV should be performed in all patients with presumed hemorrhagic fever to promptly detect outbreaks of CHIKV. This precaution would help control global epidemics of this virus.

  1. Theoretical characterization of charge transport in organic molecular crystals

    NASA Astrophysics Data System (ADS)

    Sanchez-Carrera, Roel S.

    The rapid growth in the interest to explore new synthetic crystalline organic semiconductors and their subsequent device characterization has revived the debate on the development of theoretical models to better understand the intrinsic charge transport mechanisms in organic materials. At the moment, several charge-transport theories for organic molecular crystals have been proposed and have observed a comparable agreement with experimental results. However, these models are limited in scope and restricted to specific ranges of microscopic parameters and temperatures. A general description that is applicable in all parameter regimes is still unavailable. The first step towards a complete understanding of the problem associated with the charge transport in organic molecular crystals includes the development of a first-principles theoretical methodology to evaluate with high accuracy the main microscopic charge-transport parameters and their respective couplings with intra- and intermolecular vibrational degrees of freedom. In this thesis, we have developed a first-principles methodology to investigate the impact of electron-phonon interactions on the charge-carrier mobilities in organic molecular crystals. Well-known organic materials such as oligoacene and oligothienoacene derivatives were studied in detail. To predict the charge-transport phenomena in organic materials, we rely on the Marcus theory of electron-transfer reactions. Within this context, the nature of the intramolecular vibronic coupling in oligoacenes was studied using an approach that combines high-resolution gas-phase photo-electron spectroscopy measurements with first-principles quantum-mechanical calculations. This further led to investigation of the electron interactions with optical phonons in oligoacene single crystals. The lattice phonon modes were computed at both density functional theory (DFT) and empirical force field levels. The low-frequency optical modes are found to play a significant

  2. Characterizing global evolutions of complex systems via intermediate network representations.

    PubMed

    Iwayama, Koji; Hirata, Yoshito; Takahashi, Kohske; Watanabe, Katsumi; Aihara, Kazuyuki; Suzuki, Hideyuki

    2012-01-01

    Recent developments in measurement techniques have enabled us to observe the time series of many components simultaneously. Thus, it is important to understand not only the dynamics of individual time series but also their interactions. Although there are many methods for analysing the interaction between two or more time series, there are very few methods that describe global changes of the interactions over time. Here, we propose an approach to visualise time evolution for the global changes of the interactions in complex systems. This approach consists of two steps. In the first step, we construct a meta-time series of networks. In the second step, we analyse and visualise this meta-time series by using distance and recurrence plots. Our two-step approach involving intermediate network representations elucidates the half-a-day periodicity of foreign exchange markets and a singular functional network in the brain related to perceptual alternations. PMID:22639731

  3. Characterizing global evolutions of complex systems via intermediate network representations.

    PubMed

    Iwayama, Koji; Hirata, Yoshito; Takahashi, Kohske; Watanabe, Katsumi; Aihara, Kazuyuki; Suzuki, Hideyuki

    2012-01-01

    Recent developments in measurement techniques have enabled us to observe the time series of many components simultaneously. Thus, it is important to understand not only the dynamics of individual time series but also their interactions. Although there are many methods for analysing the interaction between two or more time series, there are very few methods that describe global changes of the interactions over time. Here, we propose an approach to visualise time evolution for the global changes of the interactions in complex systems. This approach consists of two steps. In the first step, we construct a meta-time series of networks. In the second step, we analyse and visualise this meta-time series by using distance and recurrence plots. Our two-step approach involving intermediate network representations elucidates the half-a-day periodicity of foreign exchange markets and a singular functional network in the brain related to perceptual alternations.

  4. A global survey of low-molecular weight carbohydrates in lentils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lentils contain a range of low-molecular weight carbohydrates (LMWC); however, those have not been well characterized. The objectives of this study were to (1) determine the concentrations of LMWC in lentils grown in six locations, and (2) identify any genetic and environmental effects on those LMWC...

  5. A global survey of low-molecular weight carbohydrates in lentils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lentils contain a range of low-molecular weight carbohydrates (LMWC); however, they have not been well characterized. The objectives of this study were to (1) determine the concentrations of LMWC in lentils grown in different environments and (2) identify any genetic and environmental effects on tho...

  6. Metastasizing Maxillary Ameloblastoma: Report of a Case with Molecular Characterization

    PubMed Central

    Rotellini, Matteo; Maggiore, Giandomenico; Trovati, Massimo; Saraceno, Massimo Squadrelli

    2016-01-01

    ABSTRACT Background Ameloblastoma is a benign odontogenic tumour that may exhibit aggressive biological behaviour with local recurrence and metastasis following initial surgical resection. Surgery is the most acceptable modality of treatment, even if a biological approach is currently on study. We report a case of maxillary ameloblastoma with development of neck and brain metastases after repeated local recurrences. Molecular analysis was performed with the aim to better characterize this neoplasm and its peculiar behaviour. Methods We investigated the status of tumour protein p53 (TP53), epidermal growth factor receptor (EGFR), B-Raf proto-oncogene (BRAF) and human epidermal growth factor receptor 2 (HER2) genes with immunohistochemical, fluorescent in situ hybridization and/or direct sequencing in order to clarify their possible role in the development of this neoplasm and the possibility of a targeted treatment. Results The histological appearance of the tumour was the same in the primary lesion, in the recurrence and in the metastases. EGFR positivity was present in the recurrence and the brain metastasis, while HER2 was negative in all samples tested. Fluorescent in situ hybridization analysis for EGFR showed disomy of neoplastic cells. Direct DNA sequencing of TP53 gene exons 5 - 9 was carried out in tumour samples from the infratemporal recurrence and brain metastasis, with no mutational alteration detected. Similarly, sequencing analysis of BRAF exon 15 (V600) and EGFR gene showed wild type results in all samples tested. Conclusions Further studies are needed to identify molecular pathways that may provide an opportunity of alternative treatments and/or new potential predictive markers of local and distant spread of this rare tumour. PMID:27099699

  7. Molecular evolution and in vitro characterization of Botryllus histocompatibility factor.

    PubMed

    Taketa, Daryl A; Nydam, Marie L; Langenbacher, Adam D; Rodriguez, Delany; Sanders, Erin; De Tomaso, Anthony W

    2015-10-01

    Botryllus schlosseri is a colonial ascidian with a natural ability to anastomose with another colony to form a vascular and hematopoietic chimera. In order to fuse, two individuals must share at least one allele at the highly polymorphic fuhc locus. Otherwise, a blood-based inflammatory response will occur resulting in a melanin scar at the sites of interaction. The single-locus genetic control of allorecognition makes B. schlosseri an attractive model to study the underlying molecular mechanisms. Over the past decade, several candidate genes involved in allorecognition have been identified, but how they ultimately contribute to allorecognition outcome remains poorly understood. Here, we report our initial molecular characterization of a recently identified candidate allodeterminant called Botryllus histocompatibility factor (bhf). bhf, both on a DNA and protein level, is the least polymorphic protein in the fuhc locus studied so far and, unlike other known allorecognition determinants, does not appear to be under any form of balancing or directional selection. Additionally, we identified a second isoform through mRNA-Seq and an EST assembly library which is missing exon 3, resulting in a C-terminally truncated form. We report via whole-mount fluorescent in situ hybridization that a subset of cells co-express bhf and cfuhc(sec). Finally, we observed BHF's localization in HEK293T at the cytoplasmic side of the plasma membrane in addition to the nucleus via a nuclear localization signal. Given the localization data thus far, we hypothesize that BHF may function as a scaffolding protein in a complex with other Botryllus proteins, rather than functioning as an allorecognition determinant. PMID:26359175

  8. Molecular characterization of clinical multidrug-resistant Klebsiella pneumoniae isolates

    PubMed Central

    2014-01-01

    Background Klebsiella pneumoniae is a frequent nosocomial pathogen, with the multidrug-resistant (MDR) K. pneumoniae being a major public health concern, frequently causing difficult-to-treat infections worldwide. The aim of this study was to investigate the molecular characterization of clinical MDR Klebsiella pneumoniae isolates. Methods A total of 27 non-duplicate MDR K. pneumoniae isolates with a CTX-CIP-AK resistance pattern were investigated for the prevalence of antimicrobial resistance genes including extended spectrum β-lactamase genes (ESBLs), plasmid-mediated quinolone resistance (PMQR) genes, 16S rRNA methylase (16S-RMTase) genes, and integrons by polymerase chain reaction (PCR) amplification and DNA sequencing. Plasmid replicons were typed by PCR-based replicon typing (PBRT). Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were carried out to characterize the strain relatedness. Results All the isolates co-harbored 3 or more resistance determinants. OqxAB, CTX-M-type ESBLs and RmtB were the most frequent determinants, distributed among19 (70.4%),18 (66.7%) and 8 (29.6%) strains. Fourteen isolates harbored class 1 integrons, with orfD-aacA4 being the most frequent gene cassette array. Class 3 integrons were less frequently identified and contained the gene cassette array of blaGES-1-blaOXA-10-aac(6′)-Ib. IncFII replicon was most commonly found in this collection. One cluster was observed with ≥80% similarity among profiles obtained by PFGE, and one sequence type (ST) by MLST, namely ST11, was observed in the cluster. Conclusion K. pneumoniae carbapenemase (KPC)–producing ST11 was the main clone detected. Of particular concern was the high prevalence of multiple resistance determinants, classs I integrons and IncFII plasmid replicon among these MDR strains, which provide advantages for the rapid development of MDR strains. PMID:24884610

  9. A global classification and characterization of earthquake clusters

    NASA Astrophysics Data System (ADS)

    Zaliapin, Ilya; Ben-Zion, Yehuda

    2016-10-01

    We document space-dependent clustering properties of earthquakes with m ≥ 4 in the 1975-2015 worldwide seismic catalogue of the Northern California Earthquake Data Center. Earthquake clusters are identified using a nearest-neighbour distance in time-space-magnitude domain. Multiple cluster characteristics are compared with the heat flow level and type of deformation defined by parameters of the strain rate tensor. The analysis suggests that the dominant type of seismicity clusters in a region depends strongly on the heat flow, while the deformation style and intensity play a secondary role. The results show that there are two dominant types of global clustering: burst-like clusters that represent brittle fracture in relatively cold lithosphere (e.g. shallow events in subduction zones) and swarm-like clusters that represent brittle-ductile deformation in relatively hot lithosphere (e.g. mid-oceanic ridges). The global results are consistent with theoretical expectations and previous analyses of earthquake clustering in southern California based on higher quality catalogues. The observed region-specific deviations from average universal description of seismicity provide important constraints on the physics governing earthquakes and can be used to improve local seismic hazard assessments.

  10. Characterizing Uncertainty in Global Aerosol Retrievals from Multiple Spaceborne Sensors

    NASA Astrophysics Data System (ADS)

    Petrenko, M.; Smirnov, A.; Ichoku, C. M.

    2014-12-01

    Complementary global aerosol products have been routinely available from multiple spaceborne sensors, including MODIS (on Terra and Aqua), MISR, OMI, POLDER, CALIOP, SeaWiFS, and VIIRS. However, a variety of studies suggest that individual aerosol products have significant differences in the geographic distribution of their retrieval uncertainties. Nonetheless, it can be difficult or impractical to track down relevant product validation studies and invest time in mastering the proprietary file formats of these aerosol products. As a result, many studies are performed using data from one or two most familiar products that, oftentimes, may not be optimal for a given region of interest. In this presentation, we will use Aerosol Robotic Network (AERONET) and Maritime Aerosol Network (MAN) data within the framework of the Multi-sensor Aerosol Products Sampling System (MAPSS) to catalog the accuracy of aerosol retrievals from the spaceborne sensors listed above. We will report our findings in analyzing the spatial and temporal distributions of the uncertainties in the global over-land and maritime retrievals of aerosols based on inter-comparing spaceborne data with coincident ground-based measurements from both AERONET and MAN. We will also explain our vision of how this analysis can be used as a base for a multi-sensor aerosol product package that would help end users to make a more informed choice when selecting data for their regions of interest.

  11. Molecular Characterization of Organic Indicators of Petroleum Biosouring

    NASA Astrophysics Data System (ADS)

    Nowak, J.; Weber, R.; Loutey, D.; Coates, J. D.; Goldstein, A. H.

    2015-12-01

    The production of sulfide in a petroleum reservoir by anaerobic sulfate reducing microorganisms (SRM) is environmentally, industrially, and epidemiologically hazardous. More knowledge is needed about the anaerobic respiration pathway of SRM in petroleum, and whether the activity of SRM could be effectively inhibited using nitrate or perchlorate treatments. In order to understand the molecular transformations and metabolic fingerprints of SRM in petroleum reservoirs, and how they are altered by nitrate or perchlorate treatments, the Coates and Goldstein Laboratories at UC-Berkeley have run controlled column incubation studies of petroleum from an oil reservoir. By using two dimensional gas chromatography (GCxGC) with high resolution time-of-flight mass spectrometry coupled to vacuum ultraviolet radiation at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory (LBNL), detailed chemical characterizations of hydrocarbons from approximately C9-C30 have been completed, separating the complete oil sample by number of carbon atoms and chemical classes (including normal alkanes, branched alkanes, number of alkyl rings, and number of aromatic rings) corresponding to petroleum transformations in sulfate, nitrate, and perchlorate reducing environments. Results demonstrate that the anaerobic pathway of SRM preferentially involves the transformation of heavier polycyclic aromatic hydrocarbons (PAHs), and that a large number of products are created that contain either two or four oxygen atoms, suggesting fumarate additions initialize the anaerobic process.

  12. Cytological and molecular characterization of three gametoclones of Citrus clementina

    PubMed Central

    2013-01-01

    Background Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control. Conclusions The presence of few gene hybridization abnormalities, corroborated by gene dosage measurements, were hypothetically due to the segregation of hemizygous alleles and minor genomic rearrangements occurring during the haploidization procedure. In conclusion, these plants that are valuable genetic and breeding materials contain completely homozygous and essentially intact genomes. PMID:24020638

  13. Synthesis, characterization, biological evaluation and molecular docking of steroidal spirothiazolidinones

    NASA Astrophysics Data System (ADS)

    Shamsuzzaman; Abdul Baqi, Khan A. A.; Ali, Abad; Asif, Mohd; Mashrai, Ashraf; Khanam, Hena; Sherwani, Asif; Yaseen, Zahid; Owais, Mohammad

    2015-04-01

    The present work describes a convenient synthesis of steroidal spirothiazolidinone derivatives (3, 10-12) in a two-step process. All the newly synthesized compounds have been characterized by means of elemental analyses, IR, 1H NMR, 13C NMR and MS. Lipinski's 'Rule of Five' analysis and biological score predicted higher intrinsic quality of the synthesized compounds and revealed that these compounds have good passive oral absorption. The DNA binding studies of the synthesized compounds with CT-DNA were carried out by UV-vis and fluorescence spectroscopy. The molecular docking study suggested electrostatic interaction between synthesized compounds and nucleotide base pairs. The antitumor activity was tested in vitro against human leukemia cancer cell (Jurkat) and blood peripheral mononuclear normal cell (PBMCs) lines by MTT method. In addition, apoptosis and nonenzymatic degradation of DNA have been investigated. The acetylcholinesterase (AChE) inhibitor activities of the derivatives were also evaluated using Ellman's method. The present study has shown that steroidal spirothiazolidinone derivatives (3, 10-12) can be used as template to design more potent and selective cytotoxic and AChE inhibition agents through modification and derivatization.

  14. Molecular Characterization of Secondary Aerosol from Oxidation of Cyclic Methylsiloxanes

    NASA Astrophysics Data System (ADS)

    Wu, Yue; Johnston, Murray V.

    2016-03-01

    Cyclic volatile methylsiloxanes (cVMS) have been identified as important gas-phase atmospheric contaminants, but knowledge of the molecular composition of secondary aerosol derived from cVMS oxidation is incomplete. Here, the chemical composition of secondary aerosol produced from the OH-initiated oxidation of decamethylcyclopentasiloxane (D5, C10H30O5Si5) is characterized by high performance mass spectrometry. ESI-MS reveals a large number of monomeric (300 < m/z < 470) and dimeric (700 < m/z < 870) oxidation products. With the aid of high resolution and MS/MS, it is shown that oxidation leads mainly to the substitution of a CH3 group by OH or CH2OH, and that a single molecule can undergo many CH3 group substitutions. Dimers also exhibit OH and CH2OH substitutions and can be linked by O, CH2, and CH2CH2 groups. GC-MS confirms the ESI-MS results. Oxidation of D4 (C8H24O4Si4) exhibits similar substitutions and oligomerizations to D5, though the degree of oxidation is greater under the same conditions and there is direct evidence for the formation of peroxy groups (CH2OOH) in addition to OH and CH2OH.

  15. Molecular characterization of flow-sorted mammalian centromeres

    SciTech Connect

    Hamkalo, B.A.; Henschen, A.; Parseghian, M.H.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project involved experiments directed towards developing a molecular characterization of the centromere region of mammalian chromosomes. Attempts to purify this essential chromosomal locus by conventional methods have thus far been unsuccessful. However, preliminary data obtained in collaboration with the National Flow Cytometry Resource (NFCR) showed that it is possible to purify a chromosome fragment that is present in certain cultured mouse cell lines and has all the properties expected of an intact centromere region. To begin sorting this minichromosome for the identification of proteins preferentially associated with centromere regions, standard buffers utilized in chromosome sorting were evaluated for potential effects on maintenance of chromosomal proteins during sorting. The data indicate that the presence of several buffer constituents results in the extraction of all but a few chromosomal proteins. The subsequent use of a magnesium sulfate buffer resulted in the sorting of mouse chromosomes that do not suffer a significant loss of proteins. Several DNA stains were also evaluated for causing protein dissociation, but no significant losses were observed. Although flow-sorted chromosomes have been used extensively for DNA analysis and cloning, this is a pioneering effort by the NFCR, and its collaborators, to exploit chromosome sorting capabilities for the analysis of chromosomal proteins.

  16. Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics.

    PubMed

    Vermillion, Katie L; Jagtap, Pratik; Johnson, James E; Griffin, Timothy J; Andrews, Matthew T

    2015-11-01

    This study uses advanced proteogenomic approaches in a nonmodel organism to elucidate cardioprotective mechanisms used during mammalian hibernation. Mammalian hibernation is characterized by drastic reductions in body temperature, heart rate, metabolism, and oxygen consumption. These changes pose significant challenges to the physiology of hibernators, especially for the heart, which maintains function throughout the extreme conditions, resembling ischemia and reperfusion. To identify novel cardioadaptive strategies, we merged large-scale RNA-seq data with large-scale iTRAQ-based proteomic data in heart tissue from 13-lined ground squirrels (Ictidomys tridecemlineatus) throughout the circannual cycle. Protein identification and data analysis were run through Galaxy-P, a new multiomic data analysis platform enabling effective integration of RNA-seq and MS/MS proteomic data. Galaxy-P uses flexible, modular workflows that combine customized sequence database searching and iTRAQ quantification to identify novel ground squirrel-specific protein sequences and provide insight into molecular mechanisms of hibernation. This study allowed for the quantification of 2007 identified cardiac proteins, including over 350 peptide sequences derived from previously uncharacterized protein products. Identification of these peptides allows for improved genomic annotation of this nonmodel organism, as well as identification of potential splice variants, mutations, and genome reorganizations that provides insights into novel cardioprotective mechanisms used during hibernation.

  17. Molecular Cloning and Characterization of a Paramyosin from Clonorchis sinensis

    PubMed Central

    Park, Tae-Joon; Kang, Jung-Mi; Na, Byoung-Kuk

    2009-01-01

    Paramyosin is a myofibrillar protein present in helminth parasites and plays multifunctional roles in host-parasite interactions. In this study, we identified the gene encoding paramyosin of Clonorchis sinensis (CsPmy) and characterized biochemical and immunological properties of its recombinant protein. CsPmy showed a high level of sequence identity with paramyosin from other helminth parasites. Recombinant CsPmy (rCsPmy) expressed in bacteria had an approximate molecular weight of 100 kDa and bound both human collagen and complement 9. The protein was constitutively expressed in various developmental stages of the parasite. Imunofluorescence analysis revealed that CsPmy was mainly localized in the tegument, subtegumental muscles, and the muscle layer surrounding the intestine of the parasite. The rCsPmy showed high levels of positive reactions (74.6%, 56/75) against sera from patients with clonorchiasis. Immunization of experimental rats with rCsPmy evoked high levels of IgG production. These results collectively suggest that CsPmy is a multifunctional protein that not only contributes to the muscle layer structure but also to non-muscular functions in host-parasite interactions. Successful induction of host IgG production also suggests that CsPmy can be applied as a diagnostic antigen and/or vaccine candidate for clonorchiasis. PMID:19967083

  18. Molecular Characterization of Secondary Aerosol from Oxidation of Cyclic Methylsiloxanes.

    PubMed

    Wu, Yue; Johnston, Murray V

    2016-03-01

    Cyclic volatile methylsiloxanes (cVMS) have been identified as important gas-phase atmospheric contaminants, but knowledge of the molecular composition of secondary aerosol derived from cVMS oxidation is incomplete. Here, the chemical composition of secondary aerosol produced from the OH-initiated oxidation of decamethylcyclopentasiloxane (D5, C10H30O5Si5) is characterized by high performance mass spectrometry. ESI-MS reveals a large number of monomeric (300 < m/z < 470) and dimeric (700 < m/z < 870) oxidation products. With the aid of high resolution and MS/MS, it is shown that oxidation leads mainly to the substitution of a CH3 group by OH or CH2OH, and that a single molecule can undergo many CH3 group substitutions. Dimers also exhibit OH and CH2OH substitutions and can be linked by O, CH2, and CH2CH2 groups. GC-MS confirms the ESI-MS results. Oxidation of D4 (C8H24O4Si4) exhibits similar substitutions and oligomerizations to D5, though the degree of oxidation is greater under the same conditions and there is direct evidence for the formation of peroxy groups (CH2OOH) in addition to OH and CH2OH. PMID:26729452

  19. Molecular characterization of Sp110 gene in pigs.

    PubMed

    Li, Li-Zu; Wang, Qiu-Shi; Han, Li-Xin; Wang, Jin-Kui; Shao, Si-Yu; Wang, Liang; Liu, Di; Yang, Xiu-Qin

    2016-06-01

    Speckled 110 kDa (Sp110) plays an important role in infectious diseases, as revealed by studies in humans. However, little is known regarding porcine Sp110. To elucidate its potential role in porcine resistance to viral diseases, here, the complete coding sequence of porcine Sp110 gene and its 26 alternatively spliced isoforms were isolated using reverse transcription (RT)-polymerase chain reaction (PCR), and another seven splicing patterns were obtained using a minigene construct. Subcellular distribution of 11 representative isoforms was characterized in PK-15 cells transiently transfected with their respective GFP fusion constructs, and only isoforms (R and V) bearing all functional domains were localized in nucleus, indicating all the other isoforms lose normal functions of Sp110 owing to alternative splicing. Real-time quantitative PCR and competitive RT-PCR showed that both isoforms R and V had similar tissue expression profile, half-life and response to poly(I:C), a synthetic analog of viral double-stranded RNA, while the longer one (isoform R) was transcribed at a higher level. The results indicated that porcine Sp110 has a role in viral infection and that isoform R is the dominant active form. Overall the data provide potential resource for molecular breeding of pig resistant to diseases and contributes to breeding pigs resistant to viral infection. PMID:26995495

  20. Molecular cytogenetic characterization of a human thyroid cancercell line

    SciTech Connect

    Weier, Heinz-Ulrich G.; Tuton, Tiffany B.; Ito, Yuko; Chu, LisaW.; Lu, Chung-Mei; Baumgartner, Adolf; Zitzelsberger, Horst F.; Weier,Jingly F.

    2006-01-04

    The incidence of papillary thyroid carcinoma (PTC) increases significantly after exposure of the head and neck region to ionizing radiation, yet we know neither the steps involved in malignant transformation of thyroid epithelium nor the specific carcinogenic mode of action of radiation. Such increased tumor frequency became most evident in children after the 1986 nuclear accident in Chernobyl, Ukraine. In the twelve years following the accident, the average incidence of childhood PTCs (chPTC) increased over one hundred-fold compared to the rate of about 1 tumor incidence per 10{sup 6} children per year prior to 1986. To study the etiology of radiation-induced thyroid cancer, we formed an international consortium to investigate chromosomal changes and altered gene expression in cases of post-Chernobyl chPTC. Our approach is based on karyotyping of primary cultures established from chPTC specimens, establishment of cell lines and studies of genotype-phenotype relationships through high resolution chromosome analysis, DNA/cDNA micro-array studies, and mouse xenografts that test for tumorigenicity. Here, we report the application of fluorescence in situ hybridization (FISH)-based techniques for the molecular cytogenetic characterization of a highly tumorigenic chPTC cell line, S48TK, and its subclones. Using chromosome 9 rearrangements as an example, we describe a new approach termed ''BAC-FISH'' to rapidly delineate chromosomal breakpoints, an important step towards a better understanding of the formation of translocations and their functional consequences.

  1. Molecular characterization of a toluene-degrading methanogenic consortium

    SciTech Connect

    Ficker, M.; Krastel, K.; Orlicky, S.; Edwards, E.

    1999-12-01

    A toluene-degrading methanogenic consortium enriched from creosote-contaminated aquifer material was maintained on toluene as the sole carbon and energy source for 10 years. The species in the consortium were characterized by using a molecular approach. Total genomic DNA was isolated, and 16S rRBA genes were amplified by using PCR performed with kingdom-specific primers that were specific for 16S rRBA genes from either members of the kingdom Bacteria or members of the kingdom Archaea. A total of 90 eubacterial clones and 75 archaeal clones were grouped by performing a restriction fragment length polymorphism (RFLP) analysis. Six eubacterial sequences and two archaeal sequences were found in the greatest abundance (in six or more clones) based on the RFLP analysis. The relative abundance of each putative species was estimated by using fluorescent in situ hybridization (FISH), and the presence of putative species was determined qualitatively by performing slot blot hybridization with consortium DNA. Both archael species and two of the six eubacterial species were detected in the DNA and FISH hybridization experiments. A phylogenetic analysis of these four dominant organisms suggested that the two archaeal species are related to the genera methanosaeta and Methanospirillum. One of the eubacterial species is related to the genus Desulfotomaculum, which the others is not related to any previously described genus. By elimination, the authors propose that the last organism probably initiates the attack on toluene.

  2. Molecular characterization of de novo secondary trisomy 13

    SciTech Connect

    Shaffer, L.G.; McCaskill, C.; Han, Jin-Yeong; Choo, K.H.A.; Cutillo, D.M.; Donnenfeld, A.E.; Weiss, L.; Van Dyke, D.L.

    1994-11-01

    Unbalanced Robertsonian translocations are a significant cause of mental retardation and fetal wastage. The majority of homologous rearrangements of chromosome 21 in Down syndrome have been shown to be isochromosomes. Aside from chromosome 21, very little is known about other acrocentric homologous rearrangements. In this study, four cases of de novo secondary trisomy 13 are presented. FISH using alpha-satellite sequences, rDNA, and a pTRI-6 satellite I sequence specific to the short arm of chromosome 13 showed all four rearrangements to be dicentric an apparently devoid of ribosomal genes. Three of four rearrangements retained the pTRI-6 satellite I sequence. Case 1 was the exception, showing a deletion of this sequence in the rearrangement, although both parental chromosomes 13 had strong positive hybridization signals. Eleven microsatellite markers from chromosome 13 were also used to characterize the rearrangements. Of the four possible outcomes, one maternal Robertsonian translocation, two paternal isochromosomes, and one maternal isochromosomes were observed. A double recombination was observed in the maternally derived rob(13q13q). No recombination events were detected in any isochromosome. The parental origins and molecular chromosomal structure of these cases are compared with previous studies of de novo acrocentric rearrangements. 20 refs., 3 figs., 2 tabs.

  3. Molecular characterization of a Han Chinese family with essential hypertension.

    PubMed

    Zhu, J F; Zhang, X; Ling, L

    2016-01-01

    Mutations in the mitochondrial genome have been found to be associated with essential hypertension. Here, we report the clinical and molecular characterization of a three-generation Han Chinese family with maternally inherited hypertension. Most strikingly, this pedigree exhibited a high penetrance of hypertension. Sequence analysis of the mitochondrial genome showed the presence of a homoplasmic T16189C mutation in the D-loop and the intergenic CO2/tRNA(Lys) 9-bp common deletion, as well as a set of polymorphisms belonging to the East Asia haplogroup B5b1. The well-known T16189C mutation, which is in the first hypervariable segment of the mitochondrial control region, is implicated to be associated with a wide range of clinical disorders. Moreover, the genetic polymorphism 9-bp common deletion is found to be associated with hepatocellular carcinoma in the Han Chinese population. Thus, the combination of T16189C mutation and the 9-bp deletion may have caused mitochondrial dysfunction and contributed to the development of essential hypertension in this Chinese family. PMID:27323027

  4. Immunohistochemical and Molecular Characterization of the Human Periosteum

    PubMed Central

    Frey, Sönke Percy; Jansen, Hendrik; Doht, Stefanie; Filgueira, Luis; Zellweger, Rene

    2013-01-01

    Purpose. The aim of the present study was to characterize the cell of the human periosteum using immunohistological and molecular methods. Methods. Phenotypic properties and the distribution of the cells within the different layers were investigated with immunohistochemical staining techniques and RT-PCR, focussing on markers for stromal stem cells, osteoblasts, osteoclasts and immune cells. Results. Immunohistochemical results revealed that all stained cells were located in the cambium layer and that most cells were positive for vimentin. The majority of cells consisted of stromal stem cells and osteoblastic precursor cells. The density increased towards the deeper layers of the cambium. In addition, cells positive for markers of the osteoblast, chondrocyte, and osteoclast lineages were found. Interestingly, there were MHC class II-expressing immune cells suggesting the presence of dendritic cells. Using lineage-specific primer pairs RT-PCR confirmed the immunofluorescence microscopy results, supporting that human periosteum serves as a reservoir of stromal stem cells, as well as cells of the osteoblastic, and the chondroblastic lineage, osteoclasts, and dendritic cells. Conclusion. Our work elucidates the role of periosteum as a source of cells with a high regenerative capacity. Undifferentiated stromal stem cells as well as osteoblastic precursor cells are dominating in the cambium layer. A new outlook is given towards an immune response coming from the periosteum as MHC II positive immune cells were detected. PMID:23737713

  5. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  6. Clinical, biochemical and molecular characterization of prosaposin deficiency.

    PubMed

    Motta, M; Tatti, M; Furlan, F; Celato, A; Di Fruscio, G; Polo, G; Manara, R; Nigro, V; Tartaglia, M; Burlina, A; Salvioli, R

    2016-09-01

    Prosaposin (PSAP) deficiency is an ultra-rare, fatal infantile lysosomal storage disorder (LSD) caused by variants in the PSAP gene, with seven subjects reported so far. Here, we provide the clinical, biochemical and molecular characterization of two additional PSAP deficiency cases. Lysoplex, a targeted resequencing approach was utilized to identify the variant in the first patient, while quantification of plasma lysosphingolipids (lysoSLs), assessed by liquid chromatography mass spectrometry (LC-MS/MS) and brain magnetic resonance imaging (MRI), followed by Sanger sequencing allowed to attain diagnosis in the second case. Functional studies were carried out on patients' fibroblast lines to explore the functional impact of variants. The two patients were homozygous for two different truncating PSAP mutations (c.895G>T, p.Glu299*; c.834_835delGA, p.Glu278Aspfs*27). Both variants led to a complete lack of processed transcript. LC-MS/MS and brain MRI analyses consistently provided a distinctive profile in the two children. Quantification of specific plasma lysoSLs revealed elevated levels of globotriaosylsphingosine (LysoGb3) and glucosylsphingosine (GlSph), and accumulation of autophagosomes, due to a decreased autophagic flux, was observed. This report documents the successful use of plasma lysoSLs profiling in the PSAP deficiency diagnosis, as a reliable and informative tool to obtain a preliminary information in infantile cases with complex traits displaying severe neurological signs and visceral involvement. PMID:26831127

  7. Antigenic and molecular characterization of rabies virus in Argentina.

    PubMed

    Cisterna, Daniel; Bonaventura, Romina; Caillou, Susana; Pozo, Oscar; Andreau, Maria Lidia; Fontana, Liliana Dalla; Echegoyen, Cristina; de Mattos, Carlos; de Mattos, Cecilia; Russo, Susana; Novaro, Laura; Elberger, Diana; Freire, María Cecilia

    2005-05-01

    The nucleoprotein genes of 54 human, domestic and wild animals rabies isolates obtained in Argentina between 1995 and 2002 were characterized using monoclonal antibodies and partial gene sequence analysis. The antigenic and genetic diversities of rabies virus in samples from bat and bat-related cases were studied, leading to the identification of five distinct genetic variants. Rabies viruses isolated from vampire bat related cases were very similar to each other, showing 98.9% overall similarity. Specific antigenic variants (AgV) were detected associated with different insectivorous bats species, in samples from Tadarida brasiliensis and Eumops patagonicus bats. In contrast, isolates from Myotis sp. and Histiotus sp. bats could not be matched to any antigenic type. Additionally, bat rabies cases were also detected in southern provinces previously considered rabies-free. Finally, two independent antigenic and genetic variants co-circulating in northern Argentina were found in isolates obtained from dogs and dog-related cases, suggesting two independent cycles of virus transmission. This is the first national coordinated study of antigenic as well as molecular epidemiology of rabies in Argentina. The information presented here will improve our knowledge about rabies epidemiology and therefore, will assist preventing fatal human cases. PMID:15763144

  8. Molecular characterization of interferon regulatory factor 1 in Bubalus bubalis.

    PubMed

    Stafuzza, N B; Borges, M M; Amaral-Trusty, M E J

    2015-01-01

    Interferon regulatory factor 1 (IRF1) is functionally diverse in the regulation of immune response and is considered to be an important candidate gene for studying disease susceptibility in mammals. In this paper, we characterized the whole sequence of the IRF1 gene in river buffalo (Bubalus bubalis) and compared genomic and the amino acid sequences between different species. The buffalo IRF1 gene was 7099 bp long and organized into 10 exons and nine introns. Its molecular structure showed exactly the same number of exons (10) and introns (nine) in bovids, mice, horses, humans, and chickens. However, rats did not have exon 5, but had the largest exon 4, which suggests that exon 5 was incorporated into exon 4. The coding and the amino acid sequences of the gene showed that identity varied from 73 to 99% at the coding sequence level and from 61 to 100% at the amino acid level when compared with other mammals and chickens. Comparative analysis of the gene sequence between two different buffalo breeds, Murrah and Mediterranean, revealed six potential SNPs that are primarily located in the 5' and 3'UTRs. PMID:26400319

  9. Characterization of the Binding Properties of Molecularly Imprinted Polymers.

    PubMed

    Ansell, Richard J

    2015-01-01

    The defining characteristic of the binding sites of any particular molecularly imprinted material is heterogeneity: that is, they are not all identical. Nonetheless, it is useful to study their fundamental binding properties, and to obtain average properties. In particular, it has been instructive to compare the binding properties of imprinted and non-imprinted materials. This chapter begins by considering the origins of this site heterogeneity. Next, the properties of interest of imprinted binding sites are described in brief: affinity, selectivity, and kinetics. The binding/adsorption isotherm, the graph of concentration of analyte bound to a MIP versus concentration of free analyte at equilibrium, over a range of total concentrations, is described in some detail. Following this, the techniques for studying the imprinted sites are described (batch-binding assays, radioligand binding assays, zonal chromatography, frontal chromatography, calorimetry, and others). Thereafter, the parameters that influence affinity, selectivity and kinetics are discussed (solvent, modifiers of organic solvents, pH of aqueous solvents, temperature). Finally, mathematical attempts to fit the adsorption isotherms for imprinted materials, so as to obtain information about the range of binding affinities characterizing the imprinted sites, are summarized. PMID:25796622

  10. Molecular characterization of barley yellow dwarf virus in Tunisia.

    PubMed

    Bouallegue, M; Mezghani-Khemakhem, M; Bouktila, D; Makni, H; Makni, M

    2014-01-01

    Barley yellow dwarf disease is a worldwide ubiquitous virus disease of cereal crops. In order to characterize the B/CYDV isolates occurring in Tunisia, 240 barley leaves were randomly sampled from 6 fields following a North-South trend and analyzed by serological and molecular tests. DAS-ELISA results showed 40 positive samples with a prevalence of barley yellow dwarf virus (BYDV)-PAV (77.5%), followed by cereal yellow dwarf virus (CYDV)-RPV (25%) and BYDV-MAV (15%). Studies of the geographic distribution showed a high incidence of B/CYDV in the Tunisian Southern provinces. RT-PCR assays were performed to amplify the viral coat protein gene (CP) and sequence analyses revealed six BYDV-PAV haplotypes named PAV-TN1 to PAV-TN6. Phylogenetic analysis showed that the six Tunisian haplotypes were close to BYDV-PAV-II subspecies and had a strong similarity with Moroccan, Czech, French and German haplotypes. Although PAV-TN2 and PAV-TN5 showed up to 10% divergence from BYDV-PAV-II at the amino acid level, it seems to belong to the same subspecies but in a separated cluster. Our results will be important in developing appropriate control measures against BYDV disease in Tunisia.

  11. Molecular characterization of Salmonella Typhimurium highly successful outbreak strains.

    PubMed

    Petersen, Randi Føns; Litrup, Eva; Larsson, Jonas T; Torpdahl, Mia; Sørensen, Gitte; Müller, Luise; Nielsen, Eva M

    2011-06-01

    Three large clusters of Salmonella Typhimurium infections in Denmark in 2008 and 2009 were defined by multilocus variable number of tandem repeat analysis (MLVA). One of these proved to be the hereto largest Danish cluster of salmonellosis with 1446 cases. Two smaller clusters with a total of 197 and 89 cases, respectively, were seen concurrently. These clusters shared epidemiological characteristics such as age distribution, geography, and time. To investigate the possible genetic relationship between the cluster strains, these were further characterized by phage typing, pulsed-field gel electrophoresis, and Optical Mapping. Although the MLVA method proved robust and well-performing in detecting and defining clusters, the employment of a second typing method detected an additional fourth cluster among the isolates. The cluster strains were stable throughout the almost 2-year period, even though we detected changes in three of five MLVA loci in a small fraction of isolates. These changes were mainly due to the gain or loss of single repeats. Optical Mapping of the large cluster strain indicated no increased content of virulence genes; however, Optical Mapping did reveal a large insert, a probable prophage, in the main cluster. This probable prophage may give the cluster strain a competitive advantage. The molecular methods employed suggested that the four clusters represented four distinct strains, although they seemed to be epidemiologically linked and shared genotypic characteristics.

  12. Molecular and Cytogenetic Characterization of Wild Musa Species

    PubMed Central

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

    2015-01-01

    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

  13. Molecular and Cytogenetic Characterization of Wild Musa Species.

    PubMed

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

    2015-01-01

    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

  14. Molecular and serological characterization of the first Leptospira santarosai strain isolated from a dog.

    PubMed

    Miotto, Bruno Alonso; Moreno, Luisa Zanolli; Guilloux, Aline Gil Alves; Sousa, Gisele Oliveira de; Loureiro, Ana Paula; Moreno, Andrea Micke; Lilenbaum, Walter; Vasconcellos, Silvio Arruda; Heinemann, Marcos Bryan; Hagiwara, Mitika Kuribayashi

    2016-10-01

    Leptospirosis is a zoonotic disease of global importance caused by pathogenic Leptospira species. Dogs can become asymptomatically infected, acting like reservoir hosts for pathogenic Leptospira, notably Leptospira interrogans serovar Canicola. Identification of such individuals and characterization of leptospires involved in chronic infections may unravel the role of dogs in the epidemiology of particular leptospiral strains. The aim of the present work was to describe the first Leptospira santarosai strain isolated from a dog. The dog was kept in a public shelter in São Paulo city, Brazil, and presented asymptomatic urinary shedding detected by PCR. Prospective evaluation was performed to fully characterize its chronic carrier state. The dog did not present anti-Leptospira titles or clinical/laboratorial abnormalities during the evaluations; nevertheless long-term urinary shedding was confirmed by PCR and leptospires were recovered from two occasions. The isolated strain was molecularly characterized by partial 16S rRNA and secY gene sequencing and MLST analysis. Serogroup identification was performed using polyclonal antibodies. The strain was identified as Leptospira santarosai, serogroup Sejroe. This is the first evidence in the literature of the isolation of L. santarosai in dogs. Our findings show that dogs can persistently harbor leptospires other than L. interrogans.

  15. Molecular and serological characterization of the first Leptospira santarosai strain isolated from a dog.

    PubMed

    Miotto, Bruno Alonso; Moreno, Luisa Zanolli; Guilloux, Aline Gil Alves; Sousa, Gisele Oliveira de; Loureiro, Ana Paula; Moreno, Andrea Micke; Lilenbaum, Walter; Vasconcellos, Silvio Arruda; Heinemann, Marcos Bryan; Hagiwara, Mitika Kuribayashi

    2016-10-01

    Leptospirosis is a zoonotic disease of global importance caused by pathogenic Leptospira species. Dogs can become asymptomatically infected, acting like reservoir hosts for pathogenic Leptospira, notably Leptospira interrogans serovar Canicola. Identification of such individuals and characterization of leptospires involved in chronic infections may unravel the role of dogs in the epidemiology of particular leptospiral strains. The aim of the present work was to describe the first Leptospira santarosai strain isolated from a dog. The dog was kept in a public shelter in São Paulo city, Brazil, and presented asymptomatic urinary shedding detected by PCR. Prospective evaluation was performed to fully characterize its chronic carrier state. The dog did not present anti-Leptospira titles or clinical/laboratorial abnormalities during the evaluations; nevertheless long-term urinary shedding was confirmed by PCR and leptospires were recovered from two occasions. The isolated strain was molecularly characterized by partial 16S rRNA and secY gene sequencing and MLST analysis. Serogroup identification was performed using polyclonal antibodies. The strain was identified as Leptospira santarosai, serogroup Sejroe. This is the first evidence in the literature of the isolation of L. santarosai in dogs. Our findings show that dogs can persistently harbor leptospires other than L. interrogans. PMID:27282095

  16. Validation and Error Characterization for the Global Precipitation Measurement

    NASA Technical Reports Server (NTRS)

    Bidwell, Steven W.; Adams, W. J.; Everett, D. F.; Smith, E. A.; Yuter, S. E.

    2003-01-01

    The Global Precipitation Measurement (GPM) is an international effort to increase scientific knowledge on the global water cycle with specific goals of improving the understanding and the predictions of climate, weather, and hydrology. These goals will be achieved through several satellites specifically dedicated to GPM along with the integration of numerous meteorological satellite data streams from international and domestic partners. The GPM effort is led by the National Aeronautics and Space Administration (NASA) of the United States and the National Space Development Agency (NASDA) of Japan. In addition to the spaceborne assets, international and domestic partners will provide ground-based resources for validating the satellite observations and retrievals. This paper describes the validation effort of Global Precipitation Measurement to provide quantitative estimates on the errors of the GPM satellite retrievals. The GPM validation approach will build upon the research experience of the Tropical Rainfall Measuring Mission (TRMM) retrieval comparisons and its validation program. The GPM ground validation program will employ instrumentation, physical infrastructure, and research capabilities at Supersites located in important meteorological regimes of the globe. NASA will provide two Supersites, one in a tropical oceanic and the other in a mid-latitude continental regime. GPM international partners will provide Supersites for other important regimes. Those objectives or regimes not addressed by Supersites will be covered through focused field experiments. This paper describes the specific errors that GPM ground validation will address, quantify, and relate to the GPM satellite physical retrievals. GPM will attempt to identify the source of errors within retrievals including those of instrument calibration, retrieval physical assumptions, and algorithm applicability. With the identification of error sources, improvements will be made to the respective calibration

  17. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear.

  18. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear. PMID:16103373

  19. Europa: Characterization and interpretation of global spectral surface units

    USGS Publications Warehouse

    Nelson, M.L.; McCord, T.B.; Clark, R.N.; Johnson, T.V.; Matson, D.L.; Mosher, J.A.; Soderblom, L.A.

    1986-01-01

    The Voyager global multispectral mosaic of the Galilean satellite Europa (T. V. Johnson, L. A. Soderblom, J. A. Mosher, G. E. Danielson, A. F. Cook, and P. Kupferman, 1983, J. Geophys. Res. 88, 5789-5805) was analyzed to map surface units with similar optical properties (T. B. McCord, M. L. Nelson, R. N. Clark, A. Meloy, W. Harrison, T. V. Johnson, D. L. Matson, J. A. Mosher, and L. Soderblom, 1982, Bull Amer. Astron. Soc. 14, 737). Color assignments in the unit map are indicative of the spectral nature of the unit. The unit maps make it possible to infer extensions of the geologic units mapped by B. K. Lucchitta and L. A. Soderblom (1982, in Satellites of Jupiter, pp. 521-555, Univ. of Arizona Press, Tucson) beyond the region covered in the high-resolution imagery. The most striking feature in the unit maps is a strong hemispheric asymmetry. It is seen most clearly in the ultraviolet/violet albedo ratio image, because the asymmetry becomes more intense as the wavelength decreases. It appears as if the surface has been darkened, most intensely in the center of the trailing hemisphere and decreasing gradually, essentially as the cosine of the angle from the antapex of motion, to a minimum in the center of the leading hemisphere. The cosine pattern suggests that the darkening is exogenic in origin and is interpreted as evidence of alteration of the surface by ion bombardment from the Jovian magnetosphere. ?? 1986.

  20. Molecular characterization of chicken class II transactivator gene.

    PubMed

    Nikbakht Brujeni, Gholamreza; Khosravi, Mohammad

    2015-01-01

    Class II transactivator (CIITA) is an effective transcriptional factor regulating various genes in the immune system. Since the detection of CIITA in 1993, there has been considerable progress toward understanding its role as an activator of MHC II genes in human and mouse; however, there is little knowledge of this gene in other animals such as chicken. Molecular characterization of the chicken CIITA gene transcript was performed to determine its sequence and expression in different tissues. The CIITA cDNA was first generated through reverse transcriptase-polymerase chain reaction (RT-PCR) from Cobb chicken spleen cell RNA, using oligonucleotide primers based on the predicted cDNA sequence. The effect of the immune system stimulation on the CIITA gene expression in kidney, liver, thymus, and spleen were assessed by semi-quantitative RT-PCR analysis. A partial cDNA sequence (1,688 bp) encoding part of the NACHT domain followed by seven of the transactivator and one of the NLS domains were obtained. Comparison of the deduced amino acid sequence with other CIITAs reveals high level of similarities in amino acid composition, secondary structure and phosphorylation sites. Furthermore, in comparison to the Red Jungle Fowl (RJF) sequence, we found 17 single nucleotide polymorphisms in Cobb broiler chicken, ten of which were reported for the first time. Gene expression analysis indicated that CIITA RNA amounts increased in all the examined tissues following stimulation with Brucella antigen. This investigation may indicate that CIITA molecule has an important role in the chicken immune responses as well as human and other animals.

  1. Molecular characterization of Spanish infectious bursal disease virus field isolates.

    PubMed

    Majó, N; El-Attrache, J; Banda, A; Villegas, P; Ramis, A; Pagès, A; Ikuta, N

    2002-01-01

    Nine Spanish isolates of infectious bursal disease virus (IBDV) were characterized and classified after reverse transcriptase-polymerase chain reaction of a 248-bp fragment of the VP2 gene hypervariable region and restriction fragment length polymorphism (RFLP). The restriction endonucleases (REs) used were BstNI, Sad, SspI, TaqI, DraI, and StyI. Sequencing of the amplified product and further comparison of these sequences with published sequence data from other IBDV strains were also performed. Very virulent and classic strains were identified. None of the strains identified had molecular characteristics similar to that of the American variant strains. Four very virulent strains (VG-248, 5939, 6145, and 7333) were digested by the TaqI, SspI, and StyI enzymes. The sequences of these strains were closely related to other European and Japanese very virulent IBDV (vvIBDV) strains. Strains VG-311, VG-262, and VG-208 were digested by the BstNI and Sad REs and were classified as classic strains. Strains VG-276 and VG-313 had unique RFLP patterns. VG-276 exhibited the SspI RE site, which has been reported as a characteristic of vvIBDV strains, whereas the VG-313 strain exhibited a Sad and StyI RE site indicative of the classic IBDV Edgar and 52-70 strains. However, nucleotide sequence analysis of the amplified hypervariable region strain VG-276 revealed a higher identity with the classic strains STC, 52/70, and 9109 IBDV strains, whereas strain VG-313 exhibited a higher identity with the vvIBDV strains.

  2. Morphological and Molecular Characterization of Human Dermal Lymphatic Collectors

    PubMed Central

    Buttler, Kerstin; Ströbel, Philipp; Becker, Jürgen; Aung, Thiha; Felmerer, Gunther; Wilting, Jörg

    2016-01-01

    Millions of patients suffer from lymphedema worldwide. Supporting the contractility of lymphatic collectors is an attractive target for pharmacological therapy of lymphedema. However, lymphatics have mostly been studied in animals, while the cellular and molecular characteristics of human lymphatic collectors are largely unknown. We studied epifascial lymphatic collectors of the thigh, which were isolated for autologous transplantations. Our immunohistological studies identify additional markers for LECs (vimentin, CCBE1). We show and confirm differences between initial and collecting lymphatics concerning the markers ESAM1, D2-40 and LYVE-1. Our transmission electron microscopic studies reveal two types of smooth muscle cells (SMCs) in the media of the collectors with dark and light cytoplasm. We observed vasa vasorum in the media of the largest collectors, as well as interstitial Cajal-like cells, which are highly ramified cells with long processes, caveolae, and lacking a basal lamina. They are in close contact with SMCs, which possess multiple caveolae at the contact sites. Immunohistologically we identified such cells with antibodies against vimentin and PDGFRα, but not CD34 and cKIT. With Next Generation Sequencing we searched for highly expressed genes in the media of lymphatic collectors, and found therapeutic targets, suitable for acceleration of lymphatic contractility, such as neuropeptide Y receptors 1, and 5; tachykinin receptors 1, and 2; purinergic receptors P2RX1, and 6, P2RY12, 13, and 14; 5-hydroxytryptamine receptors HTR2B, and 3C; and adrenoceptors α2A,B,C. Our studies represent the first comprehensive characterization of human epifascial lymphatic collectors, as a prerequisite for diagnosis and therapy. PMID:27764183

  3. Molecular characterization of tick salivary gland glutaminyl cyclase.

    PubMed

    Adamson, Steven W; Browning, Rebecca E; Chao, Chien-Chung; Bateman, Robert C; Ching, Wei-Mei; Karim, Shahid

    2013-09-01

    Glutaminyl cyclase (QC) catalyzes the cyclization of N-terminal glutamine residues into pyroglutamate. This post-translational modification extends the half-life of peptides and, in some cases, is essential in binding to their cognate receptor. Due to its potential role in the post-translational modification of tick neuropeptides, we report the molecular, biochemical and physiological characterization of salivary gland QC during the prolonged blood feeding of the black-legged tick (Ixodes scapularis) and the gulf-coast tick (Amblyomma maculatum). QC sequences from I. scapularis and A. maculatum showed a high degree of amino acid identity to each other and other arthropods and residues critical for zinc binding/catalysis (D159, E202, and H330) or intermediate stabilization (E201, W207, D248, D305, F325, and W329) are conserved. Analysis of QC transcriptional gene expression kinetics depicts an upregulation during the bloodmeal of adult female ticks prior to fast-feeding phases in both I. scapularis and A. maculatum suggesting a functional link with bloodmeal uptake. QC enzymatic activity was detected in saliva and extracts of tick salivary glands and midguts. Recombinant QC was shown to be catalytically active. Furthermore, knockdown of QC transcript by RNA interference resulted in lower enzymatic activity, and small, unviable egg masses in both studied tick species as well as lower engorged tick weights for I. scapularis. These results suggest that the post-translational modification of neurotransmitters and other bioactive peptides by QC is critical to oviposition and potentially other physiological processes. Moreover, these data suggest that tick-specific QC-modified neurotransmitters/hormones or other relevant parts of this system could potentially be used as novel physiological targets for tick control. PMID:23770496

  4. Preliminary molecular characterization of the human pathogen Angiostrongylus cantonensis

    PubMed Central

    He, Hualiang; Cheng, Mei; Yang, Xiao; Meng, Jinxiu; He, Ai; Zheng, Xiaoying; Li, Zhuoya; Guo, Pengjuan; Pan, Zhihua; Zhan, Ximei

    2009-01-01

    Background Human angiostrongyliasis is an emerging food-borne public health problem, with the number of cases increasing worldwide, especially in mainland China. Angiostrongylus cantonensis is the causative agent of this severe disease. However, little is known about the genetics and basic biology of A. cantonensis. Results A cDNA library of A. cantonensis fourth-stage larvae was constructed, and ~1,200 clones were sequenced. Bioinformatic analyses revealed 378 cDNA clusters, 54.2% of which matched known genes at a cutoff expectation value of 10-20. Of these 378 unique cDNAs, 168 contained open reading frames encoding proteins containing an average of 238 amino acids. Characterization of the functions of these encoded proteins by Gene Ontology analysis showed enrichment in proteins with binding and catalytic activity. The observed pattern of enzymes involved in protein metabolism, lipid metabolism and glycolysis may reflect the central nervous system habitat of this pathogen. Four proteins were tested for their immunogenicity using enzyme-linked immunosorbent assays and histopathological examinations. The specificity of each of the four proteins was superior to that of crude somatic and excretory/secretory antigens of larvae, although their sensitivity was relatively low. We further showed that mice immunized with recombinant cystatin, a product of one of the four cDNA candidate genes, were partially protected from A. cantonensis infection. Conclusion The data presented here substantially expand the available genetic information about the human pathogen A. cantonensis, and should be a significant resource for angiostrongyliasis researchers. As such, this work serves as a starting point for molecular approaches for diagnosing and controlling human angiostrongyliasis. PMID:19852860

  5. Micro/Nanosatellite Mars Network for Global Lower Atmosphere Characterization

    NASA Technical Reports Server (NTRS)

    Tinker, Mike L.

    2012-01-01

    To address multiple key challenge areas for robotic exploration of Mars, to achieve scientific goals and reduce risk for future human missions, a micro/nanosatellite constellation for lower atmosphere characterization is proposed. A microsatellite design is discussed that can operate (1) in tandem with another microsat or (2) as a "mother-ship" to deploy a network of nanosatellites (CubeSats). Either configuration of the network would perform radio occultation-based atmospheric measurements. Advantages of the proposed network are low development cost based on an existing microsatellite bus, and proven performance of the bus to date. Continued efforts in miniaturization of instruments are needed to fully enable the mother-ship/nanosat version of the proposed network.

  6. MODIS and AERONET characterization of the global aerosol

    NASA Astrophysics Data System (ADS)

    Kaufman, Y. J.; Remer, L. A.; Tanre, D.

    2002-05-01

    Recently produced daily MODIS aerosol data for the whole year of 2001 are used to show the concentration and dynamics of aerosol over ocean and large parts of the continents. The data were validated against the Aerosol Robotic Network (AERONET) measurements over land and ocean. Monthly averages and a movie based on the daily data are produced and used to demonstrate the spatial and temporal evolution of aerosol. The MODIS wide spectral range is used to distinguish fine smoke and pollution aerosol from coarse dust and salt. The movie produced from the MODIS data provides a new dimension to aerosol observations by showing the dynamics of the system. For example in February smoke and dust emitted from the Sahel and West Africa is shown to travel to the North-East Atlantic. In April heavy dust and pollution from East Asia is shown to travel to North America. In May-June pollution and dust play a dynamical dance in the Arabian Sea and Bay of Bengal. In Aug-September smoke from South Africa and South America is shown to pulsate in tandem and to periodically to be transported to the otherwise pristine Southern part of the Southern Hemisphere. To use the MODIS data for global assessment of aerosol forcing AERONET data are used to answer some key critical questions: - Are MODIS data collected at 10:30 am representative of the daily forcing? - What is the concentration and properties of background aerosol and that of anthropogenic aerosol These questions and more will be answered in the talk

  7. Global-Scale Hydrology: Simple Characterization of Complex Simulation

    NASA Technical Reports Server (NTRS)

    Koster, Randal D.

    1999-01-01

    Atmospheric general circulation models (AGCMS) are unique and valuable tools for the analysis of large-scale hydrology. AGCM simulations of climate provide tremendous amounts of hydrological data with a spatial and temporal coverage unmatched by observation systems. To the extent that the AGCM behaves realistically, these data can shed light on the nature of the real world's hydrological cycle. In the first part of the seminar, I will describe the hydrological cycle in a typical AGCM, with some emphasis on the validation of simulated precipitation against observations. The second part of the seminar will focus on a key goal in large-scale hydrology studies, namely the identification of simple, overarching controls on hydrological behavior hidden amidst the tremendous amounts of data produced by the highly complex AGCM parameterizations. In particular, I will show that a simple 50-year-old climatological relation (and a recent extension we made to it) successfully predicts, to first order, both the annual mean and the interannual variability of simulated evaporation and runoff fluxes. The seminar will conclude with an example of a practical application of global hydrology studies. The accurate prediction of weather statistics several months in advance would have tremendous societal benefits, and conventional wisdom today points at the use of coupled ocean-atmosphere-land models for such seasonal-to-interannual prediction. Understanding the hydrological cycle in AGCMs is critical to establishing the potential for such prediction. Our own studies show, among other things, that soil moisture retention can lead to significant precipitation predictability in many midlatitude and tropical regions.

  8. Synthesis and characterization of low-dimensional molecular magnetic materials

    NASA Astrophysics Data System (ADS)

    Liu, Chen

    This dissertation presents experimental results from the synthesis and structural, magnetic characterization of representative low-dimensional molecule-based magnetic materials. Most of the materials reported in this dissertation, both coordination polymers and cuprate, are obtained as the result of synthesizing and characterizing spin ladder systems; except the material studied in Chapter 2, ferricenyl(III)trisferrocenyl(II)borate, which is not related to the spin ladder project. The interest in spin ladder systems is due to the discovery of high-temperature superconductivity in doped cuprates possessing ladder-like structures, and it is hoped that investigation of the magnetic behavior of ladder-like structures will help us understand the mechanism of high-temperature superconductivity. Chapter 1 reviews fundamental knowledge of molecular magnetism, general synthetic strategies for low-dimensional coordination polymers, and a brief introduction to the current status of research on spin ladder systems. Chapter 2 presents a modified synthetic procedure of a previously known monomeric complex, ferricenyl(III)trisferrocenyl(II)borate, 1. Its magnetic properties were characterized and previous results have been disproved. Chapter 3 investigates the magnetism of [CuCl2(CH3CN)] 2, 2, a cuprate whose structure consists of isolated noninterpenetrating ladders formed by the stacking of Cu(II) dimers. This material presents an unexpected ferromagnetic interaction both within the dimeric units and between the dimers, and this behavior has been rationalized based on the effect of its terminal nonbridging ligands. In Chapter 4, the synthesis and magnetism of two ladder-like coordination polymers, [Co(NO3)2(4,4'-bipyridine) 1.5(MeCN)]n, 3, and Ni2(2,6-pyridinedicarboxylic acid)2(H2O)4(pyrazine), 4, are reported. Compound 3 possesses a covalent one-dimensional ladder structure in which Co(II) ions are bridged through bipyridine molecules. Compared to the materials discussed in

  9. Molecular characterization of Hop mosaic virus: its serological and molecular relationships to Hop latent virus.

    PubMed

    Hataya, T; Arimoto, R; Suda, N; Uyeda, I

    2001-10-01

    The 3'-terminal sequence of hop mosaic virus (HpMV) genomic RNA was determined. A cDNA of approximately 1.8 kbp was amplified from the HpMV genome by 3' RACE using a degenerate primer, which was designed to anneal to the overlapping region of open reading frames (ORFs) 2 and 3 of eight carlavirus genomes. The sequence contained three ORFs, encoding proteins of 7-, 34-, and 11-kDa, which corresponded to ORFs 4, 5, and 6 of the carlavirus genome, respectively. The amino acid sequence of ORF 5, encoding the coat protein (CP) of HpMV, shows the highest identity (67%) to that of Hop latent virus (HpLV). The HpMV CP N-terminal sequence differs from that of HpLV, but the central and C-terminal sequences of the CP of both viruses are similar. The sequence similarity possibly causes the cross-reaction of heterologous antibodies of HpMV and HpLV. Phylogenetic analyses based on the CP amino acid and 3' non-coding region sequences indicate close relationships among HpMV, HpLV, and Potato virus M. We report here the first molecular characterization of HpMV genomic RNA. PMID:11722015

  10. Size-exclusion chromatography of ultrahigh molecular weight methylcellulose ethers and hydroxypropyl methylcellulose ethers for reliable molecular weight distribution characterization.

    PubMed

    Li, Yongfu; Shen, Hongwei; Lyons, John W; Sammler, Robert L; Brackhagen, Meinolf; Meunier, David M

    2016-03-15

    Size-exclusion chromatography (SEC) coupled with multi-angle laser light scattering (MALLS) and differential refractive index (DRI) detectors was employed for determination of the molecular weight distributions (MWD) of methylcellulose ethers (MC) and hydroxypropyl methylcellulose ethers (HPMC) having weight-average molecular weights (Mw) ranging from 20 to more than 1,000kg/mol. In comparison to previous work involving right-angle light scattering (RALS) and a viscometer for MWD characterization of MC and HPMC, MALLS yields more reliable molecular weight for materials having weight-average molecular weights (Mw) exceeding about 300kg/mol. A non-ideal SEC separation was observed for cellulose ethers with Mw>800kg/mol, and was manifested by upward divergence of logM vs. elution volume (EV) at larger elution volume at typical SEC flow rate such as 1.0mL/min. As such, the number-average molecular weight (Mn) determined for the sample was erroneously large and polydispersity (Mw/Mn) was erroneously small. This non-ideality resulting in the late elution of high molecular weight chains could be due to the elongation of polymer chains when experimental conditions yield Deborah numbers (De) exceeding 0.5. Non-idealities were eliminated when sufficiently low flow rates were used. Thus, using carefully selected experimental conditions, SEC coupled with MALLS and DRI can provide reliable MWD characterization of MC and HPMC covering the entire ranges of compositions and molecular weights of commercial interest. PMID:26794765

  11. Size-exclusion chromatography of ultrahigh molecular weight methylcellulose ethers and hydroxypropyl methylcellulose ethers for reliable molecular weight distribution characterization.

    PubMed

    Li, Yongfu; Shen, Hongwei; Lyons, John W; Sammler, Robert L; Brackhagen, Meinolf; Meunier, David M

    2016-03-15

    Size-exclusion chromatography (SEC) coupled with multi-angle laser light scattering (MALLS) and differential refractive index (DRI) detectors was employed for determination of the molecular weight distributions (MWD) of methylcellulose ethers (MC) and hydroxypropyl methylcellulose ethers (HPMC) having weight-average molecular weights (Mw) ranging from 20 to more than 1,000kg/mol. In comparison to previous work involving right-angle light scattering (RALS) and a viscometer for MWD characterization of MC and HPMC, MALLS yields more reliable molecular weight for materials having weight-average molecular weights (Mw) exceeding about 300kg/mol. A non-ideal SEC separation was observed for cellulose ethers with Mw>800kg/mol, and was manifested by upward divergence of logM vs. elution volume (EV) at larger elution volume at typical SEC flow rate such as 1.0mL/min. As such, the number-average molecular weight (Mn) determined for the sample was erroneously large and polydispersity (Mw/Mn) was erroneously small. This non-ideality resulting in the late elution of high molecular weight chains could be due to the elongation of polymer chains when experimental conditions yield Deborah numbers (De) exceeding 0.5. Non-idealities were eliminated when sufficiently low flow rates were used. Thus, using carefully selected experimental conditions, SEC coupled with MALLS and DRI can provide reliable MWD characterization of MC and HPMC covering the entire ranges of compositions and molecular weights of commercial interest.

  12. Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.

    PubMed

    Wang, Haihong; Shao, Yina; Zhang, Weiwei; Li, Chenghua; Lv, Zhimeng; Jin, Chunhua

    2015-10-01

    Molecular chaperones of 78 kDa glucose-regulated protein (GRP78) and protein disulfide isomerase (PDI) are involved in protein folding and assembly in the endoplasmic reticulum (ER). Increasing evidences also suggest that these two molecules play an important role in immune response. In the present study, we cloned and characterized GRP78 and PDI genes from Apostichopus japonicus by RNA-seq and RACE approaches (designated as AjGRP78 and AjPDI, respectively). The AjGRP78 cDNA was of 2355bp including an open reading frame (ORF) of 2013 bp encoding a protein of 670 amino acids with three heat shock protein 70 (HSP70) family signatures. AjGRP78 contained a 23-amino acid signal peptide at the N-terminus and a HDEL motif at the C-terminus, which supported the location of the protein in the ER. The full length cDNA of AjPDI was of 1893 bp with a 5' untranslated region (UTR) of 153 bp, a 3' UTR of 228 bp and an ORF of 1512 bp encoding a protein of 503 amino acids. A 17-amino acid signal peptide, two thioredoxin domains with two active sites of CGHC, and KDEL retention signal were totally conserved in the deduced amino acid of AjPDI. Phylogenic analysis and multiple alignments have shown that both genes shared remarkably higher degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates, further supporting that the two proteins were novel members of molecular chaperone family. Spatial expression analysis revealed that AjGRP78 mRNA transcripts were dominantly expressed in the tentacle, while AjPDI mRNA levels were abundant in the muscle, intestine and respiratory trees. For Vibrio splendidus challenged sea cucumber, the peak expression of AjGRP78 and AjPDI mRNAs in coelomocytes were detected at 24h with 1.73-fold increase and at 6h with 1.83-fold increase compared with the control group, respectively. Similarly, a significant increase in the relative mRNA levels of AjGRP78 and AjPDI was also identified in 1 μg mL(-1

  13. Longitudinal molecular characterization of endoscopic specimens from colorectal lesions

    PubMed Central

    Minarikova, Petra; Benesova, Lucie; Halkova, Tereza; Belsanova, Barbora; Suchanek, Stepan; Cyrany, Jiri; Tuckova, Inna; Bures, Jan; Zavoral, Miroslav; Minarik, Marek

    2016-01-01

    AIM: To compare molecular profiles of proximal colon, distal colon and rectum in large adenomas, early and late carcinomas. To assess feasibility of testing directed at molecular markers from this study in routine clinical practice. METHODS: A prospective 3-year study has resulted in the acquisition of samples from 159 large adenomas and 138 carcinomas along with associated clinical parameters including localization, grade and histological type for adenomas and localization and stage for carcinomas. A complex molecular phenotyping has been performed using multiplex ligation-dependent probe amplification technique for the evaluation of CpG-island methylator phenotype (CIMP), PCR fragment analysis for detection of microsatellite instability and denaturing capillary electrophoresis for sensitive detection of somatic mutations in KRAS, BRAF, TP53 and APC genes. RESULTS: Molecular types according to previously introduced Jass classification have been evaluated for large adenomas and early and late carcinomas. An increase in CIMP+ type, eventually accompanied with KRAS mutations, was notable between large adenomas and early carcinomas. As expected, the longitudinal observations revealed a correlation of the CIMP+/BRAF+ type with proximal location. CONCLUSION: Prospective molecular classification of tissue specimens is feasible in routine endoscopy practice. Increased frequency of some molecular types corresponds to the developmental stages of colorectal tumors. As expected, a clear distinction is notable for tumors located in proximal colon supposedly arising from the serrated (methylation) pathway. PMID:27239120

  14. Molecular-level characterization of fluorescent dissolved organic matter in 120 boreal lakes using ultrahigh resolution mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kellerman, Anne; Kothawala, Dolly N.; Dittmar, Thorsten; Tranvik, Lars J.

    2014-05-01

    Dissolved organic matter (DOM) is a highly diverse composite of degradation products, with its reactivity and composition central to the role inland waters play in the global carbon cycle. Thus characterizing DOM is of great interest; however, a major challenge in DOM characterization is its inherent heterogeneity. Absorbance and fluorescence spectroscopy are accessible and time-efficient characterization techniques, thus the use of such techniques continues to increase. Despite the pervasive use of these methods, the molecular basis of many commonly used indices remains a subject of great interest. We analyzed 120 lakes across Sweden using 15 Tesla ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). This method allows for precise molecular formula assignment of thousands of molecules in each sample. These data were then compared to absorbance and fluorescence properties including a six-component model derived from parallel factor analysis (PARAFAC). We found that aliphatic compounds were most highly associated with microbially derived components and vascular plant-derived polyphenols were most highly associated with terrestrial components. This state of the art analysis reveals the specific chemistry behind widely used absorbance and fluorescence fingerprinting techniques and serves as a basis for future studies looking to understand the molecular characteristics of optical parameters.

  15. Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization.

    PubMed

    Schafroth, Heather D; Floudas, Christodoulos A

    2004-02-15

    Development of a computational prediction method based on molecular modeling, global optimization, and implicit solvation has produced accurate structure and relative binding affinity predictions for peptide amino acids binding to five pockets of the MHC molecule HLA-DRB1*0101. Because peptide binding to MHC molecules is essential to many immune responses, development of such a method for understanding and predicting the forces that drive binding is crucial for pharmaceutical design and disease treatment. Underlying the development of this prediction method are two hypotheses. The first is that pockets formed by the peptide binding groove of MHC molecules are independent, separating the prediction of peptide amino acids that bind within individual pockets from those that bind between pockets. The second hypothesis is that the native state of a system composed of an amino acid bound to a protein pocket corresponds to the system's lowest free energy. The prediction method developed from these hypotheses uses atomistic-level modeling, deterministic global optimization, and three methods of implicit solvation: solvent-accessible area, solvent-accessible volume, and Poisson-Boltzmann electrostatics. The method predicts relative binding affinities of peptide amino acids for pockets of HLA-DRB1*0101 by determining computationally an amino acid's global minimum energy conformation. Prediction results from the method are in agreement with X-ray crystallography data and experimental binding assays.

  16. The effects of flow-inhomogeneities on molecular cloud formation: Local versus global collapse

    SciTech Connect

    Carroll-Nellenback, Jonathan J.; Frank, Adam; Heitsch, Fabian

    2014-07-20

    Observational evidence from local star-forming regions mandates that star formation occurs shortly after, or even during, molecular cloud formation. Models of molecular cloud formation in large-scale converging flows have identified the physical mechanisms driving the necessary rapid fragmentation. They also point to global gravitational collapse driving supersonic turbulence in molecular clouds. Previous cloud formation models have focused on turbulence generation, gravitational collapse, magnetic fields, and feedback. Here, we explore the effect of structure in the flow on the resulting clouds and the ensuing gravitational collapse. We compare two extreme cases, one with a collision between two smooth streams, and one with streams containing small clumps. We find that structured converging flows lead to a delay of local gravitational collapse ({sup c}ore formation{sup )}. Hence, the cloud has more time to accumulate mass, eventually leading to a strong global collapse, and thus to a high core formation rate. Uniform converging flows fragment hydrodynamically early on, leading to the rapid onset of local gravitational collapse and an overall low core formation rate. This is also mirrored in the core mass distribution: the uniform initial conditions lead to more low-mass cores than the clumpy initial conditions. Kinetic (E{sub k} ) and gravitational energy (E{sub g} ) budgets suggest that collapse is only prevented for E{sub k} >> E{sub g} , which occurs for large scales in the smooth flow, and for small scales for the clumpy flow. Whenever E{sub k} ≈ E{sub g} , we observe gravitational collapse on those scales. Signatures of chemical abundance variations evolve differently for the gas phase and for the stellar population. For smooth flows, the forming cloud is well mixed, while its stellar population retains more information about the initial metallicities. For clumpy flows, the gas phase is less well mixed, while the stellar population has lost most of the

  17. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

    PubMed Central

    Pääbo, S

    1989-01-01

    Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics. Images PMID:2928314

  18. A Simple Index for Characterizing Charge Transport in Molecular Materials.

    PubMed

    Jackson, Nicholas E; Savoie, Brett M; Chen, Lin X; Ratner, Mark A

    2015-03-19

    While advances in quantum chemistry have rendered the accurate prediction of band alignment relatively straightforward, the ability to forecast a noncrystalline, multimolecule system's conductivity possesses no simple computational form. Adapting the theory of classical resistor networks, we develop an index for quantifying charge transport in bulk molecular materials, without the requirement of crystallinity. The basic behavior of this index is illustrated through its application to simple lattices and clusters of common organic photovoltaic molecules, where it is shown to reproduce experimentally known performances for these materials. This development provides a quantitative computational means for determining a priori the bulk charge transport properties of molecular materials. PMID:26262862

  19. PREPARATION AND CHARACTERIZATION OF MOLECULARLY IMPRINTED ELECTROPOLYMERIZED CARBON ELECTRODES

    EPA Science Inventory

    Molecularly imprinted polymers (MIP) selective for fluorescein, rhodamine or 2,4-dichlorophenoxyacetic acid (2,4-D) were electropolymerized onto graphite electrodes using an aqueous solution equimolar in resorsinol/ortho-phenylenediamine and in the presence of the template mole...

  20. Molecular maximizing characterizes choice on Vaughan's (1981) procedure.

    PubMed

    Silberberg, A; Ziriax, J M

    1985-01-01

    Pigeons keypecked on a two-key procedure in which their choice ratios during one time period determined the reinforcement rates assigned to each key during the next period (Vaughan, 1981). During each of four phases, which differed in the reinforcement rates they provided for different choice ratios, the duration of these periods was four minutes, duplicating one condition from Vaughan's study. During the other four phases, these periods lasted six seconds. When these periods were long, the results were similar to Vaughan's and appeared compatible with melioration theory. But when these periods were short, the data were consistent with molecular maximizing (see Silberberg & Ziriax, 1982) and were incompatible with melioration, molar maximizing, and matching. In a simulation, stat birds following a molecular-maximizing algorithm responded on the short- and long-period conditions of this experiment. When the time periods lasted four minutes, the results were similar to Vaughan's and to the results of the four-minute conditions of this study; when the time periods lasted six seconds, the choice data were similar to the data from real subjects for the six-second conditions. Thus, a molecular-maximizing response rule generated choice data comparable to those from the short- and long-period conditions of this experiment. These data show that, among extant accounts, choice on the Vaughan procedure is most compatible with molecular maximizing.

  1. Molecular characterization of Clonorchis sinensis secretory myoglobin: Delineating its role in anti-oxidative survival

    PubMed Central

    2014-01-01

    Background Clonorchiasis is a globally important, neglected food-borne disease caused by Clonorchis sinensis (C. sinensis), and it is highly related to cholangiocarcinoma and hepatocellular carcinoma. Increased molecular evidence has strongly suggested that the adult worm of C. sinensis continuously releases excretory-secretory proteins (ESPs), which play important roles in the parasite-host interactions, to establish successful infection and ensure its own survival. Myoglobin, a hemoprotein, is present in high concentrations in trematodes and ESPs. To further understand the biological function of CsMb and its putative roles in the interactions of C. sinensis with its host, we explored the molecular characterization of CsMb in this paper. Methods We expressed CsMb and its mutants in E. coli BL21 and identified its molecular characteristics using bioinformatics analysis and experimental approaches. Reverse transcription PCR analysis was used to measure myoglobin transcripts of C. sinensis with different culture conditions. The peroxidase activity of CsMb was confirmed by spectrophotometry. We co-cultured RAW264.7 cells with recombinant CsMb (rCsMb), and we then measured the production of hydrogen peroxide (H2O2) and nitric oxide (NO) in addition to the mRNA levels of inducible nitric oxide synthase (iNOS), Cu-Zn superoxide dismutase (SOD1) and Mn superoxide dismutase (SOD2) in activated RAW264.7 cells. Results In the in vitro culture of adult worms, the transcripts of CsMb increased with the increase of oxygen content. Oxidative stress conditions induced by H2O2 increased the levels of CsMb transcripts in a dose-dependent manner. Furthermore, CsMb catalyzed oxidation reactions in the presence of H2O2, and amino acid 34 of CsMb played an essential role in its reaction with H2O2. In addition, CsMb significantly reduced H2O2 and NO levels in LPS-activated macrophages, and CsMb downregulated iNOS and SOD expression in activated macrophages. Conclusion The present study

  2. Applications of molecular modeling to the design and characterization of materials

    SciTech Connect

    Carlson, G.A.; Faulon, J.L.; Pohl, P.I.; Shelnutt, J.A.

    1994-06-01

    A variety of new molecular modeling tools are now available for studying molecular structures and molecular interactions, for building molecular structures from simple components using analytical data, and for studying the relationship of molecular structure to the energy of bonding and non-bonding interactions. These are proving quite valuable in characterizing molecular structures and intermolecular interactions and in designing new molecules. This paper describes the application of molecular modeling techniques to a variety of materials problems, including the probable modecular structures of coals, lignins, and hybrid inorganic-organic-organic systems (silsesquioxanes), the intercalation of small gas molecules in fullerene crystals, the diffusion of gas molecules through membranes, and the design, structure and function of biomimetic and nanocluster catalysts.

  3. Molecular Characterization of Leishmania Species Isolated from Cutaneous Leishmaniasis in Yemen

    PubMed Central

    Mahdy, Mohammed A. K.; Al-Mekhlafi, Hesham M.; Al-Mekhlafi, Abdulsalam M.; Lim, Yvonne A. L.; Bin Shuaib, Naemah O. M.; Azazy, Ahmed A.; Mahmud, Rohela

    2010-01-01

    Background Cutaneous leishmaniasis (CL) is a neglected tropical disease endemic in the tropics and subtropics with a global yearly incidence of 1.5 million. Although CL is the most common form of leishmaniasis, which is responsible for 60% of DALYs lost due to tropical-cluster diseases prevalent in Yemen, available information is very limited. Methodology/Principal Findings This study was conducted to determine the molecular characterization of Leishmania species isolated from human cutaneous lesions in Yemen. Dermal scrapes were collected and examined for Leishmania amastigotes using the Giemsa staining technique. Amplification of the ribosomal internal transcribed spacer 1(ITS-1) gene was carried out using nested PCR and subsequent sequencing. The sequences from Leishmania isolates were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. The trees identified Leishmania tropica from 16 isolates which were represented by two sequence types. Conclusions/Significance The predominance of the anthroponotic species (i.e. L. tropica) indicates the probability of anthroponotic transmission of cutaneous leishmaniasis in Yemen. These findings will help public health authorities to build an effective control strategy taking into consideration person–to-person transmission as the main dynamic of transmission of CL. PMID:20862227

  4. Molecular Characterization and TRAP Analysis of Gene in Dendranthema morifolium.

    PubMed

    Luo, Y; Li, Q; Wang, X; Yang, F; Nong, S; Li, Q; Zhu, D

    2015-01-01

    The molecular maker system - TRAP was applied to develop a novel and more accurate method to identify the variety and establish the evolutionary relationship of different categories of Dendranthema morifolium. A software - GENESIS 2.4 was used to conduct the cluster analysis and genetic dendrogram establishment. The results showed that 202 different fragments were amplified with 6 pair primers using the TRAP marker system. The polymorphic fragments number is 45, which takes up to 22.3%. The cluster analysis showed that 4 materials used in this study can be classified into 2 main groups and 3 subgroups. The genetic identity is 0.0767 and the average genetic distance is 0.9236 among the four materials. A new tool using the TRAP marker system is more accurate and can be used to identify different categories of Dendranthema morifolium at molecular level. PMID:26638892

  5. First Molecular Characterization of Echinococcus multilocularis in Turkey.

    PubMed

    Avcioglu, Hamza; Guven, Esin; Balkaya, Ibrahim; Kirman, Ridvan; Bia, Mohammed Mebarek; Gulbeyen, Hatice

    2016-09-01

    This study aimed to find out the occurrence of Echinococcus multilocularis in foxes in Erzurum province, the highest endemic region for human alveolar echinococcosis in Turkey. The sedimentation and counting technique was used to reveal adult Echinococcus spp. in the intestines of foxes. One out of the 10 foxes was infected with E. multilocularis. The adult worms were analyzed morphologically and molecularly and were confirmed to be E. multilocularis by species-specific PCR. Pairwise comparisons between the 12S rRNA sequences of the E. multilocularis isolate from Erzurum and other E. multilocularis isolates showed 100% similarity of the Erzurum isolate with European isolates. With this study, the presence of E. multilocularis in a fox in Erzurum was confirmed by PCR, and molecular identification of E. multilocularis is reported for the first time in Turkey. PMID:27463527

  6. Molecular characterization of a dual endothelin-1/Angiotensin II receptor.

    PubMed Central

    Ruiz-Opazo, N.; Hirayama, K.; Akimoto, K.; Herrera, V. L.

    1998-01-01

    BACKGROUND: The molecular recognition theory (MRT) provides a conceptual framework that could explain the evolution of intermolecular and intramolecular interaction of peptides and proteins. As such, it predicts that binding sites of peptide hormones, and its receptor binding sites were originally encoded by and evolved from complementary strands of genomic DNA. MATERIALS AND METHODS: On the basis of principles underlying the MRT, we screened a rat brain complementary DNA library using an AngII followed by an endothelin-1 (ET-1) antisense oligonucleotide probe, expecting to isolate potential cognate receptors. RESULTS: An identical cDNA clone was isolated independently from both the AngII and ET-1 oligonucleotide screenings. Structural analysis revealed a receptor polypeptide containing a single predicted transmembrane region with distinct ET-1 and AngII putative binding domains. Functional analysis demonstrated ET-1- and AngII-specific binding as well as ET-1- and AngII-induced coupling to a Ca2+ mobilizing transduction system. Amino acid substitutions within the predicted ET-1 binding domain obliterate ET-1 binding while preserving AngII binding, thus defining the structural determinants of ET-1 binding within the dual ET-1/AngII receptor, as well as corroborating the dual nature of the receptor. CONCLUSIONS: Elucidation of the dual ET-1/AngII receptor provides further molecular genetic evidence in support of the molecular recognition theory and identifies for the first time a molecular link between the ET-1 and AngII hormonal systems that could underlie observed similar physiological responses elicited by ET-1 and AngII in different organ systems. The prominent expression of the ET-1/AngII receptor mRNA in brain and heart tissues suggests an important role in cardiovascular function in normal and pathophysiological states. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:9508787

  7. Molecular characterization of primary mediastinal B cell lymphoma.

    PubMed

    Tsang, P; Cesarman, E; Chadburn, A; Liu, Y F; Knowles, D M

    1996-06-01

    Primary mediastinal B cell lymphoma (PMBL) is a diffuse large B cell lymphoma (DLCL) postulated to arise from noncirculating thymic B lymphocytes. Because of its distinctive clinical and morphological features and putative unique cellular origin, PMBL is generally considered a distinct clinicopathological entity. Little is known, however, about the molecular characteristics of PMBL. Therefore, we analyzed 16 PMBLs for molecular alterations involving the bcl-1, bcl-2, bcl-6, c-myc, H-ras, K-ras, N-ras, and p53 genes and for Epstein-Barr virus infection, which are commonly involved in lymphoid neoplasia. Employing a combination of Southern blotting and/or polymerase chain reaction and single-strand conformation polymorphism assays, we detected genetic alterations in 7 of the 16 (44%) PMBLs. Whereas the bcl-6 gene is rearranged in up to 45% of DLCLs, rearrangement of the bcl-6 gene was detected in only 1 of these 16 (6%) PMBLS. Point mutations of the 5' noncoding region of the c-myc gene were demonstrated in 3 other cases (19%), although c-myc gene rearrangements were not seen by Southern blotting. Missense point mutations of the p53 gene were identified in 3 additional PMBLs (19%). Alterations of the bcl-1, bcl-2, or ras genes and evidence of Epstein-Barr virus infection were not observed. In conclusion, a variety of molecular lesions occur in PMBLs and may be involved in their pathogenesis. This molecular genetic pattern bears little resemblance to that known for other B cell malignancies, including DLCL. In particular, the infrequent occurrence of bcl-6 gene rearrangement in PMBLs distinguishes them from other DLCLs of B cell origin, suggesting that PMBLs do not represent a distinct subtype of DLCL. PMID:8669486

  8. Molecular characterization of primary mediastinal B cell lymphoma.

    PubMed Central

    Tsang, P.; Cesarman, E.; Chadburn, A.; Liu, Y. F.; Knowles, D. M.

    1996-01-01

    Primary mediastinal B cell lymphoma (PMBL) is a diffuse large B cell lymphoma (DLCL) postulated to arise from noncirculating thymic B lymphocytes. Because of its distinctive clinical and morphological features and putative unique cellular origin, PMBL is generally considered a distinct clinicopathological entity. Little is known, however, about the molecular characteristics of PMBL. Therefore, we analyzed 16 PMBLs for molecular alterations involving the bcl-1, bcl-2, bcl-6, c-myc, H-ras, K-ras, N-ras, and p53 genes and for Epstein-Barr virus infection, which are commonly involved in lymphoid neoplasia. Employing a combination of Southern blotting and/or polymerase chain reaction and single-strand conformation polymorphism assays, we detected genetic alterations in 7 of the 16 (44%) PMBLs. Whereas the bcl-6 gene is rearranged in up to 45% of DLCLs, rearrangement of the bcl-6 gene was detected in only 1 of these 16 (6%) PMBLS. Point mutations of the 5' noncoding region of the c-myc gene were demonstrated in 3 other cases (19%), although c-myc gene rearrangements were not seen by Southern blotting. Missense point mutations of the p53 gene were identified in 3 additional PMBLs (19%). Alterations of the bcl-1, bcl-2, or ras genes and evidence of Epstein-Barr virus infection were not observed. In conclusion, a variety of molecular lesions occur in PMBLs and may be involved in their pathogenesis. This molecular genetic pattern bears little resemblance to that known for other B cell malignancies, including DLCL. In particular, the infrequent occurrence of bcl-6 gene rearrangement in PMBLs distinguishes them from other DLCLs of B cell origin, suggesting that PMBLs do not represent a distinct subtype of DLCL. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:8669486

  9. Molecular characterization of the hemolysin determinant of Serratia marcescens.

    PubMed Central

    Poole, K; Schiebel, E; Braun, V

    1988-01-01

    The nucleotide sequence of a 7.3-kilobase-pair fragment of DNA encoding a hemolytic activity from Serratia marcescens was determined. Two large open reading frames were identified, designated shlA (Serratia hemolysin) and shlB, capable of encoding polypeptides of 165, 056 and 61,897 molecular weight, respectively. Both reading frames were expressed in vivo. The shlB gene product was localized to the outer membrane of Escherichia coli cells harboring the S. marcescens hemolysin determinant. Consistent with this location, a signallike sequence was identified at the N terminus of the polypeptide predicted from the nucleotide sequence of the shlB gene. Hyperexpression of the shlB locus permitted the identification of two shlB-encoded polypeptides of 65,000 and 62,000 molecular weight, respectively. Determination of the N-terminal amino acid sequence of the purified 62,000-molecular-weight protein confirmed that it was the mature form of the ShlB protein initially synthesized as a precursor (65,000-molecular-weight protein). By using polyclonal antisera raised against the purified proteins, ShlA and ShlB were identified in the outer membrane of S. marcescens. The shlA gene product was shown to interact with erythrocyte membranes, confirming it as the hemolysin proper. Both hemolysis and the interaction of ShlA with erythrocyte membranes did, however, require the ShlB function. Progressive deletion of the C terminus of the ShlA protein gradually reduced hemolytic activity until 37% of the amino acids had been removed. Elimination of 54% of the amino acids produced a nonhemolytic protein which, however, was still capable of associating with erythrocyte membranes. Images PMID:3290200

  10. Characterizing Warm Molecular Hydrogen in Active Star-Forming Systems

    NASA Astrophysics Data System (ADS)

    Rangwala, Naseem

    2014-10-01

    Herschel observations of nearby star-forming galaxies have determined that the warm component of the molecular gas traced by the high-J CO lines dominates the luminosity (~90% of the total CO luminosity) and hence the energetics of the molecular ISM. At the temperatures (T = 300 - 2000 K) and densities (n_H < 1E6 per cubic cm) typically found in our survey, H2 emission is the dominant gas coolant, much more important than CO. A fundamental assumption of all analyses of CO emission has been that CO emission traces H2 over the entire range of physical conditions in the observed sources. However, a direct observational comparison of spatial distributions and kinematics of CO and H2 has never been made for the warm molecular gas. We propose to observe the warm H2, in S(1) and S(2) transitions, with the SOFIA-EXES instrument in a diverse sample of star-forming systems: NGC 253 (starburst nucleus), NGC 6240 (luminous infrared galaxy), NGC 1068 (Seyfert-2), and SgrB2(M)/(N) (Galactic hot cores). The primary goal is to compare these measurements with the warm CO (J = 6-5 transition) observed with the Atacama Large Millimeter Array (ALMA) to investigate differences in the kinematics and spatial distributions (for the extended targets) of the two molecules and thereby confirm whether CO is a reliable tracer of H2 in the warm gas.

  11. Molecular secondary ion mass spectrometry: New dimensions in chemical characterization

    NASA Astrophysics Data System (ADS)

    Colton, Richard J.; Campana, Joseph E.; Kidwell, David A.; Ross, Mark M.; Wyatt, Jeffrey R.

    1985-04-01

    Secondary ion mass spectrometry (SIMS) has become a diverse tool for the study of many substances other than metals and semiconductors. This paper discusses the emission of polyatomic and molecular ions from surfaces that contain various inorganic and organic compounds including polymers and biomolecules. The mass and abundance distribution of cluster ions emitted from various solids — Van der Waals, metallic, ionic and covalent — are compared. Trends in the emission patterns are discussed in terms of a recombination or direct emission mechanism. The emission of molecular ions is also discussed with respect to the method of ionization and the various sample preparation and matrix-assisted procedures used. The matrices include various solid-state and liquid matrices such as ammonium chloride, charcoal, glycerol and gallium. Various chemical derivatization procedures have been developed to enhance the sensitivity of molecular SIMS and to detect selectively components in mixtures. The procedures are demonstrated for the low-level detection of airborne contaminants from paints, for the analysis of drugs in biological fluids, and for the sequencing of biomolecules such as peptides and sugars. The emission of characteristic fragment ions from the surfaces of polymers is also described for thick, insulating films.

  12. Cytological and molecular characterization of Vicia barbazitae Ten. & Guss.

    PubMed

    Ruffini Castiglione, M; Frediani, M; Gelati, M T; Venora, G; Giorgetti, L; Caputo, P; Cremonini, R

    2012-07-01

    Vicia barbazitae, a taxon belonging to section Vicia of subgenus Vicia, was recovered and analysed by cytological, karyological and molecular methods with the aim of both proposing a general characterisation of this species and studying the relationships among the species of section Vicia . Phylogenetic relationships among the species of the section Vicia and those of the sections Microcarinae, Wiggersia and Atossa were also analysed. Automated karyotype analysis has been determined after Feulgen's reaction; chromosome banding was performed by sequence-specific fluorochrome staining. Fluorescent chromosome banding showed CMA(+)/DAPI(-) NOR-associated heterochromatin in the satellite pair. Karyomorphological parameters, based on symmetry indices, the dendrogram of linkage distance constructed on 37 chromosome parameters, as well as the molecular data based on internal transcribed spacer sequences provided information about phylogenetic position of this species inside the section Vicia and among the species belonging to the sections Microcarinae, Wiggersia, Atossa and Vicia. From our karyological and molecular results, it emerges that V. barbazitae can be considered a natural member of section Vicia.

  13. Molecular Detection and Characterization of Theileria Infecting Wildebeest (Connochaetes taurinus) in the Maasai Mara National Reserve, Kenya

    PubMed Central

    Wamuyu, Lucy; Obanda, Vincent; Kariuki, Daniel; Gakuya, Francis; Makanda, Moni; Otiende, Moses; Ommeh, Sheila

    2015-01-01

    Theileria is a genus of tick-borne protozoan that is globally widespread and infects nearly all ungulates in which they cause either latent infection or lethal disease. Wild animals are considered reservoir hosts of many species of Theileria and their diversity in wildlife species is increasingly becoming of interest. The molecular characterization and identification of Theileria infecting wildlife has been studied in a few species including buffalo, which are considered reservoir host for Theileria parva infecting cattle. In this study, we sequenced Theileria species infecting wildebeest (Connochaetes taurinus) and used molecular-genetic and phylogenetic analysis of the 18 Small Subunit of the Ribosomal RNA (18S rRNA) to identify their relationships with known species of Theileria. Our results revealed three new Theileria haplotypes infecting wildebeest. Phylogenetic analysis revealed that haplotype 1 and 2 clustered in the same clade as Theileria separata and with Theileria sp. isolated from other small to medium sized antelopes. Haplotype 3 clustered close to the Theileria ovis clade. This is the first molecular description and characterization of Theileria species infecting blue wildebeest in East Africa. This study demonstrates the potential for Theileria transmission between wildebeest and small domestic ungulates, such as sheep and goats. PMID:26295263

  14. Molecular Detection and Characterization of Theileria Infecting Wildebeest (Connochaetes taurinus) in the Maasai Mara National Reserve, Kenya.

    PubMed

    Wamuyu, Lucy; Obanda, Vincent; Kariuki, Daniel; Gakuya, Francis; Makanda, Moni; Otiende, Moses; Ommeh, Sheila

    2015-01-01

    Theileria is a genus of tick-borne protozoan that is globally widespread and infects nearly all ungulates in which they cause either latent infection or lethal disease. Wild animals are considered reservoir hosts of many species of Theileria and their diversity in wildlife species is increasingly becoming of interest. The molecular characterization and identification of Theileria infecting wildlife has been studied in a few species including buffalo, which are considered reservoir host for Theileria parva infecting cattle. In this study, we sequenced Theileria species infecting wildebeest (Connochaetes taurinus) and used molecular-genetic and phylogenetic analysis of the 18 Small Subunit of the Ribosomal RNA (18S rRNA) to identify their relationships with known species of Theileria. Our results revealed three new Theileria haplotypes infecting wildebeest. Phylogenetic analysis revealed that haplotype 1 and 2 clustered in the same clade as Theileria separata and with Theileria sp. isolated from other small to medium sized antelopes. Haplotype 3 clustered close to the Theileria ovis clade. This is the first molecular description and characterization of Theileria species infecting blue wildebeest in East Africa. This study demonstrates the potential for Theileria transmission between wildebeest and small domestic ungulates, such as sheep and goats. PMID:26295263

  15. Isolation and molecular characterization of Banna virus from mosquitoes, Vietnam.

    PubMed

    Nabeshima, Takeshi; Thi Nga, Phan; Guillermo, Posadas; Parquet, Maria del Carmen; Yu, Fuxun; Thanh Thuy, Nguyen; Minh Trang, Bui; Tran Hien, Nguyen; Sinh Nam, Vu; Inoue, Shingo; Hasebe, Futoshi; Morita, Kouichi

    2008-08-01

    We isolated and characterized a Banna virus from mosquitoes in Vietnam; 5 strains were isolated from field-caught mosquitoes at various locations; Banna virus was previously isolated from encephalitis patients in Yunnan, China, in 1987. Together, these findings suggest widespread distribution of this virus throughout Southeast Asia.

  16. Isolation and Molecular Characterization of Banna Virus from Mosquitoes, Vietnam

    PubMed Central

    Nabeshima, Takeshi; Nga, Phan Thi; Guillermo, Posadas; del Carmen Parquet, Maria; Yu, Fuxun; Thuy, Nguyen Thanh; Trang, Bui Minh; Hien, Nguyen Tran; Nam, Vu Sinh; Inoue, Shingo; Hasebe, Futoshi

    2008-01-01

    We isolated and characterized a Banna virus from mosquitoes in Vietnam; 5 strains were isolated from field-caught mosquitoes at various locations; Banna virus was previously isolated from encephalitis patients in Yunnan, China, in 1987. Together, these findings suggest widespread distribution of this virus throughout Southeast Asia. PMID:18680655

  17. Rapid molecular strategy for orbivirus detection and characterization.

    PubMed

    Palacios, Gustavo; Cowled, Chris; Bussetti, Ana V; Savji, Nazir; Weir, Richard; Wick, Ivan; Travassos da Rosa, Amelia; Calisher, Charles H; Tesh, Robert B; Boyle, David; Lipkin, W Ian

    2011-06-01

    Orbiviruses infect a wide range of hosts, including humans. The ability to detect them has been hampered by their diversity. Here we present a simple consensus reverse transcription (RT)-PCR method targeting the polymerase gene for orbivirus recognition and characterization. Phylogenetic assignment is achieved by automated Web-based sequence analysis of amplification products.

  18. Rapid molecular strategy for filovirus detection and characterization.

    PubMed

    Zhai, Junhui; Palacios, Gustavo; Towner, Jonathan S; Jabado, Omar; Kapoor, Vishal; Venter, Marietjie; Grolla, Allen; Briese, Thomas; Paweska, Janusz; Swanepoel, Robert; Feldmann, Heinz; Nichol, Stuart T; Lipkin, W Ian

    2007-01-01

    Filoviruses have the capacity to cause lethal outbreaks of hemorrhagic fever in primates. Here we present a simple consensus reverse transcription-PCR method for filovirus recognition and characterization and demonstrate its utility with all known filovirus strains. Phylogenetic assignment is achieved by automated web-based sequence analysis of amplification products.

  19. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

  20. Biological and molecular characterizations of Toxoplasma gondii strains

    USGS Publications Warehouse

    Cole, R.A.; Lindsay, D.S.; Howe, D.K.; Roderick, Constance L.; Dubey, J.P.; Thomas, N.J.; Baeten, L.A.

    2000-01-01

    Toxoplasma gondii was isolated from brain or heart tissue from 15 southern sea otters (Enhydra lutris nereis) in cell cultures. These strains were used to infect mice that developed antibodies to T. gondii as detected in the modified direct agglutination test and had T. gondii tissue cysts in their brains at necropsy. Mouse brains containing tissue cysts from 4 of the strains were fed to 4 cats. Two of the cats excreted T. gondii oocysts in their feces that were infectious for mice. Molecular analyses of 13 strains indicated that they were all type II strains, but that they were genetically distinct from one another.

  1. A New Approach to Characterizing Landslide Hazards with Global Crowd Sourcing

    NASA Astrophysics Data System (ADS)

    Bach Kirschbaum, D.; Cappelaere, P. G.; Stanley, T.; Hall, B.; Franchek, M.

    2014-12-01

    Landslide disasters cause thousands of fatalities each year and cumulatively produce more economic damage than most other natural disasters. However, the number and distribution of landslides remain poorly quantified due to their small size and the absence of local, regional or global observing or reporting mechanisms. As a result, there are very few global databases that describe landslide hazards. Characterizing the socioeconomic impacts of landslide hazards worldwide presents an even more challenging task due to the various reporting biases or information gaps in existing regional and global sources. An online system has been developed to improve reporting of landslide hazards at the global scale that leverages crowd sourcing capabilities. Through this portal, users are able to input landslide information in a series of specified fields, including the date, location, impacts, trigger, and setting of the event. They are also able to link to photos so that other users can improve the characterization of the landslide event based on additional information or expert opinion. This hazard portal and editor provides a foundation to involve citizens in reporting, visualizing and sharing landslide events while improving a global landslide database and introducing them to other geospatial data in the process. A global landslide catalog of over 6,000 events developed at NASA Goddard Space Flight Center currently anchors this system. This research presents this new crowd-based system and outlines the technology used in developing this system. Preliminary findings of societal metrics, limitations on this type of interactive crowd sourcing portal, and lessons learned from the initial launch of this system will also be presented.

  2. Molecular Characterization of a Catalase from Hydra vulgaris

    PubMed Central

    Dash, Bhagirathi; Phillips, Timothy D.

    2012-01-01

    Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp encoding a putative protein of 505 amino acids with a predicted molecular mass of 57.44 kDa. The deduced amino acid sequence of HvCatalase contained several highly conserved motifs including the heme-ligand signature sequence RLFSYGDTH and the active site signature FXRERIPERVVHAKGXGA. A comparative analysis showed the presence of conserved catalytic amino acids [His(71), Asn(145), and Tyr(354)] in HvCatalase as well. Homology modeling indicated the presence of the conserved features of mammalian catalase fold. Hydrae exposed to thermal, starvation, metal and oxidative stress responded by regulating its catalase mRNA transcription. These results indicated that the HvCatalase gene is involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. PMID:22521743

  3. Molecular characterization of the circulating Bacillus anthracis in Jordan.

    PubMed

    Aqel, Amin Abdelfattah; Hailat, Ekhlas; Serrecchia, Luigina; Aqel, Suad; Campese, Emanuele; Vicari, Nadia; Fasanella, Antonio

    2015-12-01

    To understand the biomolecular charcteristics of Bacillus anthracis in Jordan, 20 blood smear slides from dead animals with suspected anthrax were analyzed using conventional and molecular approaches. All slides were positive for B. anthracis by conventional staining but no growth of the organism on selective media was detected. However, of the 20 samples, 16 were B. anthracis DNA-positive using polymerase chain reaction (PCR). Seven samples provided enough quantity and quality of DNA, and their multilocus variable tandem repeat analysis (MLVA)-15 loci analysis revealed two different genotypes. All genotypes were belonging to A.B..r. 008/009 which is very common in Asia and Europe. Single nucleotide repeat (SNR) analysis revealed that there were no sub genotypes. Molecular diagnosis of animal anthrax in Jordan is not used routinely; henceforth, official diagnosis of anthrax is based on the observation of the slides by optical microscope and this can often cause reading errors. Therefore, the prevalence of the disease in Jordan might be slightly lower than that reported by the official bodies.

  4. Molecular characterization of ochratoxigenic fungi associated with raisins.

    PubMed

    Gashgari, Rukaia M; Shebany, Yassmin M; Gherbawy, Youssuf A

    2011-11-01

    Dried grapes (raisin) may carry a significant mycological load contaminated via cultivation, postharvest processing practices, and drying processing. The contamination of raisin with fungi can accelerate spoilage or illness, if pathogens are present. Since raisins are used as food additives in many dishes in Saudi kitchen, there are healthy concerns on the safety of raisins consumed. In this article, the mycological profile of raisins sold in different markets at Jeddah, Kingdom of Saudi Arabia, was studied. The black raisin samples showed high fungal load compared with the white samples. Aspergillus, Alternaria, Cladosporium, Epicoccum Fusarium, and Rhizopus were the most prevalent genera isolated from raisin samples. Among six Aspergillus species isolated in this study, As. carbonarius and As. niger were the most frequently isolated species. Ochratoxin A (OTA) production in raisins was investigated using a combination of chromatographical (thin layer) and molecular (random amplified polymorphic DNA and Multiplex polymerase chain reaction) techniques. The OTA was detected in 70% of the raisin samples. Also, As. carbonarius (14 out of 19 isolates) and As. niger (2 isolates out of 9) were recognized as potential producers for OTA. Also, some molecular markers for detecting the contamination of raisin samples with OTA directly without isolating the producers were tested.

  5. Extension and characterization of pressure-sensitive molecular film

    NASA Astrophysics Data System (ADS)

    Matsuda, Yu; Mori, Hideo; Sakazaki, Yoshiki; Uchida, Toru; Suzuki, Suguru; Yamaguchi, Hiroki; Niimi, Tomohide

    2009-12-01

    Pressure-sensitive paint (PSP) has the potential as a diagnostic tool for pressure measurement in high Knudsen number regime because it works as a so-called “molecular sensor”. However, there are few reports concerning application of PSP to micro-devices, because conventional PSPs are too thick owing to polymer binders. In our previous work, we adopted the Langmuir-Blodgett (LB) technique to fabricate the pressure-sensitive molecular film (PSMF) using Pd(II) Mesoporphyrin IX (PdMP), which has pressure sensitivity only in the low pressure range (below 130 Pa). In this study, aiming for pressure measurement under an atmospheric pressure condition, we have constructed four samples of PSMFs composed of Pt(II) Mesoporphyrin IX (PtMP), Pt(II) Mesoporphyrin IX dimethylester (PtMPDME), Pt(II) Protoporphyrin IX (PtPP) and Cu(II) Mesoporphyrin IX dimethylester (CuMPDME) as luminescent molecules. The pressure sensitivity of those PSMFs was measured, and it was clarified that the pressure sensitivity of PSMF-PtMP is the highest among the four samples. Moreover, the temperature dependency of PSMF-PtMP was investigated, and we found that the temperature dependency of PSMF is dominated not by the oxygen diffusion in the layer, but by non-radiative deactivation process of excited luminescent molecules.

  6. Molecular characterization of two superoxide dismutases from Hydra vulgaris

    PubMed Central

    Dash, Bhagirathi; Metz, Richard; Huebner, Henry J.; Porter, Weston; Phillips, Timothy D.

    2007-01-01

    Apparent full-length cDNA sequences coding for manganese superoxide dismutase (HvMnSOD) and extracellular superoxide dismutase (HvEC-SOD) were isolated from Hydra vulgaris in order to understand their expression and 3D structures; and explore their possibility of being used as for biomarkers for environmental stress and toxicity. The deduced HvMnSOD protein consists of 219 amino acids of which first 21 amino acids constitute a presumed mitochondria-targeting signal peptide whereas HvEC-SOD protein consists of 189 amino acids of which first 19 amino acids constitute a presumed signal peptide. Molecular model generated for HvMnSOD displayed the N-terminal long alpha antiparallel hairpin and the C-terminal mixed alpha/beta fold characteristic of MnSODs and that for HvEC-SOD displayed the characteristic CuZnSOD beta-barrel fold. Hydrae subjected to thermal, starvation, metal and oxidative stress responded by regulating MnSOD and EC-SOD mRNA transcription. These results indicated that these genes are involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. Hence the expression of these SODs in hydra may have potential as molecular biomarkers for assessing stress, toxicity and pro-oxidant quality of chemicals and aquatic environmental quality. PMID:17150313

  7. Biogeographical characterization of Saccharomyces cerevisiae wine yeast by molecular methods

    PubMed Central

    Tofalo, Rosanna; Perpetuini, Giorgia; Schirone, Maria; Fasoli, Giuseppe; Aguzzi, Irene; Corsetti, Aldo; Suzzi, Giovanna

    2013-01-01

    Biogeography is the descriptive and explanatory study of spatial patterns and processes involved in the distribution of biodiversity. Without biogeography, it would be difficult to study the diversity of microorganisms because there would be no way to visualize patterns in variation. Saccharomyces cerevisiae, “the wine yeast,” is the most important species involved in alcoholic fermentation, and in vineyard ecosystems, it follows the principle of “everything is everywhere.” Agricultural practices such as farming (organic versus conventional) and floor management systems have selected different populations within this species that are phylogenetically distinct. In fact, recent ecological and geographic studies highlighted that unique strains are associated with particular grape varieties in specific geographical locations. These studies also highlighted that significant diversity and regional character, or ‘terroir,’ have been introduced into the winemaking process via this association. This diversity of wild strains preserves typicity, the high quality, and the unique flavor of wines. Recently, different molecular methods were developed to study population dynamics of S. cerevisiae strains in both vineyards and wineries. In this review, we will provide an update on the current molecular methods used to reveal the geographical distribution of S. cerevisiae wine yeast. PMID:23805132

  8. Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

    PubMed Central

    Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

    2012-01-01

    Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

  9. Molecular and phylogenetic characterization of syntaxin genes from parasitic protozoa.

    PubMed

    Dacks, Joel B; Doolittle, W Ford

    2004-08-01

    Vesicular transport is an integral process in eukaryotic cells and the syntaxins, a member of the SNARE protein superfamily, are a critical piece of the vesicular transport machinery. We have obtained syntaxin homologues from diverse protozoan parasites (including Entamoeba, Giardia, Trichomonas and Trypanosoma), determined the paralogue affinity of the homologues by molecular phylogenetics and compared functionally critical amino acid sites identified in other syntaxins. Surprisingly, three sequences deviate at the signature glutamine residue position, conserved in all previously identified syntaxin homologues. It is known that, despite conserved structure and function of both the syntaxins and the proteins of the regulatory SM superfamily, the various syntaxin paralogues bind their respective SM partners at different regions of the syntaxin molecule. These sites of interactions have been identified down to the individual residues. The pattern of conservation at these residues, in our evolutionarily diverse sampling of syntaxin paralogues, is therefore used to gain further insight into the interaction of these proteins. Phylogenetic analysis confirms and extends previous conclusions that the syntaxin families are present in diverse eukaryotes and that the syntaxin sub-families diverged early in eukaryotic evolution. This result is expanded with the inclusion of new homologues for previously sampled taxa, newly sampled taxa, and newly sampled syntaxin sub-families. Because of their integral role in membrane trafficking, the syntaxin genes represent a valuable potential molecular marker for the experimental study of the endomembrane system of disease-causing protists.

  10. Molecular characterization of Echinococcus granulosus in Egyptian donkeys.

    PubMed

    Aboelhadid, Shawky Mohamed; El-Dakhly, Khaled Mohamed; Yanai, Tokuma; Fukushi, Hideto; Hassanin, Kamel Mohamed

    2013-03-31

    The present study was carried out during the period from August 2009 to July 2010. The purpose of this study was to identify the genotype of donkeys' echinococcosis in one of the Egyptian governorates. On post-mortem inspection taking place at the zoo of Beni-Suef, Egypt, a total number of 145 donkeys were examined for the presence of hydatid cysts. Ten of these donkeys were found to be infected by hydatid cysts; and location, number and fertility of cysts found were determined. The liver was the predominant site of infection. Molecular identification of these cystic echinococcosis isolates, based on PCR amplification and the sequence of both mitochondrial ND1 and CO1, revealed that they belonged to Echinococcus equinus (G4 genotype). An alignment of ND1 and CO1 partial nucleotide sequences with G4 partial nucleotide sequences revealed replacement of G at position 105 with A and replacement of A at position 276 with G respectively. It can be concluded that the donkeys involved in this study were harboring E. equinus. For the first time in Egypt, the present work allowed us to record the presence of the E. equinus with the molecular tools, and to report new information on the epidemiological status of this parasite in Egypt.

  11. Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

    DOE PAGES

    Guo, Chun-Jun; Sun, Wei-wen; Bruno, Kenneth S.; Wang, Clay C.

    2014-09-29

    Terreic acid is a natural product derived from 6-methylsalicylic acid (6-MSA). A compact gene cluster for its biosynthesis was characterized. Isolation of the intermediates and shunt products from the mutant strains, in combined with bioinformatic analyses, allowed us to propose a biosynthetic pathway for terreic acid. Lastly, defining the pathway and the genes involved will facilitate the engineering of this molecule with interesting antimicrobial and antitumor bioactivities.

  12. The molecular characterization of the lignin-forming peroxidase

    SciTech Connect

    Lagrimini, L.M.

    1992-01-01

    This laboratory is committed to understanding the function of plant peroxidases via a multi-disciplinary approach. We have chosen the lignin-forming peroxidase from tobacco as the first isoenzyme to be subjected to this comprehensive approach. The goals which were set out upon the initiation of this project were as follows: (1) utilize a cDNA clone to the tobacco anionic peroxidase to generate transgenic plants which either over-produced this isoenzyme or specifically under-produced this isoenzyme via antisense RNA, (2) describe any phenotypic changes resulting from altered peroxidase expression, (3) perform morphological, physiological, and biochemical analysis of the above mentioned plants to help in determining the in planta function for this enzyme, and (4) clone and characterize the gene for the tobacco anionic peroxidase. A summary of progress thus far which includes both published and unpublished work will be presented in three sections: generation and characterization of transgenic plants, description of phenotypes, and biochemical and physiological analysis of peroxidase function, and cloning and characterization of the tobacco anionic peroxidase gene.

  13. Epidemiology and molecular virus characterization of reemerging rabies, South Africa.

    PubMed

    Cohen, Cheryl; Sartorius, Benn; Sabeta, Claude; Zulu, Gugulethu; Paweska, Janusz; Mogoswane, Mamokete; Sutton, Chris; Nel, Louis H; Swanepoel, Robert; Leman, Patricia A; Grobbelaar, Antoinette A; Dyason, Edwin; Blumberg, Lucille

    2007-12-01

    The incidence of dog rabies in Limpopo Province, South Africa, increased from 5 cases in 2004 to 100 in 2006. Human rabies had last been confirmed in 1981, but investigations instituted after an index case was recognized in February 2006 identified 21 confirmed, 4 probable, and 5 possible human cases between August 5, 2005, and December 31, 2006. Twelve of these case-patients were identified retrospectively because the diagnosis of rabies was not considered: 6 of these patients consulted a traditional healer, 6 had atypical manifestations with prominent abdominal symptoms, and 6 of 7 patients tested had elevated liver enzyme activity. Molecular genetic analysis indicated that outbreak virus strains were most closely related to recent canine strains from southern Zimbabwe. Delayed recognition of the human cases may have resulted from decreased clinical suspicion after many years of effective control of the disease and the occurrence of atypical clinical presentations. PMID:18258039

  14. Molecular and Functional Characterization of Bacopa monniera: A Retrospective Review.

    PubMed

    Rajan, Koilmani Emmanuvel; Preethi, Jayakumar; Singh, Hemant K

    2015-01-01

    Over the last 50 years, laboratories around the world analyzed the pharmacological effect of Bacopa monniera extract in different dimensions, especially as a nerve tonic and memory enhancer. Studies in animal model evidenced that Bacopa treatment can attenuate dementia and enhances memory. Further, they demonstrate that Bacopa primarily either acts via antioxidant mechanism (i.e., neuroprotection) or alters different neurotransmitters (serotonin (5-hydroxytryptamine, 5-HT), dopamine (DA), acetylcholine (ACh), γ-aminobutyric acid (GABA)) to execute the pharmacological effect. Among them, 5-HT has been shown to fine tune the neural plasticity, which is a substrate for memory formation. This review focuses on the studies which trace the effect of Bacopa treatment on serotonergic system and 5-HT mediated key molecular changes that are associated with memory formation.

  15. Molecular and Functional Characterization of Bacopa monniera: A Retrospective Review

    PubMed Central

    Rajan, Koilmani Emmanuvel; Preethi, Jayakumar; Singh, Hemant K.

    2015-01-01

    Over the last 50 years, laboratories around the world analyzed the pharmacological effect of Bacopa monniera extract in different dimensions, especially as a nerve tonic and memory enhancer. Studies in animal model evidenced that Bacopa treatment can attenuate dementia and enhances memory. Further, they demonstrate that Bacopa primarily either acts via antioxidant mechanism (i.e., neuroprotection) or alters different neurotransmitters (serotonin (5-hydroxytryptamine, 5-HT), dopamine (DA), acetylcholine (ACh), γ-aminobutyric acid (GABA)) to execute the pharmacological effect. Among them, 5-HT has been shown to fine tune the neural plasticity, which is a substrate for memory formation. This review focuses on the studies which trace the effect of Bacopa treatment on serotonergic system and 5-HT mediated key molecular changes that are associated with memory formation. PMID:26413131

  16. Molecular biological characterization of equine surfactant protein A.

    PubMed

    Hospes, R; Hospes, B I L; Reiss, I; Bostedt, H; Gortner, L

    2002-12-01

    In the following, we describe the isolation and sequencing of the equine surfactant protein A (Sp-A) as found in both the cDNA and the genomic DNA. We found a length of the cDNA sequence of 747 bp (base pairs), in translation into amino acids of 248. Compared with the known molecular biological facts about Sp-A in other species, the cDNA sequence obtained showed highest homology with that of sheep (85.01%). The genomic DNA of equine Sp-A, as in other species, includes three introns. There were no hints for the existence of two different Sp-A genes. These results should form the basis for a better understanding of respiratory failure in foals and adult horses, and also lead to further studies on this item.

  17. Molecular characterization of polyphosphate kinase (ppk) gene from Serratia marcescens.

    PubMed

    Lee, Seung-Jin; Song, Ok-Ryul; Lee, Young-Choon; Choi, Yong-Lark

    2003-02-01

    To understand the mechanism of phosphate accumulation, a gene encoding polyphosphate kinase (PPK) was cloned from the genomic library of Serratia marcescens by Southern hybridization. From the nucleotide sequence of a 4 kb DNA fragment, an open reading frame of 2063 nucleotides was identified encoding a protein of 686 amino acids with molecular mass of 70 kDa. The potential CRP binding site and pho box sequence were found upstream of the putative promoter in the regulatory region. The expression of PPK resulted in the formation of inclusion bodies and the product was active at low temperature. The E. coli strain harboring plasmid pSPK5 with ppk gene increased enzyme activity of polyphosphate kinase, resulting in increased accumulation of polyphosphate in E. coli.

  18. Molecular and Functional Characterization of Bacopa monniera: A Retrospective Review.

    PubMed

    Rajan, Koilmani Emmanuvel; Preethi, Jayakumar; Singh, Hemant K

    2015-01-01

    Over the last 50 years, laboratories around the world analyzed the pharmacological effect of Bacopa monniera extract in different dimensions, especially as a nerve tonic and memory enhancer. Studies in animal model evidenced that Bacopa treatment can attenuate dementia and enhances memory. Further, they demonstrate that Bacopa primarily either acts via antioxidant mechanism (i.e., neuroprotection) or alters different neurotransmitters (serotonin (5-hydroxytryptamine, 5-HT), dopamine (DA), acetylcholine (ACh), γ-aminobutyric acid (GABA)) to execute the pharmacological effect. Among them, 5-HT has been shown to fine tune the neural plasticity, which is a substrate for memory formation. This review focuses on the studies which trace the effect of Bacopa treatment on serotonergic system and 5-HT mediated key molecular changes that are associated with memory formation. PMID:26413131

  19. Epidemiology and molecular virus characterization of reemerging rabies, South Africa.

    PubMed

    Cohen, Cheryl; Sartorius, Benn; Sabeta, Claude; Zulu, Gugulethu; Paweska, Janusz; Mogoswane, Mamokete; Sutton, Chris; Nel, Louis H; Swanepoel, Robert; Leman, Patricia A; Grobbelaar, Antoinette A; Dyason, Edwin; Blumberg, Lucille

    2007-12-01

    The incidence of dog rabies in Limpopo Province, South Africa, increased from 5 cases in 2004 to 100 in 2006. Human rabies had last been confirmed in 1981, but investigations instituted after an index case was recognized in February 2006 identified 21 confirmed, 4 probable, and 5 possible human cases between August 5, 2005, and December 31, 2006. Twelve of these case-patients were identified retrospectively because the diagnosis of rabies was not considered: 6 of these patients consulted a traditional healer, 6 had atypical manifestations with prominent abdominal symptoms, and 6 of 7 patients tested had elevated liver enzyme activity. Molecular genetic analysis indicated that outbreak virus strains were most closely related to recent canine strains from southern Zimbabwe. Delayed recognition of the human cases may have resulted from decreased clinical suspicion after many years of effective control of the disease and the occurrence of atypical clinical presentations.

  20. Characterization of molecular outflows in the substellar domain

    SciTech Connect

    Phan-Bao, Ngoc; Dang-Duc, Cuong; Lee, Chin-Fei; Ho, Paul T. P.; Li, Di E-mail: pbngoc@asiaa.sinica.edu.tw

    2014-11-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M {sub J}, which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10{sup –6} M {sub ☉} to 2.9 × 10{sup –5} M {sub ☉} and an outflow mass-loss rate from 2.7 × 10{sup –9} M {sub ☉} yr{sup –1} to 4.1 × 10{sup –8} M {sub ☉} yr{sup –1}. These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M {sub J} in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M {sub J} in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  1. 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.

  2. Molecular characterization of pulmonary sarcomatoid carcinoma: analysis of 33 cases.

    PubMed

    Terra, Simone Bsp; Jang, Jin S; Bi, Lintao; Kipp, Benjamin R; Jen, Jin; Yi, Eunhee S; Boland, Jennifer M

    2016-08-01

    Several targetable genetic alterations have been found in lung cancer, predominantly in adenocarcinomas, which have led to important therapeutic advancements with the advent of targeted therapy. In contrast, the molecular features and presence of targetable genetic abnormalities in pulmonary sarcomatoid carcinomas are largely unknown. Thirty-three cases of pulmonary sarcomatoid carcinoma were tested for approximately 2800 mutations in 50 oncogenes and tumor-suppressor genes, including EGFR, KRAS, NRAS, TP53, BRAF, ERBB2, JAK3, AKT1, ATM, MET, KIT, and PIK3CA. ALK immunostaining was performed, and ALK FISH was performed on cases with any degree of staining. Twenty-four of the 33 cases (72%) had at least one genetic abnormality: 19 cases (58%) had TP53 mutations; 10 cases (30%) had KRAS mutations; AKT1, JAK3, BRAF, NRAS, and PIK3CA mutations were observed in 1 case each (3%). Six of the 19 cases (32%) with a mutation in TP53 had simultaneous mutations in KRAS (18%). The cases with alterations in JAK3, BRAF, and NRAS also had mutations in TP53. The case showing a mutation in PIK3CA had a mutation in KRAS. No EGFR mutations were observed. One case had ALK gene rearrangement. ALK rearrangement was observed in a single case of sarcomatoid carcinoma (3%), which has currently available targeted therapy. Four tumors had mutations in genes with experimental molecular-based therapy, including BRAF, NRAS, PIK3CA, and AKT1. Testing for targetable mutations should be considered for patients with pulmonary sarcomatoid carcinoma, as a subset may benefit from currently approved drugs or clinical trials of novel therapeutic options available for other types of lung cancer.

  3. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans

    PubMed Central

    McCarver, Addison C.; Lessner, Daniel J.

    2014-01-01

    The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized the thioredoxin system from Methanosarcina acetivorans. Phylogenetic analysis of Trx homologues from methanogens revealed eight clades, with one clade containing Trxs broadly distributed among methanogens. The Methanococci and Methanobacteria each contain one additional Trx from another clade, respectively, whereas the Methanomicrobia contain an additional five distinct Trxs. M. acetivorans, a member of the Methanomicrobia, contains a single TrxR (MaTrxR) and seven Trx homologues (MaTrx1-7), with representatives from five of the methanogen Trx clades. Purified recombinant MaTrxR had DTNB reductase and oxidase activities. The apparent Km value for NADPH was 115-fold lower than the apparent Km value for NADH, consistent with NADPH as the physiological electron donor to MaTrxR. Purified recombinant MaTrx2, MaTrx6, and MaTrx7 exhibited DTT- and lipoamide-dependent insulin disulfide reductase activities. However, only MaTrx7, which is encoded adjacent to MaTrxR, could serve as a redox partner to MaTrxR. These results reveal that M. acetivorans harbors at least three functional and distinct Trxs, and a complete thioredoxin system composed of NADPH, MaTrxR, and at least MaTrx7. This is the first characterization of a complete thioredoxin system from a methanogen, which provides a foundation to understand the system in methanogens. PMID:25112424

  4. Boronate esters: Synthesis, characterization and molecular base receptor analysis

    NASA Astrophysics Data System (ADS)

    Gómez-Jaimes, Gelen; Barba, Victor

    2014-10-01

    The synthesis of three boronate esters obtained by reacting 4-fluorophenylboronic (1), 4-iodophenylboronic (2) and 3,4-chlorophenylboronic (3) acids with 2,4,5-trihidroxybenzaldehyde is reported. The structural characterization was determined by spectroscopic and spectrometric techniques. The boron atom was evaluated to acts as Lewis acid center in the reaction with pyridine (Py), triethylamine (TEA) and fluoride anion (F-). The titration method was followed by UV-Vis and 11B NMR spectroscopy; results indicate the good interaction with the fluoride ion but poor coordination towards pyridine in solution.

  5. Isolation and molecular characterization of Newcastle disease viruses from raptors.

    PubMed

    Jindal, Naresh; Chander, Yogesh; Primus, Alexander; Redig, Patrick T; Goyal, Sagar M

    2010-12-01

    The present study was undertaken to detect and characterize Newcastle disease virus (NDV) in raptors. Cloacal and oropharyngeal swab samples were collected from 60 casualty raptors during January to March 2009 in Minnesota. Inoculation of all these samples (n=120) in 9-day-old embryonated hens' eggs resulted in isolation of haemagglutinating viruses in three samples from two bald eagles and one great horned owl. These three haemagglutinating viruses were confirmed as NDV by reverse transcription-polymerase chain reaction (RT-PCR) using fusion gene-specific primers, and were negative for avian influenza virus by RT-PCR. Further characterization revealed that all three possessed (112)GKQGRL(117) at the fusion gene cleavage site, indicating that they were lentogenic strains. Phylogenetic analysis revealed that all three isolates clustered with published class II genotype II NDVs. The nucleotide sequence homology of the three NDV isolates among themselves was 98.4 to 99.6% and the sequence homology with lentogenic strains from wild birds used for comparison varied between 94.5 and 100%. Detection of NDV strains from raptors merits further epidemiological studies to determine the prevalence of different NDV strains in raptors and their impact in relation to transmission to domestic poultry. PMID:21154052

  6. Molecular mechanisms of protein aggregation from global fitting of kinetic models.

    PubMed

    Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

    2016-02-01

    The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and

  7. Global collapse of molecular clouds as a formation mechanism for the most massive stars

    NASA Astrophysics Data System (ADS)

    Peretto, N.; Fuller, G. A.; Duarte-Cabral, A.; Avison, A.; Hennebelle, P.; Pineda, J. E.; André, Ph.; Bontemps, S.; Motte, F.; Schneider, N.; Molinari, S.

    2013-07-01

    The relative importance of primordial molecular cloud fragmentation versus large-scale accretion still remains to be assessed in the context of massive core/star formation. Studying the kinematics of the dense gas surrounding massive-star progenitors can tell us the extent to which large-scale flow of material impacts the growth in mass of star-forming cores. Here we present a comprehensive dataset of the 5500(±800) M⊙ infrared dark cloud SDC335.579-0.272 (hereafter SDC335), which exhibits a network of cold, dense, parsec-long filaments. Atacama Large Millimeter Array (ALMA) Cycle 0 observations reveal two massive star-forming cores, MM1 and MM2, sitting at the centre of SDC335 where the filaments intersect. With a gas mass of 545(-385+770) M⊙ contained within a source diameter of 0.05 pc, MM1 is one of the most massive, compact protostellar cores ever observed in the Galaxy. As a whole, SDC335 could potentially form an OB cluster similar to the Trapezium cluster in Orion. ALMA and Mopra single-dish observations of the SDC335 dense gas furthermore reveal that the kinematics of this hub-filament system are consistent with a global collapse of the cloud. These molecular-line data point towards an infall velocity Vinf = 0.7( ± 0.2) km s-1, and a total mass infall rate Ṁinf ≃ 2.5(±1.0) × 10-3 M⊙ yr-1 towards the central pc-size region of SDC335. This infall rate brings 750(±300) M⊙ of gas to the centre of the cloud per free-fall time (tff = 3 × 105 yr). This is enough to double the mass already present in the central pc-size region in 3.5-1.0+2.2 × tff. These values suggest that the global collapse of SDC335 over the past million year resulted in the formation of an early O-type star progenitor at the centre of the cloud's gravitational potential well.

  8. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques.

    PubMed

    Fournier, René; Mohareb, Amir

    2016-01-14

    We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn (+) (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn (+) species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV. PMID:26772561

  9. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques

    NASA Astrophysics Data System (ADS)

    Fournier, René; Mohareb, Amir

    2016-01-01

    We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of Cu m Snn + (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each Cu m S nn + species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.

  10. Molecular Characterization of Two Major Dengue Outbreaks in Costa Rica.

    PubMed

    Soto-Garita, Claudio; Somogyi, Teresita; Vicente-Santos, Amanda; Corrales-Aguilar, Eugenia

    2016-07-01

    Dengue virus (DENV) (Flavivirus, Flaviviridae) is a reemerging arthropod-borne virus with a worldwide circulation, transmitted mainly by Aedes aegypti and Aedes albopictus mosquitoes. Since the first detection of its main transmitting vector in 1992 and the invasion of DENV-1 in 1993, Costa Rica has faced dengue outbreaks yearly. In 2007 and 2013, Costa Rica experienced two of the largest outbreaks in terms of total and severe cases. To provide genetic information about the etiologic agents producing these outbreaks, we conducted phylogenetic analysis of viruses isolated from human samples. A total of 23 DENV-1 and DENV-2 sequences were characterized. These analyses signaled that DENV-1 genotype V and DENV-2 American/Asian genotype were circulating in those outbreaks. Our results suggest that the 2007 and 2013 outbreak viral strains of DENV-1 and DENV-2 originated from nearby countries and underwent in situ microevolution. PMID:27139442

  11. Identification and Molecular Characterization of Parkin in Clonorchis sinensis

    PubMed Central

    Bai, Xuelian; Kim, Tae Im; Lee, Ji-Yun; Dai, Fuhong; Hong, Sung-Jong

    2015-01-01

    Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to Zn2+ were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis. PMID:25748711

  12. Identification and molecular characterization of Parkin in Clonorchis sinensis.

    PubMed

    Bai, Xuelian; Kim, Tae Im; Lee, Ji-Yun; Dai, Fuhong; Hong, Sung-Jong

    2015-02-01

    Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to Zn(2+) were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis. PMID:25748711

  13. Molecular Characterization of Invasive Streptococcus dysgalactiae subsp. equisimilis, Japan.

    PubMed

    Wajima, Takeaki; Morozumi, Miyuki; Hanada, Shigeo; Sunaoshi, Katsuhiko; Chiba, Naoko; Iwata, Satoshi; Ubukata, Kimiko

    2016-02-01

    We collected β-hemolytic streptococci (1,611 isolates) from patients with invasive streptococcal infections in Japan during April 2010-March 2013. Streptococcus dysgalactiae subsp. equisimilis (SDSE) was most common (n = 693); 99% of patients with SDSE infections were elderly (mean age 75 years, SD ±15 years). We aimed to clarify molecular and epidemiologic characteristics of SDSE isolates and features of patient infections. Bacteremia with no identified focus of origin and cellulitis were the most prevalent manifestations; otherwise, clinical manifestations resembled those of S. pyogenes infections. Clinical manifestations also differed by patient's age. SDSE isolates were classified into 34 emm types; stG6792 was most prevalent (27.1%), followed by stG485 and stG245. Mortality rates did not differ according to emm types. Multilocus sequence typing identified 46 sequence types and 12 novel types. Types possessing macrolide- and quinolone-resistance genes were 18.4% and 2.6%, respectively; none showed β-lactam resistance. Among aging populations, invasive SDSE infections are an increasing risk.

  14. Molecular mapping and characterization of the silkworm apodal mutant

    PubMed Central

    Chen, Peng; Tong, Xiao-Ling; Fu, Ming-Yue; Hu, Hai; Song, Jiang-Bo; He, Song-Zhen; Gai, Ting-Ting; Dai, Fang-Yin; Lu, Cheng

    2016-01-01

    The morphological diversity of insects is important for their survival; in essence, it results from the differential expression of genes during development of the insect body. The silkworm apodal (ap) mutant has degraded thoracic legs making crawling and eating difficult and the female is sterile, which is an ideal subject for studying the molecular mechanisms of morphogenesis. Here, we confirmed that the infertility of ap female moths is a result of the degradation of the bursa copulatrix. Positional cloning of ap locus and expression analyses reveal that the Bombyx mori sister of odd and bowl (Bmsob) gene is a strong candidate for the ap mutant. The expression of Bmsob is down-regulated, while the corresponding Hox genes are up-regulated in the ap mutant compared to the wild type. Analyses with the dual luciferase assay present a declined activity of the Bmsob promoter in the ap mutant. Furthermore, we demonstrate that Bmsob can inhibit Hox gene expression directly and by suppressing the expression of other genes, including the BmDsp gene. The results of this study are an important contribution to our understanding of the diversification of insect body plan. PMID:26738847

  15. Molecular characterization of Tasmanian aquabirnaviruses from 1998 to 2013.

    PubMed

    Mohr, Peter G; Moody, Nicholas J G; Williams, Lynette M; Hoad, John; St J Crane, Mark

    2015-09-17

    Tasmanian aquabirnaviruses (TABVs) have been isolated intermittently since 1998 from healthy Atlantic salmon Salmo salar and rainbow trout Oncorhynchus mykiss farmed in Macquarie Harbour, Tasmania, Australia. However, beginning in 2011, TABVs have been isolated from rainbow trout in association with mortality events. To determine if recent molecular changes in TABV were contributing to increased mortalities, next generation sequencing was undertaken on 14 TABVs isolated from 1998 to 2013. Sequencing of both genome segments and analysis of the 5 viral proteins they encode revealed that minimal changes had occurred in the past 15 yr. Of the amino acid changes detected only 1, alanine to aspartic acid at position 139 of the minor structural VP3 protein, was unique to the recent disease events. The most dramatic changes observed were in the length of the non-structural VP5 protein varying from 43 to 133 amino acids. However, the amino acid substitution in VP3 and variable VP5 length were unlikely to have resulted in increased TABV pathogenicity. The genome of a novel Australian aquabirnavirus, Victorian trout aquabirnavirus (VTAB) was also sequenced and compared to TABV isolates. PMID:26378403

  16. Molecular characterization of southern bluefin tuna myoglobin (Thunnus maccoyii).

    PubMed

    Nurilmala, Mala; Ochiai, Yoshihiro

    2016-10-01

    The primary structure of southern bluefin tuna Thunnus maccoyii Mb has been elucidated by molecular cloning techniques. The cDNA of this tuna encoding Mb contained 776 nucleotides, with an open reading frame of 444 nucleotides encoding 147 amino acids. The nucleotide sequence of the coding region was identical to those of other bluefin tunas (T. thynnus and T. orientalis), thus giving the same amino acid sequences. Based on the deduced amino acid sequence, bioinformatic analysis was performed including phylogenic tree, hydropathy plot and homology modeling. In order to investigate the autoxidation profiles, the isolation of Mb was performed from the dark muscle. The water soluble fraction was subjected to ammonium sulfate fractionation (60-90 % saturation) followed by preparative gel electrophoresis. Autoxidation profiles of Mb were delineated at pH 5.6, 6.5 and 7.4 at temperature 37 °C. The autoxidation rate of tuna Mb was slightly higher than that of horse Mb at all pH examined. These results revealed that tuna myoglobin was unstable than that of horse Mb mainly at acidic pH.

  17. Morphological and molecular characterization of Histiobalantium natans viridis (Ciliophora, Scuticociliatia).

    PubMed

    Foissner, Wilhelm; Kusuoka, Yasushi; Shimano, Satoshi

    2009-08-01

    We investigated a Histiobalantium natans viridis population from the ancient Lake Biwa in Japan, using live observation, silver impregnation, and the small subunit rRNA gene sequence. The morphological and molecular data show, with high support, a close relationship of Histiobalantium, Schizocalyptra and Pleuronema, supporting the family Pleuronematidae Kent, whose nearest relatives are the Cyclidiidae Ehrenberg. A family Histiobalantiidae Puytorac and Corliss is not supported, either by the nucleotide sequences or the morphologic data, except for the curious dorsal location of the cytopyge. Likewise, the data do not support inclusion of Histiobalantium in the family Sulcigeridae Gajewskaja, as very recently suggested by Jankowski, whose classification is based on a misidentified Sulcigera comosa. Further, there are good reasons to synonymize the genus Gajewskiella Obolkina with Histiobalantium. The European and Asian populations of H. natans differ significantly in the structure of adoral membranelle 1, suggesting that they are different species. However, there is some indication that the differences are caused by deficient data on the European H. natans, which is thus in need of detailed redescription. This applies also to the North American Histiobalantium agile Stokes which is probably not conspecific with the Eurasian H. natans. The status of the forma H. natans viridis and H. natans nigricans is not known because detailed data from nigricans are lacking. We prefer subspecific rank at the present state of knowledge.

  18. Molecular Characterization of Cryptosporidium Isolates Obtained from Humans in France

    PubMed Central

    Guyot, K.; Follet-Dumoulin, A.; Lelièvre, E.; Sarfati, C.; Rabodonirina, M.; Nevez, G.; Cailliez, J. C.; Camus, D.; Dei-Cas, E.

    2001-01-01

    Cryptosporidium parvum is usually considered the agent of human cryptosporidiosis. However, only in the last few years, molecular biology-based methods have allowed the identification of Cryptosporidium species and genotypes, and only a few data are available from France. In the present work, we collected samples of whole feces from 57 patients from France (11 immunocompetent patients, 35 human immunodeficiency virus [HIV]-infected patients, 11 immunocompromised but non-HIV-infected patients) in whom Cryptosporidium oocysts were recognized by clinical laboratories. A fragment of the Cryptosporidium 18S rRNA gene encompassing the hypervariable region was amplified by PCR and sequenced. The results revealed that the majority of the patients were infected with cattle (29 of 57) or human (18 of 57) genotypes of Cryptosporidium parvum. However, a number of immunocompromised patients were infected with C. meleagridis (3 of 57), C. felis (6 of 57), or a new genotype of C. muris (1 of 57). This is the first report of the last three species of Cryptosporidium in humans in France. These results indicate that immunocompromised individuals are susceptible to a wide range of Cryptosporidium species and genotypes. PMID:11574558

  19. Molecular characterization of an. alpha. sub 2B -adrenergic receptor

    SciTech Connect

    Harrison, J.K.; Dewan Zeng; D'Angelo, D.D.; Tucker, A.L.; Zhihong Lu; Barber, C.M.; Lynch, K.R. )

    1990-02-26

    {alpha}{sub 2}-Adrenergic receptors comprise a heterogeneous population based on pharmacologic and molecular evidence. The authors have isolated a cDNA clone (pRNG{alpha}2) encoding a previously undescribed third subtype of an {alpha}{sub 2}-adrenergic receptor from a rat kidney cDNA library. The library was screened with an oligonucleotide encoding a highly conserved region found in all biogenic amine receptors described to date. The deduced amino acid sequence displays many features of G-protein coupled receptors with exception of the absence of the consensus N-linked glycosylation site at the amino terminus. Membranes prepared from COS-1 cells transfected with pRNG{alpha}2 display high affinity and saturable binding to {sup 3}H-rauwolscine (K{sub d}=2 nM).Competition curve data analysis shows that pRNG{alpha}2 protein binds to a variety of adrenergic drugs with the following rank order of potency: yohimbine {ge} cholorpromazine > prazosin {ge} clonidine > norepinephrine {ge} oxymetazoline. pRNG{alpha}2 RNA accumulates in both adult rat kidney and rat neonatal lung (predominant species is 4.0 kb). They conclude that pRNG{alpha}2 likely represents a cDNA for the {alpha}{sub 2B}-adrenergic receptor.

  20. Molecular characterization and functional expression of the DSC1 channel.

    PubMed

    Zhang, Tianxiang; Liu, Zhiqi; Song, Weizhong; Du, Yuzhe; Dong, Ke

    2011-07-01

    Drosophila Sodium Channel 1 (DSC1) was predicted to encode a sodium channel based on a high sequence similarity with vertebrate and invertebrate sodium channel genes. However, BSC1, a DSC1 ortholog in Blattella germanica, was recently shown to encode a cation channel with ion selectivity toward Ca(2+). In this study, we isolated a total of 20 full-length cDNA clones that cover the entire coding region of the DSC1 gene from adults of Drosophila melanogaster by reverse transcription-polymerase chain reaction. Sequence analysis of the 20 clones revealed nine optional exons, four of which contain in-frame stop codons; and 13 potential A-to-I RNA editing sites. The 20 clones can be grouped into eight splice types and represent 20 different transcripts because of unique RNA editing. Three variants generated DSC1 currents when expressed in Xenopus oocytes. Like the BSC1 channel, all three functional DSC1 channels are permeable to Ca(2+) and Ba(2+), and also to Na(+) in the absence of external Ca(2+). Furthermore, the DSC1 channel is insensitive to tetrodotoxin, a potent and specific sodium channel blocker. Our study shows that DSC1 encodes a voltage-gated cation channel similar to the BSC1 channel in B. germanica. Extensive alternative splicing and RNA editing of the DSC1 transcripts suggest the molecular and functional diversity of the DSC1 channel. PMID:21571069

  1. Characterization of Sensory Properties of Flavanols - A Molecular Dynamic Approach.

    PubMed

    Ferrer-Gallego, Raúl; Quijada-Morín, Natalia; Brás, Natércia F; Gomes, Paula; de Freitas, Victor; Rivas-Gonzalo, Julián C; Escribano-Bailón, M Teresa

    2015-07-01

    In this work, sensations elicited by catechin and procyanidins in comparison with those elicited by gallocatechin and prodelphinidins were evaluated by means of a sensory panel. To obtain further insights into the mechanisms of action, molecular dynamics (MD) simulations and saturation transfer difference nuclear magnetic resonance (STD NMR) experiments have been performed. Results showed clear differences between the 2 types of flavanols. Dihydroxylated B-ring flavanols were more astringent, bitter, dry, rough, unripe, and persistent than trihydroxylated B-ring ones. Besides, these last compounds were smoother, more velvety, and viscous. MD simulations and STD NMR experiments support results obtained from tasting panel. MD results suggested that catechin binds to a human salivary proline-rich peptide IB714 faster than gallocatechin and this interaction is maintained longer. IB714 can interact with 2 catechin molecules concurrently while only interacts with 1 gallocatechin molecule. Accordingly, STD NMR experiments showed a greater affinity of catechin than gallocatechin for the peptide (K D = 2.7 and 25.7, respectively). Results indicate that the number of hydroxyl substituents present in B-ring of the flavanic nucleus is decisive for the interaction with salivary proteins and the development of astringency perception. PMID:25934978

  2. Molecular Characterization of Caveolin-induced Membrane Curvature*

    PubMed Central

    Ariotti, Nicholas; Rae, James; Leneva, Natalya; Ferguson, Charles; Loo, Dorothy; Okano, Satomi; Hill, Michelle M.; Walser, Piers; Collins, Brett M.; Parton, Robert G.

    2015-01-01

    The generation of caveolae involves insertion of the cholesterol-binding integral membrane protein caveolin-1 (Cav1) into the membrane, however, the precise molecular mechanisms are as yet unknown. We have speculated that insertion of the caveolin scaffolding domain (CSD), a conserved amphipathic region implicated in interactions with signaling proteins, is crucial for caveola formation. We now define the core membrane-juxtaposed region of Cav1 and show that the oligomerization domain and CSD are protected by tight association with the membrane in both mature mammalian caveolae and a model prokaryotic system for caveola biogenesis. Cryoelectron tomography reveals the core membrane-juxtaposed domain to be sufficient to maintain oligomerization as defined by polyhedral distortion of the caveolar membrane. Through mutagenesis we demonstrate the importance of the membrane association of the oligomerization domain/CSD for defined caveola biogenesis and furthermore, highlight the functional significance of the intramembrane domain and the CSD for defined caveolin-induced membrane deformation. Finally, we define the core structural domain of Cav1, constituting only 66 amino acids and of great potential to nanoengineering applications, which is required for caveolin-induced vesicle formation in a bacterial system. These results have significant implications for understanding the role of Cav1 in caveola formation and in regulating cellular signaling events. PMID:26304117

  3. Molecularly stabilised ultrasmall gold nanoparticles: synthesis, characterization and bioactivity

    NASA Astrophysics Data System (ADS)

    Leifert, Annika; Pan-Bartnek, Yu; Simon, Ulrich; Jahnen-Dechent, Willi

    2013-06-01

    Gold nanoparticles (AuNPs) are widely used as contrast agents in electron microscopy as well as for diagnostic tests. Due to their unique optical and electrical properties and their small size, there is also a growing field of potential applications in medical fields of imaging and therapy, for example as drug carriers or as active compounds in thermotherapy. Besides their intrinsic optical properties, facile surface decoration with (bio)functional ligands renders AuNPs ideally suited for many industrial and medical applications. However, novel AuNPs may have toxicological profiles differing from bulk and therefore a thorough analysis of the quantitative structure-activity relationship (QSAR) is required. Several mechanisms are proposed that cause adverse effects of nanoparticles in biological systems. Catalytic generation of reactive species due to the large and chemically active surface area of nanomaterials is well established. Because nanoparticles approach the size of biological molecules and subcellular structures, they may overcome natural barriers by active or passive uptake. Ultrasmall AuNPs with sizes of 2 nm or less may even behave as molecular ligands. These types of potential interactions would imply a size and ligand-dependent behaviour of any nanomaterial towards biological systems. Thus, to fully understand their QSAR, AuNPs bioactivity should be analysed in biological systems of increasing complexity ranging from cell culture to whole animal studies.

  4. Molecular characterization of southern bluefin tuna myoglobin (Thunnus maccoyii).

    PubMed

    Nurilmala, Mala; Ochiai, Yoshihiro

    2016-10-01

    The primary structure of southern bluefin tuna Thunnus maccoyii Mb has been elucidated by molecular cloning techniques. The cDNA of this tuna encoding Mb contained 776 nucleotides, with an open reading frame of 444 nucleotides encoding 147 amino acids. The nucleotide sequence of the coding region was identical to those of other bluefin tunas (T. thynnus and T. orientalis), thus giving the same amino acid sequences. Based on the deduced amino acid sequence, bioinformatic analysis was performed including phylogenic tree, hydropathy plot and homology modeling. In order to investigate the autoxidation profiles, the isolation of Mb was performed from the dark muscle. The water soluble fraction was subjected to ammonium sulfate fractionation (60-90 % saturation) followed by preparative gel electrophoresis. Autoxidation profiles of Mb were delineated at pH 5.6, 6.5 and 7.4 at temperature 37 °C. The autoxidation rate of tuna Mb was slightly higher than that of horse Mb at all pH examined. These results revealed that tuna myoglobin was unstable than that of horse Mb mainly at acidic pH. PMID:27126585

  5. Molecular cytogenetic characterization of the Amazon River dolphin Inia geoffrensis.

    PubMed

    Bonifácio, Heidi L; da Silva, Vera M F; Martin, Anthony R; Feldberg, Eliana

    2012-09-01

    Classical and molecular cytogenetic (18S rDNA, telomeric sequence, and LINE-1 retrotransposon probes) studies were carried out to contribute to an understanding of the organization of repeated DNA elements in the Amazon River dolphin (boto, Inia geoffrensis). Twenty-seven specimens were examined, each presenting 2n = 44 chromosomes, the karyotype formula 12m + 14sm + 6st + 10t + XX/XY, and fundamental number (FN) = 74. C-positive heterochromatin was observed in terminal and interstitial positions, with the occurrence of polymorphism. Interstitial telomeric sequences were not observed. The nucleolar organizer region (NOR) was located at a single site on a smallest autosomal pair. LINE-1 was preferentially distributed in the euchromatin regions, with the greatest accumulation on the X chromosome. Although the karyotype structure in cetaceans is considered to be conserved, the boto karyotype demonstrated significant variations in its formula, heterochromatin distribution, and the location of the NOR compared to other cetacean species. These results contribute to knowledge of the chromosome organization in boto and to a better understanding of karyoevolution in cetaceans.

  6. Molecular mapping and characterization of the silkworm apodal mutant.

    PubMed

    Chen, Peng; Tong, Xiao-Ling; Fu, Ming-Yue; Hu, Hai; Song, Jiang-Bo; He, Song-Zhen; Gai, Ting-Ting; Dai, Fang-Yin; Lu, Cheng

    2016-01-01

    The morphological diversity of insects is important for their survival; in essence, it results from the differential expression of genes during development of the insect body. The silkworm apodal (ap) mutant has degraded thoracic legs making crawling and eating difficult and the female is sterile, which is an ideal subject for studying the molecular mechanisms of morphogenesis. Here, we confirmed that the infertility of ap female moths is a result of the degradation of the bursa copulatrix. Positional cloning of ap locus and expression analyses reveal that the Bombyx mori sister of odd and bowl (Bmsob) gene is a strong candidate for the ap mutant. The expression of Bmsob is down-regulated, while the corresponding Hox genes are up-regulated in the ap mutant compared to the wild type. Analyses with the dual luciferase assay present a declined activity of the Bmsob promoter in the ap mutant. Furthermore, we demonstrate that Bmsob can inhibit Hox gene expression directly and by suppressing the expression of other genes, including the BmDsp gene. The results of this study are an important contribution to our understanding of the diversification of insect body plan. PMID:26738847

  7. Genetic characterization of fig tree mutants with molecular markers.

    PubMed

    Rodrigues, M G F; Martins, A B G; Desidério, J A; Bertoni, B W; Alves, M C

    2012-08-06

    The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

  8. Characterization of molecular mechanisms of in vivo UVR induced cataract.

    PubMed

    Galichanin, Konstantin; Talebizadeh, Nooshin; Söderberg, Per

    2012-01-01

    Cataract is the leading cause of blindness in the world (1). The World Health Organization defines cataract as a clouding of the lens of the eye which impedes the transfer of light. Cataract is a multi-factorial disease associated with diabetes, smoking, ultraviolet radiation (UVR), alcohol, ionizing radiation, steroids and hypertension. There is strong experimental (2-4) and epidemiological evidence (5,6) that UVR causes cataract. We developed an animal model for UVR B induced cataract in both anesthetized (7) and non-anesthetized animals (8). The only cure for cataract is surgery but this treatment is not accessible to all. It has been estimated that a delay of onset of cataract for 10 years could reduce the need for cataract surgery by 50% (9). To delay the incidence of cataract, it is needed to understand the mechanisms of cataract formation and find effective prevention strategies. Among the mechanisms for cataract development, apoptosis plays a crucial role in initiation of cataract in humans and animals (10). Our focus has recently been apoptosis in the lens as the mechanism for cataract development (8,11,12). It is anticipated that a better understanding of the effect of UVR on the apoptosis pathway will provide possibilities for discovery of new pharmaceuticals to prevent cataract. In this article, we describe how cataract can be experimentally induced by in vivo exposure to UVR-B. Further RT-PCR and immunohistochemistry are presented as tools to study molecular mechanisms of UVR-B induced cataract. PMID:23222480

  9. Molecular and biochemical characterization of carbonic anhydrases of Paracoccidioides.

    PubMed

    Tomazett, Mariana Vieira; Zanoelo, Fabiana Fonseca; Bailão, Elisa Flávia Cardoso; Bailão, Alexandre Melo; Borges, Clayton Luiz; Soares, Célia Maria de Almeida

    2016-01-01

    Carbonic anhydrases (CA) belong to the family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the present work, we characterized the cDNAs of four Paracoccidioides CAs (CA1, CA2, CA3, and CA4). In the presence of CO2, there was not a significant increase in fungal ca1, ca2 and ca4 gene expression. The ca1 transcript was induced during the mycelium-to-yeast transition, while ca2 and ca4 gene expression was much higher in yeast cells, when compared to mycelium and mycelium-to-yeast transition. The ca1 transcript was induced in yeast cells recovered directly from liver and spleen of infected mice, while transcripts for ca2 and ca4 were down-regulated. Recombinant CA1 (rCA1) and CA4 (rCA4), with 33 kDa and 32 kDa respectively, were obtained from bacteria. The enzymes rCA1 (β-class) and rCA4 (α-class) were characterized regarding pH, temperature, ions and amino acids addition influence. Both enzymes were stable at pHs 7.5-8.5 and temperatures of 30-35 °C. The enzymes were dramatically inhibited by Hg+2 and activated by Zn+2, while only rCA4 was stimulated by Fe2+. Among the amino acids tested (all in L configuration), arginine, lysine, tryptophan and histidine enhanced residual activity of rCA1 and rCA4. PMID:27560991

  10. Molecular and biochemical characterization of carbonic anhydrases of Paracoccidioides

    PubMed Central

    Tomazett, Mariana Vieira; Zanoelo, Fabiana Fonseca; Bailão, Elisa Flávia Cardoso; Bailão, Alexandre Melo; Borges, Clayton Luiz; Soares, Célia Maria de Almeida

    2016-01-01

    Abstract Carbonic anhydrases (CA) belong to the family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the present work, we characterized the cDNAs of four Paracoccidioides CAs (CA1, CA2, CA3, and CA4). In the presence of CO2, there was not a significant increase in fungal ca1, ca2 and ca4 gene expression. The ca1 transcript was induced during the mycelium-to-yeast transition, while ca2 and ca4 gene expression was much higher in yeast cells, when compared to mycelium and mycelium-to-yeast transition. The ca1 transcript was induced in yeast cells recovered directly from liver and spleen of infected mice, while transcripts for ca2 and ca4 were down-regulated. Recombinant CA1 (rCA1) and CA4 (rCA4), with 33 kDa and 32 kDa respectively, were obtained from bacteria. The enzymes rCA1 (β-class) and rCA4 (α-class) were characterized regarding pH, temperature, ions and amino acids addition influence. Both enzymes were stable at pHs 7.5-8.5 and temperatures of 30-35 °C. The enzymes were dramatically inhibited by Hg+2 and activated by Zn+2, while only rCA4 was stimulated by Fe2+. Among the amino acids tested (all in L configuration), arginine, lysine, tryptophan and histidine enhanced residual activity of rCA1 and rCA4. PMID:27560991

  11. Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat.

    PubMed

    Pearce, Stephen; Saville, Robert; Vaughan, Simon P; Chandler, Peter M; Wilhelm, Edward P; Sparks, Caroline A; Al-Kaff, Nadia; Korolev, Andrey; Boulton, Margaret I; Phillips, Andrew L; Hedden, Peter; Nicholson, Paul; Thomas, Stephen G

    2011-12-01

    The introduction of the Reduced height (Rht)-B1b and Rht-D1b semidwarfing genes led to impressive increases in wheat (Triticum aestivum) yields during the Green Revolution. The reduction in stem elongation in varieties containing these alleles is caused by a limited response to the phytohormone gibberellin (GA), resulting in improved resistance to stem lodging and yield benefits through an increase in grain number. Rht-B1 and Rht-D1 encode DELLA proteins, which act to repress GA-responsive growth, and their mutant alleles Rht-B1b and Rht-D1b are thought to confer dwarfism by producing more active forms of these growth repressors. While no semidwarfing alleles of Rht-A1 have been identified, we show that this gene is expressed at comparable levels to the other homeologs and represents a potential target for producing novel dwarfing alleles. In this study, we have characterized additional dwarfing mutations in Rht-B1 and Rht-D1. We show that the severe dwarfism conferred by Rht-B1c is caused by an intragenic insertion, which results in an in-frame 90-bp insertion in the transcript and a predicted 30-amino acid insertion within the highly conserved amino-terminal DELLA domain. In contrast, the extreme dwarfism of Rht-D1c is due to overexpression of the semidwarfing Rht-D1b allele, caused by an increase in gene copy number. We show also that the semidwarfing alleles Rht-B1d and Rht-B1e introduce premature stop codons within the amino-terminal coding region. Yeast two-hybrid assays indicate that these newly characterized mutations in Rht-B1 and Rht-D1 confer "GA-insensitive" dwarfism by producing DELLA proteins that do not bind the GA receptor GA INSENSITIVE DWARF1, potentially compromising their targeted degradation. PMID:22013218

  12. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis.

    PubMed

    Gong, Yu-Nong; Yang, Shu-Li; Shih, Shin-Ru; Huang, Yhu-Chering; Chang, Pi-Yueh; Huang, Chung-Guei; Kao, Kuo-Chin; Hu, Han-Chung; Liu, Yi-Chun; Tsao, Kuo-Chien

    2016-08-01

    Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5' untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11 genomes were

  13. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis

    PubMed Central

    Gong, Yu-Nong; Yang, Shu-Li; Shih, Shin-Ru; Huang, Yhu-Chering; Chang, Pi-Yueh; Huang, Chung-Guei; Kao, Kuo-Chin; Hu, Han-Chung; Liu, Yi-Chun; Tsao, Kuo-Chien

    2016-01-01

    Abstract Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5′ untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11

  14. Molecular characterization of dissolved organic matter (DOM): a critical review.

    PubMed

    Nebbioso, Antonio; Piccolo, Alessandro

    2013-01-01

    Advances in water chemistry in the last decade have improved our knowledge about the genesis, composition, and structure of dissolved organic matter, and its effect on the environment. Improvements in analytical technology, for example Fourier-transform ion cyclotron (FT-ICR) mass spectrometry (MS), homo and hetero-correlated multidimensional nuclear magnetic resonance (NMR) spectroscopy, and excitation emission matrix fluorimetry (EEMF) with parallel factor (PARAFAC) analysis for UV-fluorescence spectroscopy have resulted in these advances. Improved purification methods, for example ultrafiltration and reverse osmosis, have enabled facile desalting and concentration of freshly collected DOM samples, thereby complementing the analytical process. Although its molecular weight (MW) remains undefined, DOM is described as a complex mixture of low-MW substances and larger-MW biomolecules, for example proteins, polysaccharides, and exocellular macromolecules. There is a general consensus that marine DOM originates from terrestrial and marine sources. A combination of diagenetic and microbial processes contributes to its origin, resulting in refractory organic matter which acts as carbon sink in the ocean. Ocean DOM is derived partially from humified products of plants decay dissolved in fresh water and transported to the ocean, and partially from proteinaceous and polysaccharide material from phytoplankton metabolism, which undergoes in-situ microbial processes, becoming refractory. Some of the DOM interacts with radiation and is, therefore, defined as chromophoric DOM (CDOM). CDOM is classified as terrestrial, marine, anthropogenic, or mixed, depending on its origin. Terrestrial CDOM reaches the oceans via estuaries, whereas autochthonous CDOM is formed in sea water by microbial activity; anthropogenic CDOM is a result of human activity. CDOM also affects the quality of water, by shielding it from solar radiation, and constitutes a carbon sink pool. Evidence in support

  15. Purification, characterization and molecular cloning of prophenoloxidases from Sarcophaga bullata.

    PubMed

    Chase, M R; Raina, K; Bruno, J; Sugumaran, M

    2000-10-01

    Prophenoloxidase (PPO) is a key enzyme associated with both melanin biosynthesis and sclerotization in insects. This enzyme is involved in three physiologically important processes viz., cuticular hardening, defense reactions and wound healing in insects. It was isolated from the larval hemolymph of Sarcophaga bullata and purified by employing ammonium sulfate precipitation, Phenyl Sepharose chromatography, DEAE-Sepharose chromatography, and Sephacryl S-200 column chromatography. The purified enzyme exhibited two closely moving bands on 7.5% SDS-PAGE under denaturing conditions. From the estimates of molecular weight on Sephacryl S-100, TSK-3000 HPLC column and SDS-PAGE, which ranged from 90,000 to 100,000, it was inferred that the enzyme is made up of a single polypeptide chain. Activation of PPO (K(a)=40 microM) was achieved by the cationic detergent, cetyl pyridinium chloride below its critical micellar concentration (0.8 mM) indicating that the detergent molecules are binding specifically to the PPO and causing the activation. Neither anionic, nor nonionic (or zwitterionic) detergents activated the PPO. The active enzyme exhibited wide substrate specificity and marked thermal unstability. Using primers designed to conserved amino acid sequences from known PPOs, we PCR amplified and cloned two PPO genes from the sarcophagid larvae. The clones encoded polypeptides of 685 and 691 amino acids. They contained two distinct copper binding regions and lacked the signal peptide sequence. They showed a high degree of homology to dipteran PPOs. Both contained putative thiol ester site, two proteolytic activation sites and a conserved C-terminal region common to all known PPOs.

  16. Determination and characterization of 20th century global sea level rise

    NASA Astrophysics Data System (ADS)

    Kuo, Chung-Yen

    In this study, we provide a determination of the 20th Century (1900--2002) global sea level rise, the associated error budgets, and the quantifications of the various geophysical sources of the observed sea level rise, using data and geophysical models. We analyzed significant geographical variations of the global sea level including those caused by the steric component (heat and salinity) in the ocean, and the self-gravitational signal as a result of ice sheets melting, including the effects of glacial isostatic adjustment (GIA) since the Pleistocene. In particular, relative sea level data from long-term (longest is 150 year records) and over 600 tide gauge sites globally from PSMSL and other sources, and geocentric sea level data from multiple satellite altimetry (1985--2005) have been used to determine and characterize 20th century global sea level rise. Altimeter and selected tide gauge sea level data have been used for the 20th century sea level determination, accounting for relative biases between the altimeters, effects of sea level corresponding to oceanic thermal expansion, vertical motions affecting tide gauge measurements, self gravitations, and barotropic ocean response. This study is also characterized by the roles of the polar ocean in the global sea level study and addressing the question whether there is a detectable sea level rise acceleration during the last decade. Vertical motions have been estimated by combining geocentric sea level measurements from satellite altimetry (TOPEX/POSEIDON) and long-term relative (crust-fixed) sea level records from global tide gauges using the Gauss-Markov (GM) model with stochastic constraints. The study provided a demonstration of improved vertical motion solutions in semi-enclosed seas and lakes, including Fennoscandia and the Great Lakes region, showing excellent agreement with independent GPS observed radial velocities, or with predictions from GIA models. In general, the estimated uncertainty of the observed

  17. Molecular evidence of iron limitation and availability in the global diazotroph Trichodesmium

    PubMed Central

    Chappell, Phoebe Dreux; Moffett, James W; Hynes, Annette M; Webb, Eric A

    2012-01-01

    The activity of the N2-fixing cyanobacterial genus Trichodesmium is critical to the global nitrogen (N) and carbon (C) cycles. Although iron (Fe) has been shown to be an important element limiting the growth and N2 fixation of Trichodesmium, there have been no specific data demonstrating the in situ affect of Fe on Trichodesmium. We surveyed Trichodesmium populations from the Atlantic and Pacific Oceans for Fe limitation using a novel quantitative reverse transcriptase-PCR (qRT-PCR) method monitoring the expression of an Fe limitation-induced gene, isiB. Here we report the first molecular evidence of in situ Fe limitation of Trichodesmium N2 fixation, which was evident in samples from the Pacific Ocean, whereas limitation appeared minimal to nonexistent in Atlantic Ocean samples. As our method is Trichodesmium clade specific, we were also able to determine that representatives from the Trichodesmium tenue clade were the most biologically active group of Trichodesmium in the majority of our samples, which speaks to their dominance in open ocean regimes. Furthermore, comparisons of our field expression and chemical data with laboratory studies suggest that the majority of dissolved Fe in the open ocean is available to Trichodesmium colonies regardless of Fe complexation. PMID:22402399

  18. Molecular characterization of a duck Tembusu virus from China.

    PubMed

    Bai, XiaoFei; Lv, Rang; Liu, ChunGuo; Qiu, Na; He, Yilong; Yin, XiuChen; Li, XiaoJun; Liu, Ming; Zhang, Yun

    2013-12-01

    A new emerging flavivirus caused severe egg-drop in poultry and spread quickly across most duck-producing regions of China in 2010. Complete genome sequencing indicated that the virus genome is 10,989 nucleotides in length and possesses typical flavivirus genome organization, 5' untranslated region (UTR)-Cv-Ci-prM-M-E-NS1-NS2A-NS2B-NS3-NS4A-2K-NS4B-NS5-3'-UTR. The long open reading frame (ORF) encodes 3,425 amino acids (95-10,372 nt). The 94-nucleotide 5'-UTR is of intermediate size and the 617-nucleotide 3'-UTR is quite long relative to those of other flaviviruses. The polyprotein cleavage sites, potential glycosylation sites, distribution of cysteine residues, and 3'-UTR secondary structure were characterized. Phylogenetic analysis of the polyprotein sequences indicates that the HN isolate is closely related to Tembusu viruses of the Ntaya virus group. PMID:23949785

  19. Molecular characterization of epiphytic bacterial communities on charophycean green algae

    PubMed

    Fisher; Wilcox; Graham

    1998-11-01

    Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phylogenetic analysis, the cloned sequences were placed into several major lineages of the Bacteria domain: the Flexibacter/Cytophaga/Bacteroides phylum and the alpha, beta, and gamma subdivisions of the phylum Proteobacteria. Analysis at the subphylum level revealed that the majority of our sequences were not closely affiliated with those of known, cultured taxa, although the estimated evolutionary distances between our sequences and their nearest neighbors were always less than 0.1 (i.e., greater than 90% similar). This result suggests that the majority of sequences obtained in this study represent as yet phenotypically undescribed bacterial species and that the range of bacterial-algal interactions that occur in nature has not yet been fully described.

  20. Molecular Characterization of the Aphis gossypii Olfactory Receptor Gene Families

    PubMed Central

    Walker, William B.; Li, Jianhong; Wang, Guirong

    2014-01-01

    The cotton aphid, Aphis gossypii Glover, is a polyphagous pest that inflicts great damage to cotton yields worldwide. Antennal olfaction, which is extremely important for insect survival, mediates key behaviors such as host preference, mate choice, and oviposition site selection. In insects, odor detection is mediated by odorant receptors (ORs) and ionotropic receptors (IRs), which ensure the specificity of the olfactory sensory neuron responses. In this study, our aim is to identify chemosensory receptors in the cotton aphid genome, as a means to uncover olfactory encoding of the polyphagous feeding habits as well as to aid the discovery of new targets for behavioral interference. We identified a total of 45 candidate ORs and 14 IRs in the cotton aphid genome. Among the candidate AgoORs, 9 are apparent pseudogenes, while 19 can be clustered with ORs from the pea aphid, forming 16 AgoOR/ApOR orthologous subgroups. Among the candidate IRs, we identified homologs of the two highly conserved co-receptors IR8a and IR25a; no AgoIR retain the complete glutamic acid binding domain, suggesting that putative AgoIRs bind different ligands. Our results provide the necessary information for functional characterization of the chemosensory receptors of A. gossypii, with potential for new or refined applications of semiochemicals-based control of this pest insect. PMID:24971460

  1. Molecular characterization of the Aphis gossypii olfactory receptor gene families.

    PubMed

    Cao, Depan; Liu, Yang; Walker, William B; Li, Jianhong; Wang, Guirong

    2014-01-01

    The cotton aphid, Aphis gossypii Glover, is a polyphagous pest that inflicts great damage to cotton yields worldwide. Antennal olfaction, which is extremely important for insect survival, mediates key behaviors such as host preference, mate choice, and oviposition site selection. In insects, odor detection is mediated by odorant receptors (ORs) and ionotropic receptors (IRs), which ensure the specificity of the olfactory sensory neuron responses. In this study, our aim is to identify chemosensory receptors in the cotton aphid genome, as a means to uncover olfactory encoding of the polyphagous feeding habits as well as to aid the discovery of new targets for behavioral interference. We identified a total of 45 candidate ORs and 14 IRs in the cotton aphid genome. Among the candidate AgoORs, 9 are apparent pseudogenes, while 19 can be clustered with ORs from the pea aphid, forming 16 AgoOR/ApOR orthologous subgroups. Among the candidate IRs, we identified homologs of the two highly conserved co-receptors IR8a and IR25a; no AgoIR retain the complete glutamic acid binding domain, suggesting that putative AgoIRs bind different ligands. Our results provide the necessary information for functional characterization of the chemosensory receptors of A. gossypii, with potential for new or refined applications of semiochemicals-based control of this pest insect. PMID:24971460

  2. Molecular characterization and expression analysis of the duck viperin gene.

    PubMed

    Zhong, Zifu; Ji, Yanhong; Fu, Yuguang; Liu, Bin; Zhu, Qiyun

    2015-10-01

    Viperin is well known as one of the interferon-stimulated genes involved in innate immunity. Recent studies showed that this gene is mainly responsible for antiviral response to a large variety of viral infections. In this study, we successfully cloned and characterized the complete coding sequence of duck viperin gene. The duck viperin gene encodes 363 amino acids (aa) and is highly similar to viperins from other species. Moreover, secondary and 3D structures were predicted, and these structures showed two main domains, one signal peptide, and one radical S-adenosyl methionine (SAM) domain. Additionally, the duck viperin expression was analyzed in vitro and in vivo, and analysis results indicated that the duck viperin can be strongly up-regulated by poly(I:C) and Newcastle disease virus in primary duck embryo fibroblast cells. Results also demonstrated that Newcastle disease virus significantly induced duck viperin expression in the spleen, kidneys, liver, brain, and blood. Our findings will contribute to future studies on the detailed functions and potential underlying mechanisms of this novel protein in innate immunity.

  3. Molecular and biochemical characterization of Eimeria tenella hexokinase.

    PubMed

    Sun, Mingfei; Liao, Shenquan; Zhang, Longxian; Wu, Caiyan; Qi, Nanshan; Lv, Minna; Li, Juan; Lin, Xuhui; Zhang, Jianfei; Xie, Mingquan; Zhu, Guan; Cai, Jianping

    2016-09-01

    Hexokinase (HK) is one of the key enzymes in the glycolytic pathway that catalyzes the phosphorylation of glucose. In the present study, we cloned the HK gene from the coccidian Eimeria tenella (EtHK), expressed EtHK as a His-tagged fusion protein, and characterized its primary biochemical features. Mutagenesis confirmed that residues S159, N216, and D217 are essential or important to the EtHK catalytic activity. EtHK exhibited high affinity for D-glucose (Km = 0.67 to 0.79 mM), but was also able to utilize 2-deoxy-D-glucose (Km = 5.66 mM), D-fructose (Km = 13.76 mM), and D-mannose (Km = 25.41 mM). We also observed that quercetin and mangiferin could inhibit the EtHK enzyme activity (IC50 values = 6.52 and 85.82 μM, respectively). Among the two inhibitors, mangiferin also inhibited the growth of E. tenella in vitro (MIC50 = 0.12 μM). These observations suggest that EtHK may be explored as potential drug target, and mangiferin and its analogs may be explored for developing anti-coccidial therapeutics. PMID:27150971

  4. Comprehensive molecular characterization of human colon and rectal cancer.

    PubMed

    2012-07-19

    To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ε (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. PMID:22810696

  5. Molecular characterization and expression of porcine Siglec-5.

    PubMed

    Escalona, Z; Álvarez, B; Uenishi, H; Toki, D; Yuste, M; Revilla, C; Gómez del Moral, M; Alonso, F; Ezquerra, A; Domínguez, J

    2014-05-01

    In this study we describe the characterization of the porcine orthologue of Siglec-5. A cDNa clone was obtained from a porcine cDNa library derived from swine small intestine which encodes a 555 a-a type 1 transmembrane protein with sequence homology to human Siglec-5. This protein consists of four Ig-like domains, a transmembrane region, and a cytoplasmic tail with two tyrosine-based signalling motifs. When expressed as a recombinant protein fused to the Fc region of human IgG1, porcine Siglec-5 was able to bind porcine red blood cells in a sialic acid-dependent manner. Monoclonal antibodies (mAb) were developed against porcine Siglec-5 and used to analyse its expression in bone marrow and blood cells, and lymphoid tissues. Porcine Siglec-5 expression was mainly restricted to myelomonocytic cells and their precursors, being detected also, although at low levels, on plasmacytoid dendritic cells and B lymphocytes. In lymphoid tissues, ellipsoids of the spleen and subcapsular and medullar sinuses of lymph nodes were positive for Siglec-5. These mAbs were able to precipitate, from granulocyte lysates, a protein of approximately 85 kDa under non-reducing conditions, indicating that porcine Siglec-5 is expressed as a monomer in the plasma membrane.

  6. Comprehensive Molecular Characterization of Human Colon and Rectal Cancer

    PubMed Central

    2012-01-01

    Summary To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression. PMID:22810696

  7. Molecular characterization of quinolinate phosphoribosyltransferase (QPRtase) in Nicotiana.

    PubMed

    Sinclair, S J; Murphy, K J; Birch, C D; Hamill, J D

    2000-11-01

    Quinolate acid phosphoribosyltransferase (QPRTase), a key enzyme in nicotinamide adenine dinucleotide (NAD) biosynthesis, also plays an important role in ensuring nicotinic acid is available for the synthesis of defensive pyridine alkaloids in Nicotiana species. In this study, cDNAs for QPRTase were characterized from N. rustica and N. tabacum. Deduced proteins from both cDNAs are almost identical and contain a 24 amino acid N-terminal extension, not reported in other QPRTases, that has characteristics of a mitochondrial targeting sequence. In N. tabacum and N. sylvestris, both of which contain nicotine as the major pyridine alkaloid, QPRTase transcript was detected in roots, the site of nicotine synthesis, but not in leaves. QPRTase transcript levels increased markedly in roots of both species 12-24 h after damage to aerial tissues, with a concomitant rise in transcript levels of putrescine N-methyltransferase (PMT), another key enzyme in nicotine biosynthesis. In N. glauca, however, in which anabasine represents the major pyridine alkaloid, QPRTase transcript was detected in both leaf and root tissues. Moreover, wound induction of QPRTase but not PMT was observed in leaf tissues, and not in roots, 12-24 h after wounding. Southern analysis of genomic DNA from the Nicotiana species noted above, and also several others from within the genus, suggested that QPRTase is encoded by a small gene family in all the species investigated. PMID:11198422

  8. Molecular characterization and expression of porcine Siglec-5.

    PubMed

    Escalona, Z; Álvarez, B; Uenishi, H; Toki, D; Yuste, M; Revilla, C; Gómez del Moral, M; Alonso, F; Ezquerra, A; Domínguez, J

    2014-05-01

    In this study we describe the characterization of the porcine orthologue of Siglec-5. A cDNa clone was obtained from a porcine cDNa library derived from swine small intestine which encodes a 555 a-a type 1 transmembrane protein with sequence homology to human Siglec-5. This protein consists of four Ig-like domains, a transmembrane region, and a cytoplasmic tail with two tyrosine-based signalling motifs. When expressed as a recombinant protein fused to the Fc region of human IgG1, porcine Siglec-5 was able to bind porcine red blood cells in a sialic acid-dependent manner. Monoclonal antibodies (mAb) were developed against porcine Siglec-5 and used to analyse its expression in bone marrow and blood cells, and lymphoid tissues. Porcine Siglec-5 expression was mainly restricted to myelomonocytic cells and their precursors, being detected also, although at low levels, on plasmacytoid dendritic cells and B lymphocytes. In lymphoid tissues, ellipsoids of the spleen and subcapsular and medullar sinuses of lymph nodes were positive for Siglec-5. These mAbs were able to precipitate, from granulocyte lysates, a protein of approximately 85 kDa under non-reducing conditions, indicating that porcine Siglec-5 is expressed as a monomer in the plasma membrane. PMID:24382335

  9. Molecular Characterization of Cryptosporidium spp. in Children from Mexico

    PubMed Central

    Valenzuela, Olivia; González-Díaz, Mariana; Garibay-Escobar, Adriana; Burgara-Estrella, Alexel; Cano, Manuel; Durazo, María; Bernal, Rosa M.; Hernandez, Jesús; Xiao, Lihua

    2014-01-01

    Cryptosporidiosis is a parasitic disease caused by Cryptosporidium spp. In immunocompetent individuals, it usually causes an acute and self-limited diarrhea; in infants, infection with Cryptosporidium spp. can cause malnutrition and growth retardation, and declined cognitive ability. In this study, we described for the first time the distribution of C. parvum and C. hominis subtypes in 12 children in Mexico by sequence characterization of the 60-kDa glycoprotein (GP60) gene of Cryptosporidium. Altogether, 7 subtypes belonging to 4 subtype families of C. hominis (Ia, Ib, Id and Ie) and 1 subtype family of C. parvum (IIa) were detected, including IaA14R3, IaA15R3, IbA10G2, IdA17, IeA11G3T3, IIaA15G2R1 and IIaA16G1R1. The frequency of the subtype families and subtypes in the samples analyzed in this study differed from what was observed in other countries. PMID:24755606

  10. Molecular Characterization of β-Thalassemia Intermedia in Southeast Iran.

    PubMed

    Miri-Moghaddam, Ebrahim; Bahrami, Sara; Naderi, Majid; Bazi, Ali; Karimipoor, Morteza

    2016-06-01

    Inheritance of mild mutations within the β-globin gene and coinheritance of α-thalassemia (α-thal) are known as two important genetic modifiers in β-thalassemia (β-thal) intermedia (β-TI). We aimed to evaluate the spectrum of β- and α-thal mutations in β-TI patients in Southeast Iran. Common β- and α-globin gene mutations were detected by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and multiplex gap-PCR, respectively. There were 26 male (57.8%) and 19 female (42.2%) patients. HBB: c.92 + 5T > C [IVS-I-5 (G > C)] and HBB: c.-138C + 1G > A [IVS-II-I (G > A)] represented the prevalent alleles with respective frequencies of 60.0 and 10.0%. Other β-globin mutations included HBB: c.-138C > T [-88 (C > T)], HBB: c.27_28insG [frameshift codons (FSC) 8/9 (+G)], HBB: c.46delT [codon 15 (-T)], HBB: c.93-22_95del (IVS-I, 25 del), and the 619 bp deletion (NG_000007.3: g.71609_72227del619). The predominant genotypic combinations were β(0)/β(0) (68.9%), β(0)/β(+ )(8.9%) and β(+)/β(+ )(2.2%). Coinheritance of α-thal was observed in 33.0% of the patients, with the -α(3.7) (rightward) (NG_000006.1: g.34164_37967del3804) as the most common deletion (86.0%). One patient was diagnosed with the -α(4.2) (leftward) (AF221717) and one with the - -(MED) (g.24664_41064del16401) deletions, while no patients carried the -(α)(20.5) (g.15164_37864del22701), α(-5 nt) (HBA2: c.95 + 2_95_6delTGAGG) or codon 19 (-G) (HBA2: c.56delG) mutations. The alleviating molecular mechanism was not explainable by β(+ )or concurrent α-thal in more than half of our β-TI patients. This encourages conducting more studies to identify other contributing factors, especially Hb F-inducing genetic modifiers. PMID:27117567

  11. Molecular characterization of mutations in white-flowered torenia plants

    PubMed Central

    2014-01-01

    Background Torenia (Torenia fournieri Lind.) is a model plant increasingly exploited in studies in various disciplines, including plant engineering, biochemistry, physiology, and ecology. Additionally, cultivars with different flower colors have been bred and made commercially available. Flower color in torenia is mainly attributed to the accumulation of anthocyanins, but the molecular mechanisms inducing flower color mutations in torenia have not been well elucidated. In this study, we therefore attempted to identify the cause of white coloration in torenia by comparing the white-flowered cultivar Crown White (CrW) with Crown Violet (CrV), a violet-flowered variety. Results In an expression analysis, no flavanone 3-hydroxylase (TfF3H) transcript accumulation was detected in CrW petals. Sequence analyses revealed that a novel long terminal repeat (LTR)-type retrotransposable element, designated as TORE1 (Torenia retrotransposon 1), is inserted into the 5′-upstream region of the TfF3H gene in CrW. A transient expression assay using torenia F3H promoters with or without TORE1 insertion showed that the TORE1 insertion substantially suppressed F3H promoter activity, suggesting that this insertion is responsible for the absence of F3H transcripts in white petals. Furthermore, a transformation experiment demonstrated that the introduction of a foreign gentian F3H cDNA, GtF3H, into CrW was able to recover pink-flower pigmentation, indicating that F3H deficiency is indeed the cause of the colorless flower phenotype in CrW. Detailed sequence analysis also identified deletion mutations in flavonoid 3′-hydroxylase (TfF3′H) and flavonoid 3′,5′- hydroxylase (TfF3′5′H) genes, but these were not directly responsible for white coloration in this cultivar. Conclusions Taken together, a novel retrotransposable element, TORE1, inserted into the F3H 5′-upstream region is the cause of deficient F3H transcripts in white-flowered torenia, thereby leading to reduced petal

  12. Biochemical and molecular characterization of the calcineurin in Echinococcus granulosus larval stages.

    PubMed

    Nicolao, María Celeste; Cumino, Andrea C

    2015-06-01

    Calcineurin (CaN) is a Ca(2+)-calmodulin activated serine-threonine protein phosphatase that couples the local or global calcium signals, thus controlling important cellular functions in physiological and developmental processes. The aim of this study was to characterize CaN in Echinococcus granulosus (Eg-CaN), a human cestode parasite of clinical importance, both functionally and molecularly. We found that the catalytic subunit isoforms have predicted sequences of 613 and 557 amino acids and are substantially similar to those of the human counterpart, except for the C-terminal end. We also found that the regulatory subunit consists of 169 amino acids which are 87% identical to the human ortholog. We cloned a cDNA encoding for one of the two catalytic subunit isoforms of CaN (Eg-can-A1) as well as the only copy of the Eg-can-B gene, both constitutively transcribed in all Echinococcus larval stages and responsible for generating a functionally active heterodimer. Eg-CaN native enzyme has phosphatase activity, which is enhanced by Ca(2+)/Ni(2+) and reduced by cyclosporine A and Ca(2+) chelators. Participation of Eg-CaN in exocytosis was demonstrated using the FM4-64 probe and Eg-CaN-A was immunolocalized in the cytoplasm of tegumental cells, suckers and excretory bladder of protoscoleces. We also showed that the Eg-can-B transcripts were down-regulated in response to low Ca(2+) intracellular level, in agreement with decreased enzyme activity. Confocal microscopy revealed a striking pattern of Eg-CaN-A in discrete fluorescent spots in the protoscolex posterior bladder and vesicularized protoscoleces beginning the vesicular differentiation. In contrast, Eg-CaN-A was undetectable during the pre-microcyst closing stage while a high DDX-like RNA helicase expression was evidenced. Finally, we identified and analyzed the expression of CaN-related endogenous regulators.

  13. Characterization of Rhizobial Isolates of Phaseolus vulgaris by Staircase Electrophoresis of Low-Molecular-Weight RNA

    PubMed Central

    Velázquez, Encarna; Martínez-Romero, Esperanza; Rodríguez-Navarro, Dulce Nombre; Trujillo, Martha E.; Daza, Antonio; Mateos, Pedro F.; Martínez-Molina, Eustoquio; van Berkum, Peter

    2001-01-01

    Low-molecular-weight (LMW) RNA molecules were analyzed to characterize rhizobial isolates that nodulate the common bean growing in Spain. Since LMW RNA profiles, determined by staircase electrophoresis, varied across the rhizobial species nodulating beans, we demonstrated that bean isolates recovered from Spanish soils presumptively could be characterized as Rhizobium etli, Rhizobium gallicum, Rhizobium giardinii, Rhizobium leguminosarum bv. viciae and bv. trifolii, and Sinorhizobium fredii. PMID:11157280

  14. Molecular identification, immunolocalization, and characterization of Clonorchis sinensis triosephosphate isomerase.

    PubMed

    Zhou, Juanjuan; Liao, Hua; Li, Shan; Zhou, Chenhui; Huang, Yan; Li, Xuerong; Liang, Chi; Yu, Xinbing

    2015-08-01

    Clonorchis sinensis triosephosphate isomerase (CsTIM) is a key regulatory enzyme of glycolysis and gluconeogenesis, which catalyzes the interconversion of glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. In this study, the biochemical characterizations of CsTIM have been examined. A full-length complementary DNA (cDNA; Cs105350) sequence encoding CsTIM was obtained from our C. sinensis cDNA library. The open reading frame of CsTIM contains 759 bp which encodes 252 amino acids. The amino acid sequence of CsTIM shares 60-65% identity with other species. Western blot analysis displayed that recombinant CsTIM (rCsTIM) can be probed by anti-rCsTIM rat serum and anti-C. sinensis excretory/secretory products (anti-CsESPs) rat serum. Quantitative reverse transcription (RT)-PCR and western blotting analysis revealed that CsTIM messenger RNA (mRNA) and protein were differentially expressed in development cycle stages of the parasite, including adult worm, metacercaria, excysted metacercaria, and egg. In addition, immunolocalization assay showed that CsTIM was located in the seminal vesicle, eggs, and testicle. Moreover, rCsTIM exhibited active enzyme activity in catalytic reactions. The Michaelis constant (K m) of rCsTIM was 0.33 mM, when using glyceraldehyde 3-phosphate as the substrate. The optimal temperature and pH of CsTIM were 37 °C and 7.5-9.5, respectively. Collectively, these results suggest that CsTIM is an important protein involved in glycometabolism, and CsTIM possibly take part in many biological functions in the growth and development of C. sinensis. PMID:25990061

  15. Molecular characterization of Bacillus thuringiensis strains from Argentina.

    PubMed

    Franco-Rivera, Alejandro; Benintende, Graciela; Cozzi, Jorge; Baizabal-Aguirre, Victor Manuel; Valdez-Alarcón, Juan José; López-Meza, Joel Edmundo

    2004-07-01

    Bacillus thuringiensis INTA 7-3, INTA 51-3, INTA Mo9-5 and INTA Mo14-4 strains were obtained from Argentina and characterized by determination of serotype, toxicity, plasmid composition, insecticidal gene content ( cry and vip ) and the cloning of the single- vip3A gene of the INTA Mo9-5 strain. The serotype analysis identified the serovars tohokuensis and darmstadiensis for the INTA 51-3 and INTA Mo14-4 strains, respectively, whereas the INTA Mo9-5 strain was classified as "autoagglutinated". In contrast to the plasmid patterns of INTA 7-3, INTA 51-3 and INTA Mo9-5 (which were similar to B. thuringiensis HD-1 strain), strain INTA Mo14-4 showed a unique plasmid array. PCR analysis of the four strains revealed the presence of cry genes and vip3A genes. Interestingly, it was found that B. thuringiensis 4Q7 strain, which is a plasmid cured strain, contained vip3A genes indicating the presence of these insecticidal genes in the chromosome. Bioassays towards various lepidopteran species revealed that B. thuringiensis INTA Mo9-5 and INTA 7-3 strains were highly active. In particular, the mean LC(50) obtained against A. gemmatalis larvae with the INTA Mo9-5 and INTA 7-3 strains were 7 (5.7-8.6) and 6.7 (5.6-8.0) ppm, respectively. The INTA Mo14-4 strain was non-toxic and strain INTA 51-3 showed only a weak larvicidal activity. PMID:15103240

  16. Molecular Characterization of δ-Thalassemia in Iran.

    PubMed

    Kordafshari, Alireza; Amirian, Azam; Zeinali, Sirous; Valaei, Atefeh; Maryami, Fereshteh; Karimipoor, Morteza

    2016-01-01

    δ-Thalassemia (δ-thal) (OMIM #142000) resulting from mutations on the HBD gene usually has no clinical consequences. However, it may cause the misdiagnosis of β-thalassemia (β-thal) carriers by lowering the Hb A2 level to the normal range. Therefore, a study for δ-thal should be considered as a step in the detection of at-risk couple in our region. The aim of the present study was to characterize the mutations of the HBD gene in β-thal carriers with normal Hb A2 levels, and also in normal individuals with Hb A2 of less than 2.0%. Four β-thal carriers with normal Hb A2 and 39 individuals with Hb A2 of less than 2.0% were enrolled. Genomic DNA was extracted by the salting out method and the HBD gene was investigated by polymerase chain reaction (PCR) and direct DNA sequencing. Hb A2-Yialousa (HBD: c.82 G > T) was the most common variant found in the HBD gene, but the following mutations were also found: Hb A2-NYU (HBD: c.39 T > A), Hb A2-Coburg (HBD: c.350 G > A), Hb A2-Etolia (HBD: c.257 T > C), Hb A2-Fitzroy (HBD: c.428 C > A) and the δ-IVS-I-5 (G > T) (HBD: c.92 + 5 G > T). One case was a compound heterozygote for δ-IVS-I-5/Hb A2-Fitzroy. The results of this single center study suggest that the mutations in the HBD gene in the Iranian population are heterogeneous and should be considered in genetic counseling of families. PMID:26754299

  17. Molecular Characterization of Staphylococcus sciuri Strains Isolated from Humans

    PubMed Central

    Couto, Isabel; Sanches, Ilda Santos; Sá-Leão, Raquel; de Lencastre, Hermínia

    2000-01-01

    We previously characterized over 100 Staphylococcus sciuri isolates, mainly of animal origin, and found that they all carried a genetic element (S. sciuri mecA) closely related to the mecA gene of methicillin-resistant Staphylococcus aureus (MRSA) strains. We also found a few isolates that carried a second copy of the gene, identical to MRSA mecA. In this work, we analyzed a collection of 28 S. sciuri strains isolated from both healthy and hospitalized individuals. This was a relatively heterogeneous group, as inferred from the different sources, places, and dates of isolation and as confirmed by pulsed-field gel electrophoresis analysis. All strains carried the S. sciuri mecA copy, sustaining our previous proposal that this element belongs to the genetic background of S. sciuri. Moreover, 46% of the strains also carried the MRSA mecA copy. Only these strains showed significant levels of resistance to beta-lactams. Strikingly, the majority of the strains carrying the additional MRSA mecA copy were obtained from healthy individuals in an antibiotic-free environment. Most of the 28 strains were resistant to penicillin, intermediately resistant to clindamycin, and susceptible to tetracycline, erythromycin, and gentamicin. Resistance to these last three antibiotics was found in some strains only. The findings reported in this work confirmed the role of S. sciuri in the evolution of the mechanism of resistance to methicillin in staphylococci and suggested that this species (like the pathogenic staphylococci) may accumulate resistance markers for several classes of antibiotics. PMID:10699009

  18. Molecular Characterization of Vitellogenin and Vitellogenin Receptor of Bemisia tabaci.

    PubMed

    Upadhyay, Santosh Kumar; Singh, Harpal; Dixit, Sameer; Mendu, Venugopal; Verma, Praveen C

    2016-01-01

    Vitellogenin (Vg) plays vital role in oocytes and embryo development in insects. Vg is synthesized in the fat body, moves through haemolymph and accumulates in oocytes. Vitellogenin receptors (VgR) present on the surface of oocytes, are responsible for Vg transportation from haemolymph to oocytes. Here, we cloned and characterized these genes from Bemisia tabaci Asia1 (BtA1) species. The cloned BtA1Vg and BtA1VgR genes consisted of 6,330 and 5,430 bp long open reading frames, which encoded 2,109 and 1,809 amino acid (AA) residues long protein. The BtA1Vg protein comprised LPD_N, DUF1943 and VWFD domains, typical R/KXXR/K, DGXR and GL/ICG motifs, and polyserine tracts. BtA1VgR protein contained 12 LDLa, 10 LDLb and 7 EGF domains, and a trans-membrane and cytoplasmic region at C-terminus. Phylogenetic analyses indicated evolutionary association of BtA1Vg and BtA1VgR with the homologous proteins from various insect species. Silencing of BtA1VgR by siRNA did not affect the transcript level of BtA1Vg. However, BtA1Vg protein accumulation in oocytes was directly influenced with the expression level of BtA1VgR. Further, BtA1VgR silencing caused significant mortality and reduced fecundity in adult whiteflies. The results established the role of BtA1VgR in transportation of BtA1Vg in oocytes. Further, these proteins are essential for fecundity, and therefore these can be potential RNAi targets for insect control in crop plants. PMID:27159161

  19. Biochemical and molecular characterization of Staphylococcus simulans lipase.

    PubMed

    Sayari, A; Agrebi, N; Jaoua, S; Gargouri, Y

    2001-09-01

    Staphylococcus simulans strain secretes a non-induced lipase in the culture medium. Staphylococcus simulans lipase (SSL), purified to homogeneity, is a tetrameric protein (160 kDa) corresponding to the association of four lipase molecules. The 30 N-terminal amino acid residues were sequenced. This sequence is identical to the one of Staphylococcus aureus PS54 lipase (SAL PS54) and exhibits a high degree of homology with Staphylococcus aureus NCTC8530 lipase (SAL NCTC8530), Staphylococcus hyicus lipase (SHL) and Staphylococcus epidermis RP62A lipase (SEL RP62A) sequences. But the cloning and sequencing of the part of the gene encoding the mature lipase show some differences from SAL PS54 sequence, which suggest that it is a new sequence. The lipase activity was maximal at pH 8.5 and 37 degrees C. SSL is able to hydrolyze triacylglycerols without chain length specificity. A specific activity of about 1000 U/mg was measured on tributyrin or triolein as substrate at 37 degrees C and at pH 8.5 in the presence of 3 mM CaCl(2). In contrast to other staphylococcal lipases previously characterized, Ca(2+) is not required to express the activity of SSL. SSL was found to be stable between pH 4 and pH 9. The enzyme is inactivated after a few minutes when incubated at 60 degrees C. Using tripropionin as substrate, SSL does not present the interfacial activation phenomenon. In contrast to many lipases, SSL is able to hydrolyze its substrate in the presence of bile salts or amphiphilic proteins. PMID:11698108

  20. Molecular Characterization of Vitellogenin and Vitellogenin Receptor of Bemisia tabaci

    PubMed Central

    Upadhyay, Santosh Kumar; Singh, Harpal; Dixit, Sameer; Mendu, Venugopal; Verma, Praveen C.

    2016-01-01

    Vitellogenin (Vg) plays vital role in oocytes and embryo development in insects. Vg is synthesized in the fat body, moves through haemolymph and accumulates in oocytes. Vitellogenin receptors (VgR) present on the surface of oocytes, are responsible for Vg transportation from haemolymph to oocytes. Here, we cloned and characterized these genes from Bemisia tabaci Asia1 (BtA1) species. The cloned BtA1Vg and BtA1VgR genes consisted of 6,330 and 5,430 bp long open reading frames, which encoded 2,109 and 1,809 amino acid (AA) residues long protein. The BtA1Vg protein comprised LPD_N, DUF1943 and VWFD domains, typical R/KXXR/K, DGXR and GL/ICG motifs, and polyserine tracts. BtA1VgR protein contained 12 LDLa, 10 LDLb and 7 EGF domains, and a trans-membrane and cytoplasmic region at C-terminus. Phylogenetic analyses indicated evolutionary association of BtA1Vg and BtA1VgR with the homologous proteins from various insect species. Silencing of BtA1VgR by siRNA did not affect the transcript level of BtA1Vg. However, BtA1Vg protein accumulation in oocytes was directly influenced with the expression level of BtA1VgR. Further, BtA1VgR silencing caused significant mortality and reduced fecundity in adult whiteflies. The results established the role of BtA1VgR in transportation of BtA1Vg in oocytes. Further, these proteins are essential for fecundity, and therefore these can be potential RNAi targets for insect control in crop plants. PMID:27159161

  1. Identification and Molecular Characterization of Microneme 5 of Eimeria acervulina

    PubMed Central

    Zhang, ZhenChao; Huang, JingWei; Li, MengHui; Sui, YuXia; Wang, Shuai; Liu, LianRui; Xu, LiXin; Yan, RuoFeng; Song, XiaoKai; Li, XiangRui

    2014-01-01

    In the present study, the microneme 5 gene of Eimeria acervulina (E. acervulina) (EaMIC5) was cloned and characterized. Specific primers for the rapid amplification of cDNA ends (RACE) were designed based on the expressed sequence tag (EST, GenBank Accession No. EH386430.1) to amplify the 3′- and 5′-ends of EaMIC5. The full length cDNA of this gene was obtained by overlapping the sequences of 3′- and 5′-extremities and amplification by reverse transcription PCR. Sequence analysis revealed that the open reading frame (ORF) of EaMIC5 was 336 bp and encoded a protein of 111 amino acids with 12.18 kDa. The ORF was inserted into pET-32a (+) to produce recombinant EaMIC5. Using western blotting assay, the recombinant protein was successfully recognized by the sera of chicks experimentally infected with E. acervulina, while the native protein in the somatic extract of sporozoites was as well detected by sera from rats immunized with the recombinant protein of EaMIC5. Immunofluorescence analysis using antibody against recombinant protein EaMIC5 indicated that this protein was expressed in the sporozoites and merozoites stages of E. acervulina. Animal challenge experiments demonstrated that the recombinant protein of EaMIC5 could significantly increase the average body weight gains, decrease the mean lesion scores and the oocyst outputs of the immunized chickens, and presented anti-coccidial index (ACI) more than 160. All the above results suggested that the EaMIC5 was a novel E. acervulina antigen and could be an effective candidate for the development of a new vaccine against this parasite. PMID:25531898

  2. Molecular Characterization of δ-Thalassemia in Iran.

    PubMed

    Kordafshari, Alireza; Amirian, Azam; Zeinali, Sirous; Valaei, Atefeh; Maryami, Fereshteh; Karimipoor, Morteza

    2016-01-01

    δ-Thalassemia (δ-thal) (OMIM #142000) resulting from mutations on the HBD gene usually has no clinical consequences. However, it may cause the misdiagnosis of β-thalassemia (β-thal) carriers by lowering the Hb A2 level to the normal range. Therefore, a study for δ-thal should be considered as a step in the detection of at-risk couple in our region. The aim of the present study was to characterize the mutations of the HBD gene in β-thal carriers with normal Hb A2 levels, and also in normal individuals with Hb A2 of less than 2.0%. Four β-thal carriers with normal Hb A2 and 39 individuals with Hb A2 of less than 2.0% were enrolled. Genomic DNA was extracted by the salting out method and the HBD gene was investigated by polymerase chain reaction (PCR) and direct DNA sequencing. Hb A2-Yialousa (HBD: c.82 G > T) was the most common variant found in the HBD gene, but the following mutations were also found: Hb A2-NYU (HBD: c.39 T > A), Hb A2-Coburg (HBD: c.350 G > A), Hb A2-Etolia (HBD: c.257 T > C), Hb A2-Fitzroy (HBD: c.428 C > A) and the δ-IVS-I-5 (G > T) (HBD: c.92 + 5 G > T). One case was a compound heterozygote for δ-IVS-I-5/Hb A2-Fitzroy. The results of this single center study suggest that the mutations in the HBD gene in the Iranian population are heterogeneous and should be considered in genetic counseling of families.

  3. Fine binding characteristics of human autoantibodies-partial molecular characterization.

    PubMed

    Kumar, Sanjeev; Kalsi, Jatinderpal; Bunting, Karen; Ravirajan, Chelliah T; Latchman, David S; Pearl, Laurence H; Isenberg, David A

    2004-07-01

    The fine binding characteristics of three well-characterized human autoantibodies B3, RH14 (anti-DNA) and UK4 (anti-cardiolipin) in their IgG and cloned Fab formats, were investigated. Although in severe combined immunodeficiency (SCID) mice B3 and RH14 both induce proteinuria, only RH14 induces early features of lupus nephritis, whereas UK4 exhibits lupus anticoagulant activity. RH14 exhibited up to 10 fold higher binding to DNA compared to that shown by B3 or UK4 and involved significant electrostatic and phosphate group interactions. Only RH14 exhibited strong anti-Sm cross-reactivity residing on the C-terminus of the antigen as determined by the use of 76 overlapping 15mer peptides. Chain shuffling experiments indicate that anti-Sm/RNP and anti-Jo-1 activities of B3 and UK4 co-exist on one of the two chains (light, B3; heavy, UK4). The present study provides evidence that a human anti-DNA antibody can also be an anti-ENA antibody. Furthermore, the anti-DNA antibodies also exhibited cross-reactivity against glutathione-S-transferase and DNA polymerase PolIV of bacterial origin. This is the first demonstration of the presence of such cross-reactivities on lupus anti-DNA antibodies. We now demonstrate that subsets of sera from the patients with lupus, recognise these antigens. This observation may in some cases provide a mechanism for the common expression of a variety of autoantibodies observed in systemic lupus erythematosus (SLE).

  4. Microbiological and Molecular Characterization of Staphylococcus hominis Isolates from Blood

    PubMed Central

    Mendoza-Olazarán, Soraya; Morfin-Otero, Rayo; Rodríguez-Noriega, Eduardo; Llaca-Díaz, Jorge; Flores-Treviño, Samantha; González-González, Gloria Ma; Villarreal-Treviño, Licet; Garza-González, Elvira

    2013-01-01

    Background Among Coagulase-Negative Staphylococci (CoNS), Staphylococcus hominis represents the third most common organism recoverable from the blood of immunocompromised patients. The aim of this study was to characterize biofilm formation, antibiotic resistance, define the SCCmec (Staphylococcal Chromosomal Cassette mec) type, and genetic relatedness of clinical S. hominis isolates. Methodology S. hominis blood isolates (n = 21) were screened for biofilm formation using crystal violet staining. Methicillin resistance was evaluated using the cefoxitin disk test and the mecA gene was detected by PCR. Antibiotic resistance was determined by the broth microdilution method. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE) and SCCmec typed by multiplex PCR using two different methodologies described for Staphylococcus aureus. Results Of the S. hominis isolates screened, 47.6% (10/21) were categorized as strong biofilm producers and 23.8% (5/21) as weak producers. Furthermore, 81% (17/21) of the isolates were methicillin resistant and mecA gene carriers. Resistance to ampicillin, erythromycin, and trimethoprim was observed in >70% of isolates screened. Each isolate showed a different PFGE macrorestriction pattern with similarity ranging between 0–95%. Among mecA-positive isolates, 14 (82%) harbored a non-typeable SCCmec type: eight isolates were not positive for any ccr complex; four contained the mec complex A ccrAB1 and ccrC, one isolate contained mec complex A, ccrAB4 and ccrC, and one isolate contained the mec complex A, ccrAB1, ccrAB4, and ccrC. Two isolates harbored the association: mec complex A and ccrAB1. Only one strain was typeable as SCCmec III. Conclusions The S. hominis isolates analyzed were variable biofilm producers had a high prevalence of methicillin resistance and resistance to other antibiotics, and high genetic diversity. The results of this study strongly suggested that S. hominis isolates harbor new SCCmec

  5. Molecular cloning and characterization of presenilin gene in Bombyx mori.

    PubMed

    Zheng, Zeng-Zhang; Chao, Meng-Ling; Fan, Zong-Biao; Zhao, Yi-Jiao; Song, Hong-Sheng

    2015-10-01

    Presenilin (PS), the catalytic core of the γ-secretase complex, is considered to be a causative protein of the early‑onset familial form of Alzheimer's disease. Aging is a risk factor for Alzheimer's disease and a number of genetic studies have utilized Bombyx mori (B. mori) as a model, making it possible to use B. mori to investigate Alzheimer's disease. However, the homologous gene of human PS in B. mori has remained to be elucidated. In the present study, the PS homologue gene in B. mori was identified and characterized, and six B. mori presenilin (BmPS) mRNA transcripts were generated by selecting multiple transcription start sites and/or alternative splice sites. The longest mRNA of BmPS (termed BmPS1) contains a 153 nt 5' untranslated region (UTR), a 1,440 nt open reading frame and a 1,063 nt 3' UTR. The predicted protein of BmPS1 consists of 479 amino acid residues and has two highly‑conserved aspartate residues, which form the catalytic core of aspartic proteases. It exhibits a sequence identity of ~44 and 51% with homologues in Homo sapiens and Drosophila melanogaster, respectively. However, the amino acid sequence of the BmPS loop region does not completely match between the two B. mori strains R13Q and Dazao. Genomic analysis revealed that B. mori had a single copy of the BmPS gene, which was composed of 14 exons. A total of four isoforms of BmPS (BmPS‑A, ‑B, ‑C and ‑D) owing to multiple transcriptional start sites and alternative splice sites were identified. The alternative splicing events occurring in the loop region improved the diversity of the BmPS protein and were detectable in all tissues, as determined using reverse transcription quantitative polymerase chain reaction (RT‑qPCR). Furthermore, the expression levels of BmPS in the brain at different developmental stages were detected using RT‑qPCR, and significantly higher expression levels of BmPS were found in the adult stage compared with those in the larval and pupal stages

  6. Adenosquamous carcinoma of the pancreas: Molecular characterization of 23 patients along with a literature review

    PubMed Central

    Borazanci, Erkut; Millis, Sherri Z; Korn, Ron; Han, Haiyong; Whatcott, Clifford J; Gatalica, Zoran; Barrett, Michael T; Cridebring, Derek; Von Hoff, Daniel D

    2015-01-01

    Adenosquamous carcinoma of the pancreas (ASCP) is a rare entity. Like adenocarcinoma of the pancreas, overall survival is poor. Characteristics of ASCP include central tumor necrosis, along with osteoclasts and hypercalcemia. Various theories exist as to why this histological subtype exists, as normal pancreas tissue has no benign squamous epithelium. Due to the rarity of this disease, limited molecular analysis has been performed, and those reports indicate unique molecular features of ASCP. In this paper, we characterize 23 patients diagnosed with ASCP through molecular profiling using immunohistochemistry staining, fluorescent in situ hybridization, chromogenic in situ hybridization, and gene sequencing, Additionally, we provide a comprehensive literature review of what is known to date of ASCP. Molecular characterization revealed overexpression in MRP1 (80%), MGMT (79%), TOP2A (75), RRM1 (42%), TOPO1 (42%), PTEN (45%), CMET (40%), and C-KIT (10%) among others. One hundred percent of samples tested were positive for KRAS mutations. This analysis shows heretofore unsuspected leads to be considered for treatments of this rare type of exocrine pancreas cancer. Molecular profiling may be appropriate to provide maximum information regarding the patient’s tumor. Further work should be pursued to better characterize this disease. PMID:26380056

  7. Molecular characterization of bacterial respiration of minerals. Final technical report, March 1, 1985--February 29, 1996

    SciTech Connect

    Blake, R. II

    1996-08-01

    The goals of this project were to continue the identification, separation, and characterization of the cellular components necessary for aerobic respiration on iron, and to initiate an investigation of the molecular principles whereby these bacteria recognize and adhere to their insoluble inorganic substrates. Progress is described.

  8. Morphometric and molecular characterization of Dactylogyrus vastator and D. intermedius in goldfish (Carassius auratus).

    PubMed

    Ling, Fei; Tu, Xiao; Huang, Aiguo; Wang, Gaoxue

    2016-05-01

    Goldfish is known to be parasitized by at least seven species of Dactylogyrus and considered as one of the most common hosts. Dactylogyrus vastator and Dactylogyrus intermedius are the dominant species living on the gills of goldfish. However, little information on morphometric characterization is available, which easily causes misidentification. The purpose of this study is to provide comprehensive morphometric and molecular characterization of D. vastator and D. intermedius collected form a fish farm in Henan, China. The characterization was presented based on the high-resolution images and standard molecular markers (18S ribosomal DNA subunit and the internal transcribed spacer region), as well as a total of 10 point-to-point morphometrics characters. In addition, a detailed comparison of morphometric and phylogenetic characterization in D. vastator versus D. intermedius was performed. The results demonstrated that all parameters measured differed significantly between these two species of Dactylogyrus, whereas molecular comparison showed subtle differences between them in nucleotide divergence and genetic distances. These findings suggested that these two species of Dactylogyrus can be distinguished more easily based on morphometric measurements than molecular data for 18S ribosomal DNA + internal transcribed spacer region (ITS-1).

  9. Morphometric and molecular characterization of Dactylogyrus vastator and D. intermedius in goldfish (Carassius auratus).

    PubMed

    Ling, Fei; Tu, Xiao; Huang, Aiguo; Wang, Gaoxue

    2016-05-01

    Goldfish is known to be parasitized by at least seven species of Dactylogyrus and considered as one of the most common hosts. Dactylogyrus vastator and Dactylogyrus intermedius are the dominant species living on the gills of goldfish. However, little information on morphometric characterization is available, which easily causes misidentification. The purpose of this study is to provide comprehensive morphometric and molecular characterization of D. vastator and D. intermedius collected form a fish farm in Henan, China. The characterization was presented based on the high-resolution images and standard molecular markers (18S ribosomal DNA subunit and the internal transcribed spacer region), as well as a total of 10 point-to-point morphometrics characters. In addition, a detailed comparison of morphometric and phylogenetic characterization in D. vastator versus D. intermedius was performed. The results demonstrated that all parameters measured differed significantly between these two species of Dactylogyrus, whereas molecular comparison showed subtle differences between them in nucleotide divergence and genetic distances. These findings suggested that these two species of Dactylogyrus can be distinguished more easily based on morphometric measurements than molecular data for 18S ribosomal DNA + internal transcribed spacer region (ITS-1). PMID:26779922

  10. Molecular Characterization of a Functional Type VI Secretion System from a Clinical Isolate of Aeromonas hydrophilia

    EPA Science Inventory

    Our laboratory recently molecularly characterized the type II secretion system (T2SS)-associated cytotoxic enterotoxin (Act) and the T3SS-secreted AexU effector from a diarrheal isolate SSU of Aeromonas hydrophila. The role of these toxin proteins in the pathogenesis of A. hydrop...

  11. Molecular characterization of a functional type VI secretion system from a clinical isolate of Aeromonas hydrophila

    EPA Science Inventory

    Our laboratory recently molecularly characterized the type II secretion system (T2SS)-associated cytotoxic enterotoxin (Act) and the T3SS-secreted AexU effector from a diarrheal isolate SSU of Aeromonas hydrophila. The role of these toxin proteins in the pathogenesis of A. hydrop...

  12. Global reaction route mapping of isomerization pathways of exotic C{sub 6}H molecular species

    SciTech Connect

    Vikas, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet

    2013-12-14

    C{sub 6}H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C{sub 6}H is explored to search isomers of C{sub 6}H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C{sub 6}H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF/aug-cc-pVTZ, CCSD(T)/6-311++G(d,p)//DFT/B3LYP/6-311++G(d,p), and DFT/B3LYP/aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C{sub 6}H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C{sub 6}H can readily isomerize to a six-member ring isomer.

  13. Characterizing the Global Impact of P2P Overlays on the AS-Level Underlay

    NASA Astrophysics Data System (ADS)

    Rasti, Amir Hassan; Rejaie, Reza; Willinger, Walter

    This paper examines the problem of characterizing and assessing the global impact of the load imposed by a Peer-to-Peer (P2P) overlay on the AS-level underlay. In particular, we capture Gnutella snapshots for four consecutive years, obtain the corresponding AS-level topology snapshots of the Internet and infer the AS-paths associated with each overlay connection. Assuming a simple model of overlay traffic, we analyze the observed load imposed by these Gnutella snapshots on the AS-level underlay using metrics that characterize the load seen on individual AS-paths and by the transit ASes, illustrate the churn among the top transit ASes during this 4-year period, and describe the propagation of traffic within the AS-level hierarchy.

  14. Molecular basis of a shattering resistance boosting global dissemination of soybean.

    PubMed

    Funatsuki, Hideyuki; Suzuki, Masaya; Hirose, Aya; Inaba, Hiroki; Yamada, Tetsuya; Hajika, Makita; Komatsu, Kunihiko; Katayama, Takeshi; Sayama, Takashi; Ishimoto, Masao; Fujino, Kaien

    2014-12-16

    Pod dehiscence (shattering) is essential for the propagation of wild plant species bearing seeds in pods but is a major cause of yield loss in legume and crucifer crops. Although natural genetic variation in pod dehiscence has been, and will be, useful for plant breeding, little is known about the molecular genetic basis of shattering resistance in crops. Therefore, we performed map-based cloning to unveil a major quantitative trait locus (QTL) controlling pod dehiscence in soybean. Fine mapping and complementation testing revealed that the QTL encodes a dirigent-like protein, designated as Pdh1. The gene for the shattering-resistant genotype, pdh1, was defective, having a premature stop codon. The functional gene, Pdh1, was highly expressed in the lignin-rich inner sclerenchyma of pod walls, especially at the stage of initiation in lignin deposition. Comparisons of near-isogenic lines indicated that Pdh1 promotes pod dehiscence by increasing the torsion of dried pod walls, which serves as a driving force for pod dehiscence under low humidity. A survey of soybean germplasm revealed that pdh1 was frequently detected in landraces from semiarid regions and has been extensively used for breeding in North America, the world's leading soybean producer. These findings point to a new mechanism for pod dehiscence involving the dirigent protein family and suggest that pdh1 has played a crucial role in the global expansion of soybean cultivation. Furthermore, the orthologs of pdh1, or genes with the same role, will possibly be useful for crop improvement. PMID:25468966

  15. Molecular basis of a shattering resistance boosting global dissemination of soybean

    PubMed Central

    Funatsuki, Hideyuki; Suzuki, Masaya; Hirose, Aya; Inaba, Hiroki; Yamada, Tetsuya; Hajika, Makita; Komatsu, Kunihiko; Katayama, Takeshi; Sayama, Takashi; Ishimoto, Masao; Fujino, Kaien

    2014-01-01

    Pod dehiscence (shattering) is essential for the propagation of wild plant species bearing seeds in pods but is a major cause of yield loss in legume and crucifer crops. Although natural genetic variation in pod dehiscence has been, and will be, useful for plant breeding, little is known about the molecular genetic basis of shattering resistance in crops. Therefore, we performed map-based cloning to unveil a major quantitative trait locus (QTL) controlling pod dehiscence in soybean. Fine mapping and complementation testing revealed that the QTL encodes a dirigent-like protein, designated as Pdh1. The gene for the shattering-resistant genotype, pdh1, was defective, having a premature stop codon. The functional gene, Pdh1, was highly expressed in the lignin-rich inner sclerenchyma of pod walls, especially at the stage of initiation in lignin deposition. Comparisons of near-isogenic lines indicated that Pdh1 promotes pod dehiscence by increasing the torsion of dried pod walls, which serves as a driving force for pod dehiscence under low humidity. A survey of soybean germplasm revealed that pdh1 was frequently detected in landraces from semiarid regions and has been extensively used for breeding in North America, the world’s leading soybean producer. These findings point to a new mechanism for pod dehiscence involving the dirigent protein family and suggest that pdh1 has played a crucial role in the global expansion of soybean cultivation. Furthermore, the orthologs of pdh1, or genes with the same role, will possibly be useful for crop improvement. PMID:25468966

  16. Global Characterization and Monitoring of Forest Cover Using Landsat Data: Opportunities and Challenges

    NASA Technical Reports Server (NTRS)

    Townshend, John R.; Masek, Jeffrey G.; Huang, ChengQuan; Vermote, Eric F.; Gao, Feng; Channan, Saurabh; Sexton, Joseph O.; Feng, Min; Narasimhan, Ramghuram; Kim, Dohyung; Song, Kuan; Song, Danxia; Song, Xiao-Peng; Noojipady, Praveen; Tan, Bin; Hansen, Matthew C.; Li, Mengxue; Wolfe, Robert E.

    2012-01-01

    The compilation of global Landsat data-sets and the ever-lowering costs of computing now make it feasible to monitor the Earth's land cover at Landsat resolutions of 30 m. In this article, we describe the methods to create global products of forest cover and cover change at Landsat resolutions. Nevertheless, there are many challenges in ensuring the creation of high-quality products. And we propose various ways in which the challenges can be overcome. Among the challenges are the need for atmospheric correction, incorrect calibration coefficients in some of the data-sets, the different phenologies between compilations, the need for terrain correction, the lack of consistent reference data for training and accuracy assessment, and the need for highly automated characterization and change detection. We propose and evaluate the creation and use of surface reflectance products, improved selection of scenes to reduce phenological differences, terrain illumination correction, automated training selection, and the use of information extraction procedures robust to errors in training data along with several other issues. At several stages we use Moderate Resolution Spectroradiometer data and products to assist our analysis. A global working prototype product of forest cover and forest cover change is included.

  17. Characterization and control of molecular ordering on adsorbate-induced reconstructed surfaces

    NASA Astrophysics Data System (ADS)

    Pai, Woei Wu; Hsu, C. L.; Lin, K. C.; Sin, L. Y.; Tang, Tong B.

    2005-02-01

    Understanding molecular ordering is a critical step in achieving molecular self-assembly for the fabrication of nanomaterials, and molecular ordering in the adsorption of large molecules on atomically flat surfaces can be characterized with precision by scanning tunneling microscopy (STM). Complications arise therein from the expanded possibility of various adsorption structures, conformations and surface reconstructions. Here we present two cases of C 60 adsorbed on Ag(1 0 0) and Cu(1 1 1) that illustrate the importance of competitive interactions in the presence of adsorbate-induced reconstruction. In both studies, strong STM contrasts derive from topographic features arising from reconstructed substrates. C 60/Ag(1 0 0) presents a unique uniaxially incommensurate molecular packing. We have also found that one can control molecular ordering with a stepped surface to produce a single-domain film. In C 60/Cu(1 1 1), we are able to obtain metastable, yet well-defined, molecular ordering with precise annealing procedures. These metastable states exhibit a clear correlation between molecular contrast patterns and the adlayer rotation angle, as a consequence of competitive interactions between optimizing C 60 bonding at preferred reconstructive sites and C 60-C 60 repulsion. Finer control of selective preparation of these metastable structures offers a plausible way of fabricating nanostructures by design.

  18. Molecular intermediates of fitness gain of an RNA virus: characterization of a mutant spectrum by biological and molecular cloning.

    PubMed

    Arias, A; Lázaro, E; Escarmís, C; Domingo, E

    2001-05-01

    The mutant spectrum of a virus quasispecies in the process of fitness gain of a debilitated foot-and-mouth disease virus (FMDV) clone has been analysed. The mutant spectrum was characterized by nucleotide sequencing of three virus genomic regions (internal ribosome entry site; region between the two AUG initiation codons; VP1-coding region) from 70 biological clones (virus from individual plaques formed on BHK-21 cell monolayers) and 70 molecular clones (RT--PCR products cloned in E. coli). The biological and molecular clones provided statistically indistinguishable definitions of the mutant spectrum with regard to the distribution of mutations among the three genomic regions analysed and with regard to the types of mutations, mutational hot-spots and mutation frequencies. Therefore, the molecular cloning procedure employed provides a simple protocol for the characterization of mutant spectra of viruses that do not grow in cell culture. The number of mutations found repeated among the clones analysed was higher than expected from the mean mutation frequencies. Some components of the mutant spectrum reflected genomes that were dominant in the prior evolutionary history of the virus (previous passages), confirming the presence of memory genomes in virus quasispecies. Other components of the mutant spectrum were genomes that became dominant at a later stage of evolution, suggesting a predictive value of mutant spectrum analysis with regard to the outcome of virus evolution. The results underline the observation that greater insight into evolutionary processes of viruses may be gained from detailed clonal analyses of the mutant swarms at the sequence level.

  19. Theoretical Characterization of Visual Signatures and Calculation of Approximate Global Harmonic Frequency Scaling Factors

    NASA Astrophysics Data System (ADS)

    Kashinski, D. O.; Nelson, R. G.; Chase, G. M.; di Nallo, O. E.; Byrd, E. F. C.

    2016-05-01

    We are investigating the accuracy of theoretical models used to predict the visible, ultraviolet, and infrared spectra, as well as other properties, of product materials ejected from the muzzle of currently fielded systems. Recent advances in solid propellants has made the management of muzzle signature (flash) a principle issue in weapons development across the calibers. A priori prediction of the electromagnetic spectra of formulations will allow researchers to tailor blends that yield desired signatures and determine spectrographic detection ranges. Quantum chemistry methods at various levels of sophistication have been employed to optimize molecular geometries, compute unscaled harmonic frequencies, and determine the optical spectra of specific gas-phase species. Electronic excitations are being computed using Time Dependent Density Functional Theory (TD-DFT). Calculation of approximate global harmonic frequency scaling factors for specific DFT functionals is also in progress. A full statistical analysis and reliability assessment of computational results is currently underway. Work supported by the ARL, DoD-HPCMP, and USMA.

  20. Molecular characterization of natural orchid in South slopes of Mount Merapi, Sleman regency, Yogyakarta

    NASA Astrophysics Data System (ADS)

    Ferdiani, Defika I.; Devi, Fera L.; Koentjana, Johan P.; Milasari, Asri F.; Nur'aini, Indah; Semiarti, Endang

    2015-09-01

    Natural orchid is one of the most important tropical biodiversity. In Indonesia there are ± 6000 species out of 30000 orchids species in the world, of which there are ± 60 species at Mount Merapi. Repetitive eruption of Merapi have wiped out the biodiversity of orchids, therefore the efforts to conserve the orchids and to establish the database of natural orchids in Mount Merapi are needed. The orchid's database can be created based on DNA analysis, and establish barcoding DNA. DNA-barcodes can be used as molecular markers. The different character of morphology usually shows different pattern in DNA fragments. This research aims to characterize the phenotype and genotype of natural orchids of Mt. Merapi based on morphology and the structure of DNA in trnL-F intergenic region of chloroplasts DNA of orchid. Amplified Fragment Length Polymorphism (AFLP) technique was used to characterize the molecular types of orchids in silico of intergenic space area of orchid chloroplast. In this study, 11 species of orchids were characterized based on morphological and molecular characters. The molecular characters were obtained from trnL-F intergenic region of leaves chloroplasts. The data indicates that there is a conserve DNA pattern in all orchids and the distinctive characters of some orchids. In this study, based on trnL-F intergenic region of chloroplast genome, the phylogenetic tree revealed that 11 species of orchids at Mt. Merapi can be grouped into 2 clades, that matched with morphological characters.

  1. Molecular and chemical characterization of vetiver, Chrysopogon zizanioides (L.) Roberty, germplasm.

    PubMed

    Celestino, R S; Zucchi, M I; Pinheiro, J B; Campos, J B; Pereira, A A; Bianchini, F G; Lima, R N; Arrigoni-Blank, M F; Alves, P B; Blank, A F

    2015-08-14

    Due to the economic interests in vetiver, Chrysopogon zizanioides (L.) Roberty, molecular and chemical studies are essential to generate information for its sustainable exploitation. The aim of this study was to undertake a molecular and chemical characterization of vetiver accessions of the active germplasm bank of the Universidade Federal de Sergipe. The molecular characteristics of the accessions were studied using amplified fragment length polymorphism markers, with a total of 14 primer combinations that generated 442 loci, allowing us to observe that these accessions have similar genomes. The vetiver accessions were divided into three distinct groups, where accession UFS-VET005 was the most differentiated and accession UFS-VET004 had the lowest essential oil content (0.70%). The content of the chemical constituents of the essential oils was observed to vary, with a predominance of khusimol, which ranged from 18.97 to 25.02%. It was possible to divide the vetiver accessions into two groups based on chemical composition, and these groups do not correlate with the molecular grouping. Therefore, it is necessary to perform molecular and chemical analyses to characterize vetiver accessions.

  2. Pyrolysis-Molecular Beam Mass Spectrometry to Characterize Soil Organic Matter Composition in Chemically Isolated Fractions from Differing Land Uses

    SciTech Connect

    Plante, A. F.; Magrini-Bair, K.; Vigil, M.; Paul, E. A.

    2009-01-01

    Today's questions concerning the role of soil organic matter (SOM) in soil fertility, ecosystem functioning and global change can only be addressed through knowledge of the controls on SOM stabilization and their interactions. Pyrolysis molecular beam mass spectrometry (py-MBMS) provides a powerful and rapid means of assessing the biochemical composition of SOM. However, characterization of SOM composition alone is insufficient to predict its dynamic behavior. Chemical fractionation is frequently used to isolate more homogeneous SOM components, but the composition of fractions is frequently unknown. We characterized biochemical SOM composition in two previously studied soils from the USA, under contrasting land uses: cultivated agriculture and native vegetation. Bulk soils, as well as chemically isolated SOM fractions (humic acid, humin and non-acid hydrolysable), were analyzed using py-MBMS. Principal components analysis (PCA) showed distinct differences in the SOM composition of isolated fractions. Py-MBMS spectra and PCA loadings were dominated by low molecular weight fragments associated with peptides and other N-containing compounds. The py-MBMS spectra were similar for native whole-soil samples under different vegetation, while cultivation increased heterogeneity. An approach based on previously published data on marker signals also suggests the importance of peptides in distinguishing samples. While the approach described here represents significant progress in the characterization of changing SOM composition, a truly quantitative analysis will only be achieved using multiple internal standards and by correcting for inorganic interference during py-MBMS analysis. Overall, we have provided proof of principle that py-MBMS can be a powerful tool to understand the controls on SOM dynamics, and further method development is underway.

  3. Surveying the global virome: Identification and characterization of HCV-related animal hepaciviruses

    PubMed Central

    Scheel, Troels K. H.; Simmonds, Peter; Kapoor, Amit

    2015-01-01

    Recent advances in sequencing technologies have greatly enhanced our abilities to identify novel microbial sequences. Thus, our understanding of the global virome and the virome of specific host species in particular is rapidly expanding. Identification of animal viruses is important for understanding animal disease, the origin and evolution of human viruses, as well as zoonotic reservoirs for emerging infections. Although the human hepacivirus, hepatitis C virus (HCV), was identified 25 years ago, its origin has remained elusive. In 2011, the first HCV homolog was reported in dogs but subsequent studies showed the virus to be widely distributed in horses. This indicated a wider hepacivirus host range and paved the way for identification of rodent, bat and non-human primate hepaciviruses. The equine non-primate hepacivirus (NPHV) remains the closest relative of HCV and is so far the best characterized. Identification and characterization of novel hepaciviruses may in addition lead to development of tractable animal models to study HCV persistence, immune responses and pathogenesis. This could be particular important, given the current shortage of immunocompetent models for robust HCV infection. Much remains to be learned on the novel hepaciviruses, including their association with disease, and thereby how relevant they will become as HCV model systems and for studies of animal disease. This review discusses how virome analysis led to identification of novel hepaci- and pegiviruses, their genetic relationship and characterization and the potential use of animal hepaciviruses as models to study hepaciviral infection, immunity and pathogenesis. This article forms part of a symposium in Antiviral Research on “Hepatitis C: Next steps toward global eradication.” PMID:25545071

  4. Formation of giant molecular clouds in global spiral structures: The role of orbital dynamics and cloud-cloud collisions

    NASA Technical Reports Server (NTRS)

    Roberts, W. W., Jr.; Stewart, G. R.

    1987-01-01

    The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.

  5. Labeling quality and molecular characterization studies of products containing Lactobacillus spp. strains.

    PubMed

    Blandino, Giovanna; Fazio, Davide; Petronio, Giulio Petronio; Inturri, Rosanna; Tempera, Gianna; Furneri, Pio Maria

    2016-03-01

    The objective of the study was to characterize at species level by phenotypic and different molecular methods the strains of Lactobacillus spp. used as constituents of five oral and four vaginal products. Susceptibilities to representative antibiotics were evaluated. In addition, total viable counts at mid and 3 months to deadline of shelf life, in the different formulations and the presence of eventual contaminant microorganisms were investigated.In all oral products the molecular characterization at species level of the strains of Lactobacillus spp. confirmed the strains stated on the label, except for one strain cited on the label as Lactobacillus casei, that our study characterized as Lactobacillus paracasei. In oral products total viable cell content complied with content claimed on the label. In three out four vaginal products (one product claimed "bacillo di Döderlein"), molecular characterization complied with the bacterial name stated on the label. Two vaginal products reported viable counts on the label that were confirmed by our study. The other vaginal products, which did not report bacterial counts on the label, showed a similar decrease of viable counts at different dates to deadline compared to the others. From all the tested products, contaminant microorganisms and acquired resistance to representative antibiotics by the probiotic strains were not detected.

  6. Global scale observations of atmospheric molecular hydrogen and its stable isotopic composition

    NASA Astrophysics Data System (ADS)

    Batenburg, A. M.

    2012-09-01

    With average mixing ratios (χ) around 550 ppb (nmole/mole), molecular hydrogen (H2) is the most abundant reduced gas in our atmosphere after methane (CH4), but considerably less studied. H2 is also a promising energy carrier that might replace fossil fuels in vehicles with great sustainability advantages, but there may be environmental side effects. Large-scale leakage of H2 into the atmosphere might affect the atmosphere’s oxidative capacity and stratospheric ozone chemistry. To assess these risks, a better understanding of the atmospheric H2 cycle is needed. Stable isotopic composition measurements can be used to constrain the source and sink terms in the budgets of atmospheric trace gases, as the different processes affect the stable isotopic composition of the gases in different ways. For H2, the effects are particularly large, due to the large relative mass difference between the isotopes (H and D). The largest source, hydrocarbon oxidation, yields D-enriched H2, whereas the smaller combustion-related sources and the minor microbial sources yield D-depleted and extremely D-depleted H2, respectively. Both sink processes, uptake in soils and reaction with hydroxyl radicals (OH), have a D-enriching effect, but the effect is much stronger for OH. Despite its usefulness, few environmental observations of H2 isotopic composition (δD(H2)) are available. We present three new χ(H2) and δD(H2) datasets to fill this gap. First, we present one- to five-year long time series from six globally distributed, predominantly background stations. As expected, average χ(H2) and δD(H2) values were larger in the southern hemisphere (SH) than in the northern hemisphere (NH). The minimum in δD(H2) was found at the NH midlatitude stations, likely a result of fossil fuel combustion. At the three NH coastal and island stations, seasonal δD(H2)-cycles were observed, which were five to six months out-of-phase with the χ(H2)-cycles. No δD(H2)-cycles were observed at the other

  7. Chemical characterization of high molecular weight dissolved organic matter in fresh and marine waters

    NASA Astrophysics Data System (ADS)

    Repeta, Daniel J.; Quan, Tracy M.; Aluwihare, Lihini I.; Accardi, AmyMarie

    2002-03-01

    The high molecular weight fraction of dissolved organic matter in a suite of lakes, rivers, seawater, and marine sediment interstitial water samples was collected by ultrafiltration and characterized by molecular level and spectroscopic techniques. Proton nuclear magnetic resonance spectra of all samples show a high degree of similarity, with major contributions from carbohydrates, bound acetate, and lipids. Molecular level analyses of neutral sugars show seven monosaccharides, rhamnose, fucose, arabinose, xylose, mannose, glucose, and galactose, to be abundant, and to occur in comparable relative amounts in each sample. Previous studies have emphasized the distinctive composition of dissolved humic substances in fresh and marine waters, and have attributed these differences to sources and transformations of organic matter unique to each environment. In contrast we find a large fraction of freshwater high molecular weight dissolved organic matter (HMWDOM; > 1kD) to be indistinguishable from marine HMWDOM in bulk and molecular-level chemical properties. Aquatic HMWDOM is similar in chemical composition to biologically derived acylated heteropolysaccharides isolated from marine algal cultures, suggesting a biological source for some fraction of persistent HMWDOM. High molecular weight DOC contributes 51 ± 26% of the total DOC, and monosaccharides 18 ± 8% of the total HMWDOC in our freshwater samples. These contributions are on average higher and more variable, but not significantly different than for surface seawater (30% and 16% respectively). Biogeochemical processes that produce, accumulate, and recycle DOM may therefore share important similarities and be broadly comparable across a range of environmental settings.

  8. Characterization and Molecular Simulation of Poly(p-phenylene/m-phenylene) Copolymers

    NASA Astrophysics Data System (ADS)

    Bubeck, Robert; Keinath, Steven

    Characterization and molecular simulation of the molecular structure and microstructure of poly(p-phenylene/m-phenylene) copolymers were carried out. Tensile modulus, yield stress, and entanglement molecular weight were modeled as amorphous polymers as a function of m-phenylene content. Significant biphasic character, however, was observed for two copolymers in the melt near 300ºC using variable temperature synchrotron-based WAXS. The biphasic nature of the melt may be a contributor to difficulty in melt processing. Precise experimental determinations of entanglement molecular weights were frustrated by the occurrence of significant amounts of nematic mesophasic order in the rubbery and melt regimes of two commercial poly(p-phenylene/m-phenylene) examples. Nonetheless, entanglement molecular weights obtained by molecular modeling can be useful for experimental guidance because the level of order in the glassy phase near ambient temperature was found to be low (5 %) regardless of melt processing history. Based on both the modeling and WAXS measurements, it is believed that increasing m-phenylene content reduces modulus, and improves toughness and processibility. Beamtime at the Cornell High Energy Synchrotron Source is gratefully acknowledged.

  9. Molecular characterization of canine parvovirus (CPV) infection in dogs in Turkey.

    PubMed

    Timurkan, Mehmet; Oğuzoğlu, Tuba

    2015-01-01

    This study provides data about canine parvovirus (CPV) types circulating among dogs in Turkey. Sixty-five samples from dogs with and without clinical signs of parvovirus infection were collected between April 2009 and February 2010. The samples were subsequently tested for CPV using polymerase chain reaction (PCR). Twenty-five samples (38.4%) were positive; when positive samples were characterized by sequence analysis, results showed that both CPV-2a (17/25, 68%) and CPV-2b (8/25, 32%) strains are circulating among domestic dogs in Turkey. This is the first molecular characterization study of CPVs from dogs based on partial VP2 gene sequences in Turkey.

  10. Molecular Characterization, Antioxidant and Protein Solubility-Related Properties of Polyphenolic Compounds from Walnut (Juglans regia).

    PubMed

    Labuckas, Diana; Maestri, Damián; Lamarque, Alicia

    2016-05-01

    Aqueous ethanol extraction of partially defatted walnut flours provides a simple and reliable method to obtain extracts with high content of polyphenolic compounds. These were characterized by means of HPLC-ESI-MS/MS analytical techniques and molecular parameters. Considering the whole set of polyphenolic compounds identified, a high average number of phenolic-OH groups was found. Although these represent potential hydrogen-atom transfer sites, which are associated with high free-radical scavenging capacity, results show that such a property could be strongly limited by the low lipophilicity of polyphenols affecting the accessibility of these molecules to lipid substrates. Variations in pH values were found to change the ionization behavior of phenolic compounds. These changes, however, had minor effects on walnut protein solubility-related properties. The results obtained in this study highlight the importance of molecular characterization of walnut phenolic compounds in order to assess better their bioactive properties.

  11. Molecular Characterization, Antioxidant and Protein Solubility-Related Properties of Polyphenolic Compounds from Walnut (Juglans regia).

    PubMed

    Labuckas, Diana; Maestri, Damián; Lamarque, Alicia

    2016-05-01

    Aqueous ethanol extraction of partially defatted walnut flours provides a simple and reliable method to obtain extracts with high content of polyphenolic compounds. These were characterized by means of HPLC-ESI-MS/MS analytical techniques and molecular parameters. Considering the whole set of polyphenolic compounds identified, a high average number of phenolic-OH groups was found. Although these represent potential hydrogen-atom transfer sites, which are associated with high free-radical scavenging capacity, results show that such a property could be strongly limited by the low lipophilicity of polyphenols affecting the accessibility of these molecules to lipid substrates. Variations in pH values were found to change the ionization behavior of phenolic compounds. These changes, however, had minor effects on walnut protein solubility-related properties. The results obtained in this study highlight the importance of molecular characterization of walnut phenolic compounds in order to assess better their bioactive properties. PMID:27319138

  12. The fabrication and characterization of a formaldehyde odor sensor using molecularly imprinted polymers.

    PubMed

    Feng, Liang; Liu, Yongjun; Zhou, Xiaodong; Hu, Jiming

    2005-04-15

    The fabrication and characterization of odor sensors based on molecularly imprinted polymers is reported as the first case of imprinting formaldehyde. A quartz crystal microbalance is employed as a sensitive apparatus of a sensor for the determination of odor formaldehyde. An equation is deduced to characterize the interaction between molecularly imprinted films and the template. A linear relationship between the frequency shifts and the concentration of analyte in the range of 1.25 to 14.25 microM is found. The detection limit is about 20.5 microM. The sensor can selectively distinguish gaseous formaldehyde. It is envisaged that this novel and handy method could be employed to determine formaldehyde gas in the atmosphere.

  13. Molecular characterization of the horse isolate of Echinococcus granulosus in Turkey.

    PubMed

    Utuk, A E; Simsek, S

    2013-09-01

    Cystic echinococcosis is one of the most important helminthozoonoses, affecting various species of intermediate hosts and humans. In this report, we present Echinococcus granulosus infection in a horse and its molecular characterization. Polymerase chain reaction (PCR) amplification of mitochondrial 12S rRNA (mt-12S rRNA) and partial sequencing of mitochondrial cytochrome c oxidase subunit 1 (mt-CO1) genes were performed. According to the mt-12S rRNA-PCR result, the horse isolate was grouped with E. granulosus sensu stricto (G1-G3) and the partial mt-CO1 sequence corresponded to the G1 strain. This is the first study of the molecular characterization of the horse isolate of E. granulosus in Turkey.

  14. Preliminary Molecular Characterizations of Sarcoptes scaibiei (Acari: Sarcoptidae) from Farm Animals in Egypt

    PubMed Central

    Amer, Said; Wahab, Taher Abd El; Metwaly, Abd El Naby; Ye, Jianbin; Roellig, Dawn; Feng, Yaoyu; Xiao, Lihua

    2014-01-01

    Little is known about the genetic diversity of Sarcoptes scabiei mites in farm animals in Egypt. In this study, we characterized S. scabiei in 25 skin scrapes from water buffalo, cattle, sheep, and rabbits at the nuclear marker ITS2 and mitochondrial markers COX1 and 16S rRNA. Sequences of the ITS2 showed no host segregation or geographical isolation, whereas those of the mitochondrial COX1 and 16S rRNA genes indicated the presence of both host-adapted and geographically segregated populations of S. scabiei. Host adaptation may limit inter-species transmission of. S. scabiei, thus restrict gene flow among S. scabiei from different hosts. This is the first report on the molecular characterization of sarcoptic mites in Egypt. Further genetic studies involving larger numbers of specimens, especially those from humans and companion animals, are needed to understand the molecular epidemiology of sarcoptic mange in Egypt. PMID:24728386

  15. Preliminary molecular characterizations of Sarcoptes scaibiei (Acari: Sarcoptidae) from farm animals in Egypt.

    PubMed

    Amer, Said; El Wahab, Taher Abd; Metwaly, Abd El Naby; Ye, Jianbin; Roellig, Dawn; Feng, Yaoyu; Xiao, Lihua

    2014-01-01

    Little is known about the genetic diversity of Sarcoptes scabiei mites in farm animals in Egypt. In this study, we characterized S. scabiei in 25 skin scrapes from water buffalo, cattle, sheep, and rabbits at the nuclear marker ITS2 and mitochondrial markers COX1 and 16S rRNA. Sequences of the ITS2 showed no host segregation or geographical isolation, whereas those of the mitochondrial COX1 and 16S rRNA genes indicated the presence of both host-adapted and geographically segregated populations of S. scabiei. Host adaptation may limit inter-species transmission of. S. scabiei, thus restrict gene flow among S. scabiei from different hosts. This is the first report on the molecular characterization of sarcoptic mites in Egypt. Further genetic studies involving larger numbers of specimens, especially those from humans and companion animals, are needed to understand the molecular epidemiology of sarcoptic mange in Egypt.

  16. Morphological and molecular characterization of Explanatum explanatum from cattle and buffaloes in Myanmar.

    PubMed

    Ichikawa, Madoka; Kondoh, Daisuke; Bawn, Saw; Maw, Ni Ni; Htun, Lat Lat; Thein, Myint; Gyi, Aung; Sunn, Kyaw; Katakura, Ken; Itagaki, Tadashi

    2013-01-01

    A robust molecular marker is needed for discrimination of amphistome species, because identification based on morphology alone requires specialized knowledge and techniques. In this study, we performed morphological and molecular characterization of Explanatum explanatum, a species that causes severe liver damage in definitive host species. Fifty-five adult amphistomes were collected from cattle and water buffaloes in Myanmar. Eighteen of the amphistomes, arbitrarily chosen, were morphologically identified as E. explanatum using sagittal sections. All of the 55 amphistome isolates had identical second internal transcribed spacer (ITS2) of ribosomal DNA sequences; these sequences differed at 7 nucleotide sites from those of the closest species, Paramphistomum leydeni. Our data indicate that the ITS2 sequence could be a useful molecular marker for epidemiological studies on E. explanatum.

  17. Molecular diversity and characterization of tetracycline-resistant Staphylococcus aureus isolates from a poultry processing plant.

    PubMed

    Huys, Geert; D'Haene, Klaas; Van Eldere, Johan; von Holy, Alexander; Swings, Jean

    2005-01-01

    DNA fingerprinting and molecular characterization showed that the tetracycline-resistant Staphylococcus aureus population of a South African poultry processing plant comprised one or possibly several tet(K)-containing endemic clones that contaminated chicken and machinery surfaces at all sampled processing stages. The tet(K) gene was transferable by filter mating to S. aureus recipient 80CR5 and was located on a pT181-like plasmid.

  18. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    PubMed Central

    2011-01-01

    Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp.. PMID:21658284

  19. Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

    PubMed Central

    Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

    2015-01-01

    Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

  20. Cytological and molecular characterization of Vicia esdraelonensis Warb. & Eig: a rare taxon.

    PubMed

    Ruffini Castiglione, M; Frediani, M; Gelati, M T; Ravalli, C; Venora, G; Caputo, P; Cremonini, R

    2007-01-01

    Vicia esdraelonensis, a rare taxon belonging to section Hypechusa of subgenus Vicia, was recovered and analyzed by cytological, karyological, and molecular methods, with the aim of both characterizing this species and furthering our knowledge of the phylogeny of subgenus Vicia. Automated karyotype analysis, nuclear DNA content, and chromatin organization were determined by the Feulgen reaction, as well as chromosome banding after double staining with 4',6-diamidino-2-phenylindole (DAPI) and chromomycin A3. The chromosome number and the nuclear DNA content were in agreement with the values of the species of section Hypechusa. The GC- and AT-rich preferential sites were determined by chromomycin A3 and DAPI staining. Karyomorphological parameters indicated that V. esdraelonensis is in an intermediate position in the spatial representation of the species of section Hypechusa on the basis of symmetry indices, as well as in the dendrogram of linkage distance constructed on 37 chromosome parameters. Molecular data based on internal transcribed spacer sequences show that V. esdraelonensis can doubtlessly be included in section Hypechusa and document its closeness to V. noeana. A cladistic analysis combining the molecular data set with karyological characters is also reported. Karyological, cytological, and molecular data allow characterization of the V. esdraelonensis genome and provide information about the phylogenetic position of this species within the Hyrcanicae series of section Hypechusa.

  1. Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly.

    PubMed

    Martín-Rodríguez, Juan F; Muñoz-Bravo, Jose L; Ibañez-Costa, Alejandro; Fernandez-Maza, Laura; Balcerzyk, Marcin; Leal-Campanario, Rocío; Luque, Raúl M; Castaño, Justo P; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso; Cano, David A

    2015-01-01

    Acromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic, and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors. PMID:26549306

  2. Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly

    PubMed Central

    Martín-Rodríguez, Juan F.; Muñoz-Bravo, Jose L.; Ibañez-Costa, Alejandro; Fernandez-Maza, Laura; Balcerzyk, Marcin; Leal-Campanario, Rocío; Luque, Raúl M.; Castaño, Justo P.; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso; Cano, David A.

    2015-01-01

    Acromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic, and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors. PMID:26549306

  3. Portuguese contributions to the discovery and characterization of the embryonic molecular clock.

    PubMed

    Pascoal, Susana; Palmeirim, Isabel

    2009-01-01

    Embryonic development is strictly regulated both in time and in space. This extraordinary control is clearly evidenced during the process of somitogenesis. In this process, pairs of somites are formed periodically, such that the time required to form a new somite pair is constant and species specific. The tight temporal control underlying somitogenesis has been shown to depend upon a molecular clock, manifested by the cyclic expression of an increasing number of genes in the unsegmented paraxial mesoderm. Portuguese researchers have been intimately connected to the achievements that have been made in this new field of research: the somitogenesis molecular clock. This article intends to report the Portuguese contributions to the discovery and characterization of the molecular clock underlying somite formation and possibly other embryonic processes. This work inspired many scientists around the world and it has been followed in Portugal by teams that keep on pursuing the characterization of the machinery of this molecular oscillator and its function in the acquisition of both temporal and positional information during development.

  4. Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly.

    PubMed

    Martín-Rodríguez, Juan F; Muñoz-Bravo, Jose L; Ibañez-Costa, Alejandro; Fernandez-Maza, Laura; Balcerzyk, Marcin; Leal-Campanario, Rocío; Luque, Raúl M; Castaño, Justo P; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso; Cano, David A

    2015-11-09

    Acromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic, and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors.

  5. Characterization of global flow and local fluctuations in 3D SPH simulations of protoplanetary discs

    NASA Astrophysics Data System (ADS)

    Arena, S. E.; Gonzalez, J.-F.

    2013-07-01

    A complete and detailed knowledge of the structure of the gaseous component in protoplanetary discs is essential to the study of dust evolution during the early phases of pre-planetesimal formation. The aim of this paper is to determine if three-dimensional accretion discs simulated by the smoothed particle hydrodynamics (SPH) method can reproduce the observational data now available and the expected turbulent nature of protoplanetary discs. The investigation is carried out by setting up a suite of diagnostic tools specifically designed to characterize both the global flow and the fluctuations of the gaseous disc. The main result concerns the role of the artificial viscosity implementation in the SPH method: in addition to the already known ability of SPH artificial viscosity to mimic a physical-like viscosity under specific conditions, we show how the same artificial viscosity prescription behaves like an implicit turbulence model. In fact, we identify a threshold for the parameters in the standard artificial viscosity above which SPH disc models present a cascade in the power spectrum of velocity fluctuations, turbulent diffusion and a mass accretion rate of the same order of magnitude as measured in observations. Furthermore, the turbulence properties observed locally in SPH disc models are accompanied by meridional circulation in the global flow of the gas, proving that the two mechanisms can coexist.

  6. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae

    PubMed Central

    Diaz, Maureen H.; Winchell, Jonas M.

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen. PMID:27014191

  7. Surveillance and molecular characterization of group A rotaviruses in Goroka, Papua New Guinea.

    PubMed

    Horwood, Paul Francis; Luang-Suarkia, Dagwin; Bebes, Sauli; Boniface, Karen; Datta, Siddhartha Sankar; Siba, Peter Max; Kirkwood, Carl Dunn

    2012-12-01

    In this study, we investigated the molecular epidemiology of group A rotaviruses in cases of acute gastroenteritis in Goroka, Papua New Guinea. From April 2008 through November 2010, 813 diarrheal stool samples were collected from children < 5 years of age hospitalized with acute gastroenteritis. Rotavirus antigen was detected in 31.2% of samples using a commercial enzyme-linked immunosorbent assay. Genotyping revealed the presence of the globally circulating strains G1P[8] (50.0%), G3P[8] (23.0%), and G2P[4] (8.2%). The globally emerging strains G9 and G12 were detected in 1.2% and 6.1% of samples, respectively. Mixed infections were detected in a high proportion of samples (11.9%), with 9.0% and 3.7% of samples displaying multiple G and P genotypes, respectively.

  8. Molecular characterization of DNA sequences from the Primula vulgaris S-locus.

    PubMed

    Manfield, Iain W; Pavlov, Vassily K; Li, Jinhong; Cook, Holly E; Hummel, Florian; Gilmartin, Philip M

    2005-04-01

    Primula species provide possibly the best known examples of heteromorphic flower development and this breeding system has attracted considerable attention, including that of Charles Darwin. However, despite considerable recent advances in molecular genetics, nothing is known about the molecular basis of floral heteromorphy. The first molecular marker for the Primula S-locus is reported here. This DNA sequence was identified by random amplification of polymorphic DNA (RAPD)-PCR, further defined as a sequence characterized amplified region (SCAR) marker, and subsequently shown to correspond to a restriction fragment length polymorphism (RFLP) that is linked to the thrum allele of the Primula S-locus. The sequence of 8.8 kb of genomic DNA encompassing this thrum-specific RFLP is presented. Analysis of this DNA reveals a highly repetitive sequence structure similar to that found at the S-locus in other species; it also contains sequences similar to elements of a Gypsy-like retrotransposon. The identification of a specific DNA sequence associated with the thrum allele of the Primula S-locus provides the first molecular probe with which to investigate the molecular basis of heteromorphic flower development in Primula.

  9. Global Threat Reduction Initiative Fuel-Thermo-Physical Characterization Project Quality Assurance Plan

    SciTech Connect

    Pereira, Mario M.; Slonecker, Bruce D.

    2012-06-01

    The charter of the Fuel Thermo-Physical Characterization Project is to ready Pacific Northwest National Laboratory (PNNL) facilities and processes for the receipt of unirradiated and irradiated low enriched uranium (LEU) molybdenum (U-Mo) fuel element samples, and to perform analysis to support the Global Threat Reduction Initiative conversion program. PNNL’s support for the program will include the establishment of post-irradiation examination processes, including thermo-physical properties, unique to the U.S. Department of Energy laboratories. These processes will ultimately support the submission of the base fuel qualification (BFQ) to the U.S. Nuclear Regulatory Commission (NRC) and revisions to High Performance Research Reactor Safety Analysis Reports to enable conversion from highly enriched uranium to LEU fuel. This quality assurance plan (QAP) provides the quality assurance requirements and processes that support the NRC BFQ. This QAP is designed to be used by project staff, and prescribes the required management control elements that are to be met and how they are implemented. Additional controls are captured in Fuel Thermo-Physical Characterization Project plans, existing procedures, and procedures to be developed that provide supplemental information on how work is conducted on the project.

  10. Global Threat Reduction Initiative Fuel Thermo-Physical Characterization Project: Sample Management Plan

    SciTech Connect

    Casella, Amanda J.; Pereira, Mario M.; Steen, Franciska H.

    2013-01-01

    This sample management plan provides guidelines for sectioning, preparation, acceptance criteria, analytical path, and end-of-life disposal for the fuel element segments utilized in the Global Threat Reduction Initiative (GTRI), Fuel Thermo-Physical Characterization Project. The Fuel Thermo-Physical Characterization Project is tasked with analysis of irradiated Low Enriched Uranium (LEU) Molybdenum (U-Mo) fuel element samples to support the GTRI conversion program. Sample analysis may include optical microscopy (OM), scanning electron microscopy (SEM) fuel-surface interface analysis, gas pycnometry (density) measurements, laser flash analysis (LFA), differential scanning calorimetry (DSC), thermogravimetry and differential thermal analysis with mass spectroscopy (TG /DTA-MS), Inductively Coupled Plasma Spectrophotometry (ICP), alpha spectroscopy, and Thermal Ionization Mass Spectroscopy (TIMS). The project will utilize existing Radiochemical Processing Laboratory (RPL) operating, technical, and administrative procedures for sample receipt, processing, and analyses. Test instructions (TIs), which are documents used to provide specific details regarding the implementation of an existing RPL approved technical or operational procedure, will also be used to communicate to staff project specific parameters requested by the Principal Investigator (PI). TIs will be developed, reviewed, and issued in accordance with the latest revision of the RPL-PLN-700, RPL Operations Plan. Additionally, the PI must approve all project test instructions and red-line changes to test instructions.

  11. Characterization of novel mechanisms for steatosis from global protein hyperacetylation in ethanol-induced mouse hepatocytes.

    PubMed

    Kim, Sun Ju; Kwon, Oh Kwang; Ki, Sung Hwan; Jeong, Tae Cheon; Lee, Sangkyu

    2015-08-01

    Steatosis is the earliest and most common disease of the liver due to chronic ethanol consumption, and stems from alterations in the function of transcription factors related to lipid metabolism. Protein acetylation at the lysine residue (Kac) is known to have diverse functions in cell metabolism. Recent studies showed that ethanol exposure induces global protein hyperacetylation by reducing the deacetylase activities of SIRT1 and SIRT3. Although global acetylome analyses have revealed the involvement of a variety of lysine acetylation sites, the exact sites directly regulated by ethanol exposure are unknown. In this study, to elucidate the exact hyperacetylation sites that contribute to SIRT1 and SIRT3 downregulation, we identified and quantified a total of 1285 Kac sites and 686 Kac proteins in AML-12 cells after ethanol treatment (100 mM) for 3 days. All quantified Kac sites were divided into four quantiles: Q1 (0-15%), Q2 (15-50%), Q3 (50-85%), and Q4 (85-100%). Q4 had 192 Kac sites indicating ethanol-induced hyperacetylation. Using the Motif-x program, the [LXKL], [KH], and [KW] motifs were included in the Q4 category, where [KW] was a specific residue for SIRT3. We also performed gene ontology term and KEGG pathway enrichment analyses. Hyperacetylation sites were significantly enriched in biosynthetic processes and ATPase activities within the biological process and molecular function categories, respectively. In conclusion, ethanol regulates the acetylation of proteins in a variety of metabolic pathways mediated by SIRT1 and SIRT3. As a result, ethanol stimulates increased de novo fatty acid synthesis in hepatocytes.

  12. Characterizing Molecular Structure by Combining Experimental Measurements with Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Lopez-Encarnacion, Juan M.

    2016-06-01

    In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21

  13. [Morphological and molecular characterization of isolates of Macrophomina phaseolina associated with sugarcane in Mexico].

    PubMed

    Leyva-Mir, Santos G; Velázquez-Martínez, Guadalupe C; Tlapal-Bolaños, Bertha; Tovar-Pedraza, Juan M; Rosas-Saito, Greta H; Alvarado-Gómez, Omar G

    2015-01-01

    Charcoal rot caused by Macrophomina phaseolina is an important disease of sugarcane in Mexico. This study was carried out to characterize isolates of M. phaseolina obtained from sugarcane by the combination of morphological and molecular analyses. The morphological characterization of 10 isolates was performed using scanning electron microscopy and light microscopy. To confirm the morphological identification, rDNA from two representative isolates was extracted, and the internal transcribed spacer (ITS) region was amplified by polymerase chain reaction and sequenced using specific primers MpKF1 and MpKR1. Based on their morphological characteristics, all isolates were identified as M. phaseolina. Moreover, the analysis of two ITS sequences showed 100% similarity with the M. phaseolina sequences deposited in the GenBank. To our knowledge, this is the first study in the world aimed at characterizing isolates of M. phaseolina obtained from sugarcane.

  14. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept.

    PubMed

    Allec, Nicholas; Choi, Mina; Yesupriya, Nikhil; Szychowski, Brian; White, Michael R; Kann, Maricel G; Garcin, Elsa D; Daniel, Marie-Christine; Badano, Aldo

    2015-01-01

    Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species. PMID:26160052

  15. Molecular Epidemiological and Antibiotic Susceptibility Characterization of Brucella Isolates from Humans in Sicily, Italy▿

    PubMed Central

    Marianelli, Cinzia; Graziani, Caterina; Santangelo, Carmela; Xibilia, Maria Teresa; Imbriani, Alida; Amato, Rosa; Neri, Domenico; Cuccia, Mario; Rinnone, Sebastiano; Di Marco, Vincenzo; Ciuchini, Franco

    2007-01-01

    Brucellosis is a serious problem in Sicily. Brucella melitensis was identified as the species most frequently isolated in humans in Italy. No data, however, are available about the molecular epidemiological characterization of Brucella isolates from humans. We have conducted this study to molecularly characterize clinical isolates of Brucella spp. and to evaluate their antimicrobial susceptibilities. Twenty Brucella isolates were studied. Differential growth characteristics and DNA polymorphisms such as the restriction patterns of the PCR-amplified omp2a and omp2b genes, rpoB nucleotide sequencing, and multiple-locus variable-number tandem repeat analysis of 16 loci (MLVA-16) were used to characterize the strains. In vitro antibiotic susceptibility was determined by the E-test method on two different agar media, and the results were compared. All isolates were identified as B. melitensis biovar 3. rpoB nucleotide sequence analysis allowed the identification of two different genotypes of B. melitensis biovar 3. On the other hand, the MLVA-16 typing assay recognized 17 distinct genotypes. All isolates were sensitive to all tested antibiotics (rifampin, doxycycline, ciprofloxacin, ceftriaxone, and trimethoprim-sulfamethoxazole), and the Mueller-Hinton agar plate is recommended for antibiotic susceptibility testing by the E-test method. Our findings identify B. melitensis biovar 3 as the etiological agent isolated in Sicily and encourage the use of both molecular methods, and in particular of the MLVA-16 assay, in epidemiological trace-back analysis. This study represents the first epidemiological data from molecular typing of Brucella strains circulating in Italy and, in particular, in eastern Sicily. PMID:17634297

  16. Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria.

    PubMed

    Zait, Houria; Kouidri, Mokhtaria; Grenouillet, Florence Elisabeth; Umhang, Gérald; Millon, Laurence; Hamrioui, Boussad; Grenouillet, Frédéric

    2016-06-01

    In Algeria, previous studies investigated genotypes of Echinococcus granulosus sensu lato in animals and identified E. granulosus sensu stricto (s.s.) genotypes G1 and G3 whereas Echinococcus canadensis genotype G6 was only reported from dromedary cysts. Molecular data on human cystic echinococcosis (CE) were limited. We implemented a large genotyping study of hydatid cysts from humans and livestock animals to specify CE's molecular epidemiology and the genetic diversity in Algeria. Fifty-four human CE cysts from patients predominantly admitted in surgical units from Mustapha Hospital, Algiers, and 16 cysts from livestock animals gathered in two geographically distinct slaughterhouses, Tiaret and Tamanrasset, were collected. Molecular characterization was performed using sequencing of two mitochondrial genes, cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit I (NDI). In humans, G1 of E. granulosus s.s. was the main genotype (90.7 %); four samples (7.4 %) were characterized as E. granulosus s.s. G3 and one cyst as E. canadensis G6 (1.8 %). This molecular confirmation of E. canadensis G6 human infection in Algeria was observed in a Tuareg female living in a desertic area in Tamanrasset. All cysts from sheep, cattle, and goat were identified as E. granulosus s.s. G1 and the two cysts originating from dromedary as E. canadensis G6. Twenty concatenated haplotypes (COI + NDI) were characterized. Among E. granulosus s.s., one haplotype (HL1) was highly predominant in both humans and animals cysts (71.6 %). This study revealed main occurrence of E. granulosus s.s. in humans and livestock animals, with description of a predominant shared haplotype corresponding to the main worldwide observed haplotype E.granulosus s.s. G1. E. canadensis G6 was limited to South Algeria, in dromedary as well as in human.

  17. Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria.

    PubMed

    Zait, Houria; Kouidri, Mokhtaria; Grenouillet, Florence Elisabeth; Umhang, Gérald; Millon, Laurence; Hamrioui, Boussad; Grenouillet, Frédéric

    2016-06-01

    In Algeria, previous studies investigated genotypes of Echinococcus granulosus sensu lato in animals and identified E. granulosus sensu stricto (s.s.) genotypes G1 and G3 whereas Echinococcus canadensis genotype G6 was only reported from dromedary cysts. Molecular data on human cystic echinococcosis (CE) were limited. We implemented a large genotyping study of hydatid cysts from humans and livestock animals to specify CE's molecular epidemiology and the genetic diversity in Algeria. Fifty-four human CE cysts from patients predominantly admitted in surgical units from Mustapha Hospital, Algiers, and 16 cysts from livestock animals gathered in two geographically distinct slaughterhouses, Tiaret and Tamanrasset, were collected. Molecular characterization was performed using sequencing of two mitochondrial genes, cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit I (NDI). In humans, G1 of E. granulosus s.s. was the main genotype (90.7 %); four samples (7.4 %) were characterized as E. granulosus s.s. G3 and one cyst as E. canadensis G6 (1.8 %). This molecular confirmation of E. canadensis G6 human infection in Algeria was observed in a Tuareg female living in a desertic area in Tamanrasset. All cysts from sheep, cattle, and goat were identified as E. granulosus s.s. G1 and the two cysts originating from dromedary as E. canadensis G6. Twenty concatenated haplotypes (COI + NDI) were characterized. Among E. granulosus s.s., one haplotype (HL1) was highly predominant in both humans and animals cysts (71.6 %). This study revealed main occurrence of E. granulosus s.s. in humans and livestock animals, with description of a predominant shared haplotype corresponding to the main worldwide observed haplotype E.granulosus s.s. G1. E. canadensis G6 was limited to South Algeria, in dromedary as well as in human. PMID:27021186

  18. The vaginal microbiota: what have we learned after a decade of molecular characterization?

    PubMed

    van de Wijgert, Janneke H H M; Borgdorff, Hanneke; Verhelst, Rita; Crucitti, Tania; Francis, Suzanna; Verstraelen, Hans; Jespers, Vicky

    2014-01-01

    We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB. PMID:25148517

  19. Combining differential expression, chromosomal and pathway analyses for the molecular characterization of renal cell carcinoma

    PubMed Central

    Furge, Kyle A; Dykema, Karl; Petillo, David; Westphal, Michael; Zhang, Zhongfa; Kort, Eric J; Teh, Bin Tean

    2007-01-01

    Using high-throughput gene-expression profiling technology, we can now gain a better understanding of the complex biology that is taking place in cancer cells. This complexity is largely dictated by the abnormal genetic makeup of the cancer cells. This abnormal genetic makeup can have profound effects on cellular activities such as cell growth, cell survival and other regulatory processes. Based on the pattern of gene expression, or molecular signatures of the tumours, we can distinguish or subclassify different types of cancers according to their cell of origin, behaviour, and the way they respond to therapeutic agents and radiation. These approaches will lead to better molecular subclassification of tumours, the basis of personalized medicine. We have, to date, done whole-genome microarray gene-expression profiling on several hundreds of kidney tumours. We adopt a combined bioinformatic approach, based on an integrative analysis of the gene-expression data. These data are used to identify both cytogenetic abnormalities and molecular pathways that are deregulated in renal cell carcinoma (RCC). For example, we have identified the deregulation of the VHL-hypoxia pathway in clear-cell RCC, as previously known, and the c-Myc pathway in aggressive papillary RCC. Besides the more common clear-cell, papillary and chromophobe RCCs, we are currently characterizing the molecular signatures of rarer forms of renal neoplasia such as carcinoma of the collecting ducts, mixed epithelial and stromal tumours, chromosome Xp11 translocations associated with papillary RCC, renal medullary carcinoma, mucinous tubular and spindle-cell carcinoma, and a group of unclassified tumours. Continued development and improvement in the field of molecular profiling will better characterize cancer and provide more accurate diagnosis, prognosis and prediction of drug response. PMID:18542781

  20. Complete Genome Sequence of Hepatitis B Virus Genotype E: The First Molecular Characterization from an Imported Case in Mexico

    PubMed Central

    Escobar-Escamilla, Noé; Fragoso-Fonseca, David Esaú; Arreguín-Porras, Dulce María; Esteban-Valencia, María del Carmen; Corona-Valdespino, Estela; Falcón-Acosta, Jaime Israel; Vázquez-Campuzano, Roberto; Garcés-Ayala, Fabiola; Ortiz-Alcantara, Joanna María; López-Martinez, Irma

    2016-01-01

    Hepatitis B virus infection is currently a global public health problem. Here, we present the first characterization and complete genome sequence of a strain belonging to genotype E in Mexico, obtained from a foreign carrier with chronic infection. PMID:27034495

  1. New insights from molecular characterization of the tick Rhipicephalus (Boophilus) microplus in Brazil.

    PubMed

    Csordas, Bárbara Guimarães; Garcia, Marcos Valério; Cunha, Rodrigo Casquero; Giachetto, Poliana Fernanda; Blecha, Isabella Maiumi Zaidan; Andreotti, Renato

    2016-01-01

    The Rhipicephalus (Boophilus) microplus complex currently consists of five taxa, namely R. australis, R. annulatus, R. (B.) microplus clade A sensu, R. microplus clade B sensu, and R. (B.) microplus clade C sensu. Mitochondrial DNA-based methods help taxonomists when they are facing the morpho-taxonomic problem of distinguishing members of the R. (B.) microplus complex. The purpose of this study was to perform molecular characterization of ticks in all five regions of Brazil and infer their phylogenetic relationships. Molecular analysis characterized 10 haplotypes of the COX-1 gene. Molecular network analysis revealed that haplotype H-2 was the most dispersed of the studied populations (n = 11). Haplotype H-3 (n = 2) had the greatest genetic differentiation when compared to other Brazilian populations. A Bayesian phylogenetic tree of the COX-1 gene obtained strong support. In addition, it was observed that the population of R. (B.) microplus haplotype H-3 exhibited diverging branches among the other Brazilian populations in the study. The study concludes that the different regions of Brazil have R. (B.) microplus tick populations with distinct haplotypes.

  2. Molecular Characterization and Risk Factors of Giardia duodenalis among School Children from La Habana, Cuba

    PubMed Central

    Jerez Puebla, Luis Enrique; Núñez, Fidel A.; Martínez Silva, Isabel; Rojas Rivero, Lázara; Martínez González, Marta; Méndez Sutil, Yuliet; Ayllón Valdés, Lucía; Atencio Millán, Iraís; Müller, Norbert

    2015-01-01

    Giardia duodenalis is considered the most common protozoan infecting humans worldwide. Molecular characterization of G. duodenalis isolates has revealed the existence of eight groups (assemblages A to H) which differ in their host distribution. A cross-sectional study was conducted in 639 children from La Habana between January and December 2013. Two assemblage-specific PCRs were carried out for the molecular characterization. The overall prevalence of Giardia infection was 11.9%. DNA from 63 of 76 (82.9%) samples was successfully amplified by PCR-tpi, while 58 from 76 (76.3%) were detected by PCRE1-HF. Similar results by both PCRs were obtained in 54 from 76 samples (71%). According to these analyses, assemblage B and mixed assemblages A + B account for most of the Giardia infections in the cohort of children tested. Our current study identified assemblage B as predominant genotype in children infected with Giardia. Univariate analysis indicated that omission of washing hands before eating and keeping dogs at home were significant risk factors for a Giardia infection. In the future, novel molecular tools for a better discrimination of assemblages at the subassemblages level are needed to verify possible correlations between Giardia genotypes and symptomatology of giardiasis. PMID:26693345

  3. New insights from molecular characterization of the tick Rhipicephalus (Boophilus) microplus in Brazil.

    PubMed

    Csordas, Bárbara Guimarães; Garcia, Marcos Valério; Cunha, Rodrigo Casquero; Giachetto, Poliana Fernanda; Blecha, Isabella Maiumi Zaidan; Andreotti, Renato

    2016-01-01

    The Rhipicephalus (Boophilus) microplus complex currently consists of five taxa, namely R. australis, R. annulatus, R. (B.) microplus clade A sensu, R. microplus clade B sensu, and R. (B.) microplus clade C sensu. Mitochondrial DNA-based methods help taxonomists when they are facing the morpho-taxonomic problem of distinguishing members of the R. (B.) microplus complex. The purpose of this study was to perform molecular characterization of ticks in all five regions of Brazil and infer their phylogenetic relationships. Molecular analysis characterized 10 haplotypes of the COX-1 gene. Molecular network analysis revealed that haplotype H-2 was the most dispersed of the studied populations (n = 11). Haplotype H-3 (n = 2) had the greatest genetic differentiation when compared to other Brazilian populations. A Bayesian phylogenetic tree of the COX-1 gene obtained strong support. In addition, it was observed that the population of R. (B.) microplus haplotype H-3 exhibited diverging branches among the other Brazilian populations in the study. The study concludes that the different regions of Brazil have R. (B.) microplus tick populations with distinct haplotypes. PMID:27579530

  4. Luminal B breast cancer: molecular characterization, clinical management, and future perspectives.

    PubMed

    Ades, Felipe; Zardavas, Dimitrios; Bozovic-Spasojevic, Ivana; Pugliano, Lina; Fumagalli, Debora; de Azambuja, Evandro; Viale, Giuseppe; Sotiriou, Christos; Piccart, Martine

    2014-09-01

    Gene expression profiling has reshaped our understanding of breast cancer by defining and characterizing four main intrinsic molecular subtypes: human epidermal growth factor receptor 2-enriched, basal-like, luminal A, and luminal B subtypes. Luminal B breast cancer has been reported to have lower expression of hormone receptors, higher expression of proliferation markers, and higher histologic grade than luminal A. It also exhibits worse prognosis and has a distinct profile of response to hormone therapy and chemotherapy. Although luminal cancers share similarities, the studies conducted in recent years using next-generation sequencing technology show that luminal A and B breast cancers should be perceived as distinct entities, with specific oncogenic drivers, rather than more proliferative varieties of luminal tumors. This review discusses the definition and molecular characterization of luminal B breast cancer and presents the available clinical evidence for chemotherapy and endocrine therapy patterns of response. It also provides an overview of ongoing research on molecularly targeted agents for this disease. PMID:25049332

  5. Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

    PubMed

    van Eerden, Floris J; de Jong, Djurre H; de Vries, Alex H; Wassenaar, Tsjerk A; Marrink, Siewert J

    2015-06-01

    The thylakoid membrane is mainly composed of non-common lipids, so called galactolipids. Despite the importance of these lipids for the function of the photosynthetic reaction centers, the molecular organization of these membranes is largely unexplored. Here we use multiscale molecular dynamics simulations to characterize the thylakoid membrane of both cyanobacteria and higher plants. We consider mixtures of up to five different galactolipids plus phosphatidylglycerol to represent these complex membranes. We find that the different lipids generally mix well, although nanoscale heterogeneities are observed especially in case of the plant membrane. The fluidity of the cyanobacterial membrane is markedly reduced compared to the plant membrane, even considering elevated temperatures at which thermophilic cyanobacteria are found. We also find that the plant membrane more readily undergoes a phase transformation to an inverted hexagonal phase. We furthermore characterized the conformation and dynamics of the cofactors plastoquinone and plastoquinol, revealing of the fast flip-flop rates for the non-reduced form. Together, our results provide a molecular view on the dynamical organization of the thylakoid membrane. PMID:25749153

  6. Epidemiology and Molecular Characterization of Human Respiratory Syncytial Virus in Senegal after Four Consecutive Years of Surveillance, 2012–2015

    PubMed Central

    Cisse, El Hadj Abdel Kader; Kiori, Davy E.; Sarr, Fatoumata Diene; Sy, Sara; Goudiaby, Debora; Richard, Vincent; Niang, Mbayame Ndiaye

    2016-01-01

    Background The burden of respiratory syncytial virus (RSV) infection remains poorly defined in Africa. To address this, we carried out a descriptive and retrospective pilot study, with a focus on the epidemiology of RSV in Senegal after 4 years of surveillance. Methodology and Results From January 2012 to October 2015 swabs were collected from consenting ILI outpatients. Viral detection was performed using RV16 kit enabling direct subtyping of RSV-A and B. For the molecular characterization of HRSV, the second hypervariable region of the Glycoprotein (G) gene was targeted for sequencing. We enrolled 5338 patients with 2803 children younger than five years of age (52.5%). 610 (11.4%) were positive for RSV infection: 276 (45.2%) were group A infections, 334 (54.8%) were group B infections and 21 (3.4%) were A/B co-infections. RSV detection rate is significantly higher (P < 0.0001) in children below 5 years. We noted that the annual distribution of RSV varied substantially by season and for the predominant subtype. Globally, results show a clear circulation pattern in the second half of each year; between June and September and possibly extended into November. The majority of RSV-A strains from Senegal clustered with strains that were previously assigned NA1 and novel ON1 genotype sequences. RSV-B sequences from Senegal clustered with the BA9 genotype. At the amino acid level, RSV-A strains from Senegal show proximity with the genotype ON1 characterized by a 72 nt insertion in G, resulting in 24 extra amino acids of which 23 are duplications of aa 261–283. Conclusion Globally our results show a clear circulation pattern of RSV in the second half of each year, between June and September and possibly extending into November, with children under 5 being more susceptible. Molecular studies identified the novel strains ON1 and BA9 as the major genotypes circulating in Senegal between 2012 and 2015. PMID:27315120

  7. Land Surface Phenology from MODIS: Characterization of the Collection 5 Global Land Cover Dynamics Product

    NASA Technical Reports Server (NTRS)

    Ganguly, Sangram; Friedl, Mark A.; Tan, Bin; Zhang, Xiaoyang; Verma, Manish

    2010-01-01

    Information related to land surface phenology is important for a variety of applications. For example, phenology is widely used as a diagnostic of ecosystem response to global change. In addition, phenology influences seasonal scale fluxes of water, energy, and carbon between the land surface and atmosphere. Increasingly, the importance of phenology for studies of habitat and biodiversity is also being recognized. While many data sets related to plant phenology have been collected at specific sites or in networks focused on individual plants or plant species, remote sensing provides the only way to observe and monitor phenology over large scales and at regular intervals. The MODIS Global Land Cover Dynamics Product was developed to support investigations that require regional to global scale information related to spatiotemporal dynamics in land surface phenology. Here we describe the Collection 5 version of this product, which represents a substantial refinement relative to the Collection 4 product. This new version provides information related to land surface phenology at higher spatial resolution than Collection 4 (500-m vs. 1-km), and is based on 8-day instead of 16-day input data. The paper presents a brief overview of the algorithm, followed by an assessment of the product. To this end, we present (1) a comparison of results from Collection 5 versus Collection 4 for selected MODIS tiles that span a range of climate and ecological conditions, (2) a characterization of interannual variation in Collections 4 and 5 data for North America from 2001 to 2006, and (3) a comparison of Collection 5 results against ground observations for two forest sites in the northeastern United States. Results show that the Collection 5 product is qualitatively similar to Collection 4. However, Collection 5 has fewer missing values outside of regions with persistent cloud cover and atmospheric aerosols. Interannual variability in Collection 5 is consistent with expected ranges of

  8. Molecular characterization of Antarctic actinobacteria and screening for antimicrobial metabolite production.

    PubMed

    Lee, Learn-Han; Cheah, Yoke-Kqueen; Mohd Sidik, Shiran; Ab Mutalib, Nurul-Syakima; Tang, Yi-Li; Lin, Hai-Peng; Hong, Kui

    2012-05-01

    The present study aimed to isolate actinobacteria from soil samples and characterized them using molecular tools and screened their secondary metabolites for antimicrobial activities. Thirty-nine strains from four different location of Barrientos Island, Antarctica using 12 types of isolation media was isolated. The isolates were preceded to screening of secondary metabolites for antimicrobial and antifungal activities. Using high-throughput screening methods, 38% (15/39) of isolates produced bioactive metabolites. Approximately 18% (7/39), 18% (7/39), 10% (4/39) and 2.5% (1/39) of isolates inhibited growth of Candida albicans ATCC 10231(T), Staphylococcus aurues ATCC 51650(T), methicillin-resistant Staphylococcus aurues (MRSA) ATCC BAA-44(T) and Pseudomonas aeruginosa ATCC 10145(T), respectively. Molecular characterization techniques like 16S rRNA analysis, Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), Random amplified polymorphic DNA (RAPD) and composite analyses were used to characterize the actinobacteria strains. Analysis of 16S rRNA sequences is still one of the most powerful methods to determine higher taxonomic relationships of Actinobacteria. Both RAPD and ERIC-PCR fingerprinting have shown good discriminatory capability but RAPD proved to be better in discriminatory power than ERIC-PCR. Our results demonstrated that composite analysis of both fingerprinting generally increased the discrimination ability and generated best clustering for actinobacteria strains in this study.

  9. Molecular characterization of Hepatitis A virus causing an outbreak among Thai navy recruits.

    PubMed

    Theamboonlers, A; Rianthavorn, P; Jiamsiri, S; Kumthong, S; Silaporn, P; Thongmee, C; Poovorawan, Y

    2009-12-01

    Hepatitis A virus (HAV) infection is a communicable disease, typically transmitted by faecal-oral contamination. HAV outbreaks usually occur in endemic areas. We report an outbreak of HAV from June to July, 2008 among Thai navy recruits who had received training at the Sattahip Navy Base, Chonburi province, Thailand. Upon conclusion of the training, the recruits were deployed to serve at several navy bases across the country. Secondary cases of HAV infection were reported among military personnel from these navy bases. To elucidate origin and distribution of these outbreaks, we characterized the genome and genotype of HAV isolated from the different navy bases. Sera and stool from the subjects were tested for antiHAV IgM, antiHAV IgG and HAV RNA. Subsequently, molecular characterization of HAV was performed by nucleotide sequencing of the VP1-P2A region, BLAST/FASTA and phylogenetic analysis. HAV RNA was detected in specimens obtained from different areas. All isolated strains clustered in the same lineage and belonged to genotype 1A. They shared nearly 100% genome homology indicating a single point source of this outbreak. This study provides essential baseline data as a reference for genetic analysis of HAV strains causing future outbreaks. Early detection of HAV infection and identification of the source by using molecular characterization and prompt preventive measures will hopefully prevent further outbreaks.

  10. Mass spectrometric techniques for characterizing low-molecular-weight resins used as paint varnishes.

    PubMed

    Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

    2013-01-01

    The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

  11. Molecular characterization of a gene affecting potassium channels in Drosophila melanogaster

    SciTech Connect

    Drysdale, R.A.

    1988-01-01

    This study describes the molecular isolation and characterization of the ether-a-go-go (eag) gene of Drosophila melanogaster. Electrophysiological and genetic evidence suggest that the product of the eag locus is intimately involved in the normal functioning of voltage-gated potassium channels. A molecular analysis of eag was undertaken in order to elucidate the contribution of eag{sup +} to the proper operation of the nervous system. An inverted chromosome, In(1)sc{sup 29}, broken in the scute complex and in the eag locus, was used to isolate DNA from the eag region. 85kb of DNA around this starting point were isolated by chromosome waling. Analysis of the corresponding genomic DNA identified the molecular lesions associated with three additional eag allels: two dysgeneis-induced insertion mutations and a lambda-ray-induced insertional translocation. The molecular defects associated with these alleles are spread throughout 27kb within the chromosome walk. Several cDNAs have been isolated on the basis of homology to parts of the chromosome walk. One of these is multiply spliced over 32kb of genomic DNA in a pattern that strongly suggests that it represents at least part of the eag message.

  12. Molecular prevalence and genetic characterization of piroplasms in dogs from Tunisia.

    PubMed

    Rjeibi, Mohamed R; Amairia, Safa; Rouatbi, Mariem; Ben Salem, Fatma; Mabrouk, Moez; Gharbi, Mohamed

    2016-10-01

    In this study, the prevalence of piroplasms in dogs was assessed using polymerase chain reaction (PCR) to identify Babesia and Theileria species in 200 dogs from Northern and Central Tunisia between spring and autumn 2014. The overall molecular prevalence for piroplasms was 14·5% ± 0·05 (29/200); PCR detected 2 species, namely Babesia vogeli and Theileria annulata with an overall prevalence of 12·5 ± 0·04 and 2% ± 0·02, respectively. No differences in the molecular prevalences of B. vogeli were revealed for age and sex (P > 0·05). The molecular prevalence of B. vogeli was significantly higher in central Tunisia (26·5% ± 0·01) compared with the North (9·6% ± 0·04) (P 0·05). Comparison of the partial sequences of 18S rRNA and Tams 1 genes confirmed the presence of 2 novel B. vogeli and T. annulata genotypes. This is the first molecular detection of T. annulata and genetic characterization of dogs' piroplasms in Tunisia. Further studies are needed to better assess the epidemiological feature of piroplasms infection in North Africa. PMID:27417681

  13. Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

    NASA Technical Reports Server (NTRS)

    Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

    1993-01-01

    This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

  14. Global Studies of Molecular Clouds in the Galaxy, the Magellanic Cloud and M31

    NASA Technical Reports Server (NTRS)

    Thaddeus, Patrick

    1998-01-01

    Over the past five years we have used our extensive CO surveys of the Galaxy and M31 in conjunction with spacecraft observations to address central problems in galactic structure and the astrophysics of molecular clouds. These problems included the nature of the molecular ring and its relation to the spiral arms and central bar, the cosmic ray distribution, the origin of the diffuse X-ray background, the distribution and properties of x-ray sources and supernova remnants, and the Galactic stellar mass distribution. For many of these problems, the nearby spiral M31 provided an important complementary perspective.

  15. Molecular characterization of toxicity mechanism of single-walled carbon nanotubes.

    PubMed

    Chen, Po-Hsuan; Hsiao, Kuang-Ming; Chou, Cheng-Chung

    2013-07-01

    Carbon nanotubes (CNTs) are one of widely used nanomaterials in industry and biomedicine. The potential impact of single-walled carbon nanotubes (SWCNTs) was evaluated using Caenorhabditis elegans (C. elegans) as a toxicological animal model. SWCNTs are extremely hydrophobic to form large agglomerates in aqueous solutions. Highly soluble amide-modified SWCNTs (a-SWCNTs) were therefore used in the present study so that the exact impact of SWCNTs could be studied. No significant toxicity was observed in C. elegans due to the amide modification. a-SWCNTs were efficiently taken up by worms and caused acute toxicity, including retarded growth, shortened lifespan and defective embryogenesis. The resulting toxicity was reversible since C. elegans could recover from a-SWCNT-induced toxicity once the exposure terminates. Chronic exposure to low doses of a-SWCNTs during all development stages could also cause a toxic accumulation in C. elegans. Genome-wide gene expression analysis was performed to investigate the toxic molecular mechanisms. Functional genomic analysis and molecular biology validation suggest that defective endocytosis, the decreased activity of the citrate cycle and the reduced nuclear translocation of DAF-16 transcription factor play key roles in inducing the observed a-SWCNT toxicity in worms. The present study presents an integrated approach to evaluating the toxicity of nanomaterials at the organism and molecular level for human and environmental health and demonstrates that traditional toxicological endpoints associated with functional genomic analysis can provide global and thorough insight into toxicity.

  16. Consortium for Molecular Characterization of Screen-Detected Lesions Created: Eight Grants Awarded | Division of Cancer Prevention

    Cancer.gov

    The NCI has awarded eight grants to create the Consortium for Molecular Characterization of Screen-Detected Lesions. The consortium has seven molecular characterization laboratories (MCLs) and a coordinating center, and is supported by the Division of Cancer Prevention and the Division of Cancer Biology. | 7 laboratories and a coordinating center focused on identifying screening-detected pre-cancers and early cancers, including within the tumor microenvironment.

  17. Molecular mechanisms responsive to dehydration may impact the invasiveness of perennial weeds under global climate change

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leafy spurge is an invasive perennial weed in the great plains of the US and Canada. The ability of this herbaceous weed to regenerate new shoot growth from an abundance of crown and root buds after severe abiotic stress is critical for survival. Due to its adaptable and aggressive nature, global cl...

  18. Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist.

    PubMed

    Darling, Kate F; Kucera, Michal; Wade, Christopher M

    2007-03-20

    The high-latitude planktonic foraminifera have proved to be particularly useful model organisms for the study of global patterns of vicariance and gene flow in the oceans. Such studies demonstrate that gene flow can occur over enormous distances in the pelagic marine environment leading to cosmopolitanism but also that there are ecological and geographical barriers to gene flow producing biogeographic structure. Here, we have undertaken a comprehensive global study of genetic diversity within a marine protist species, the high-latitude planktonic foraminiferan Neogloboquadrina pachyderma. We present extensive new data sets from the North Pacific and Arctic Oceans that, in combination with our earlier data from the North Atlantic and Southern Oceans, allow us to determine the global phylogeography of this species. The new genetic data reveal a pattern of Arctic circumpolar isolation and bipolar asymmetry between the Atlantic and Pacific Oceans. We show that the ancestry of North Pacific N. pachyderma is relatively recent. It lies within the upwelling systems and subpolar waters of the Southern Hemisphere and remarkably not within the neighboring Arctic Ocean. Instead, the Arctic Ocean population forms a genetic continuum with the North Atlantic population, which became isolated from the southern populations much earlier, after the onset of Northern hemisphere glaciation. Data from the planktonic foraminiferal morphospecies Globigerina bulloides is also introduced to highlight the isolation and endemism found within the subpolar North Pacific gyre. These data provide perspective for interpretation and discussion of global gene flow and speciation patterns in the plankton.

  19. Redescription and molecular characterization of Placobdella cryptobranchii (Johnson & Klemm, 1977) (Glossiphoniidae, Hirudinida)

    PubMed Central

    Moser, William E.; Briggler, Jeffrey T.; Richardson, Dennis J.; Schuette, Chawna D.; Hammond, Charlotte I.; Hopkins, William A.; Lazo-Wasem, Eric A.

    2013-01-01

    Abstract Placobdella cryptobranchii (Johnson & Klemm, 1977) was originally described from specimens collected from Ozark Hellbenders (Cryptobranchus alleganiensis bishopi) from the North Fork of the White River in Missouri, U.S.A. Leeches collected during August 2009 to August 2011 from five localities in Missouri (including the type locality) facilitated a redescription and molecular characterization of Placobdella cryptobranchii. Placobdella cryptobranchii has a rusty, reddish-brown dorsum with 2 lateral rows of unpigmented papillae, two unpigmented nuchal bands, unpigmented patches, and pair of four pre-anal papillae. Molecular comparison of CO-I sequence data from Placobdella cryptobranchii revealed a 93–94% similarity to Placobdella ornata and 10–17% difference among other species of Placobdella. PMID:24146580

  20. Investigations of bisacodyl with modified β-cyclodextrins: Characterization, molecular modeling, and effect of PEG.

    PubMed

    Li, Shanshan; Wang, Lili; Jiang, Jian; Tang, Peixiao; Wang, Qing; Wu, Di; Li, Hui

    2015-12-10

    Bisacodyl inclusion into hydroxypropyl-β-cyclodextrin and 2,6-di-O-methyl-β-cyclodextrin cavities was experimentally and theoretically investigated, and the effect of PEG 4000 on these inclusions was studied. Isothermal calorimetry titration curves indicated that the binary inclusion processes are enthalpy- and entropy-driven. The solid-state complexes were fully characterized by FT-IR, XRPD, DSC and SEM analyses. FT-IR, (1)H NMR, and ROESY studies provided the most favorable encapsulation modes of binary complexes, and results were further confirmed by molecular docking and molecular dynamics studies. The presence of PEG 4000 slightly enhanced encapsulation efficiency, solubility and dissolution rates of the binary complexes. In vivo studies showed that complexes with CDs markedly accelerated gastrointestinal transit time compared with pure bisacodyl, whereas addition of PEG 4000 showed no further significant improvement of the bioavailability. PMID:26428103

  1. Synthesis, characterization and molecular dynamic simulation on dendronized poly(diphtalimidoalky phenyl) methacrylates

    NASA Astrophysics Data System (ADS)

    Radić, D.; Alegría, L.; Sandoval, C.; Gargallo, L.

    2012-07-01

    Dendronized methacrylates containing 3,5-diphtalimido alkylphenyl moieties with ethyl (M-EthylG1), propyl (M-PropylG1) and butyl (M-ButylG1) spacer groups were synthesized. Monomers of the first generation were polymerized by radical polymerization using AIBN as initiator. The corresponding polymers (P-EthylG1), (P-PropylG1) and (P-ButylG1) were obtained. Monomers and polymers were characterized by 1H-NMR, 13C-NMR, FTIR spectroscopic measurements. Molecular weight was estimated by following the nitrogen content in the obtained polymers. Molecular Dynamic Simulation (MDS) was performed in order to evaluate the radius of gyration (Rg) and the end-to-end distance (ree) to estimate the stiffness of the backbone and of the dendrimers. According to the conformational analysis it is possible to observe different spacial arrangements depending on the length of the spacer group.

  2. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  3. Field-free molecular alignment induced by elliptically polarized laser pulses: Noninvasive three-dimensional characterization

    SciTech Connect

    Hertz, E.; Guerin, S.; Jauslin, H. R.; Lavorel, B.; Faucher, O.; Daems, D.

    2007-10-15

    An investigation of field-free molecular alignment produced by elliptically polarized laser pulses is reported. Experiments are conducted in CO{sub 2} at room temperature. A noninvasive all-optical technique, based on the cross defocusing of a probe pulse, is used to measure the alignment along two orthogonal directions which is sufficient to provide a three-dimensional characterization. The field-free molecular alignment produced by a laser of elliptical polarization is in good agreement in terms of amplitude and shape with theoretical predictions. It turns out to be almost equivalent to the superposition of the effects that one would obtain with two individual cross-polarized pulses. The investigation highlights notably the occurrence of field-free two-direction alignment alternation for a suitably chosen degree of ellipticity. The analogy between this specific ellipticity and the well-known 'magic angle' used in time-resolved spectroscopy to prevent rotational contributions is discussed.

  4. Redescription and molecular characterization of Placobdella cryptobranchii (Johnson & Klemm, 1977) (Glossiphoniidae, Hirudinida).

    PubMed

    Moser, William E; Briggler, Jeffrey T; Richardson, Dennis J; Schuette, Chawna D; Hammond, Charlotte I; Hopkins, William A; Lazo-Wasem, Eric A

    2013-01-01

    Placobdella cryptobranchii (Johnson & Klemm, 1977) was originally described from specimens collected from Ozark Hellbenders (Cryptobranchus alleganiensis bishopi) from the North Fork of the White River in Missouri, U.S.A. Leeches collected during August 2009 to August 2011 from five localities in Missouri (including the type locality) facilitated a redescription and molecular characterization of Placobdella cryptobranchii. Placobdella cryptobranchii has a rusty, reddish-brown dorsum with 2 lateral rows of unpigmented papillae, two unpigmented nuchal bands, unpigmented patches, and pair of four pre-anal papillae. Molecular comparison of CO-I sequence data from Placobdella cryptobranchii revealed a 93-94% similarity to Placobdella ornata and 10-17% difference among other species of Placobdella. PMID:24146580

  5. Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

    PubMed

    Marshall, David C; Hill, Kathy B R; Moulds, Max; Vanderpool, Dan; Cooley, John R; Mohagan, Alma B; Simon, Chris

    2016-01-01

    Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non

  6. Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

    PubMed

    Marshall, David C; Hill, Kathy B R; Moulds, Max; Vanderpool, Dan; Cooley, John R; Mohagan, Alma B; Simon, Chris

    2016-01-01

    Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non

  7. Characterization of the Aerosol Instrument Package for the In-service Aircraft Global Observing System IAGOS

    NASA Astrophysics Data System (ADS)

    Bundke, Ulrich; Berg, Marcel; Tettig, Frank; Franke, Harald; Petzold, Andreas

    2015-04-01

    The atmospheric aerosol influences the climate twofold via the direct interaction with solar radiation and indirectly effecting microphysical properties of clouds. The latter has the largest uncertainty according to the last IPPC Report. A measured in situ climatology of the aerosol microphysical properties is needed to reduce the reported uncertainty of the aerosol climate impact. The European Research Infrastructure IAGOS (In-service Aircraft for a Global Observing System; www.iagos.org) responds to the increasing requests for long-term, routine in situ observational data by using commercial passenger aircraft as measurement platform. However, scientific instrumentation for the measurement of atmospheric constituents requires major modifications before being deployable aboard in-service passenger aircraft. The IAGOS Aerosol Package (IAGOS-P2C) consists of two modified Butanol based CPCs (Model Grimm 5.410) and one optical particle counter (Model Grimm Sky OPC 1.129). A thermodenuder at 250°C is placed upstream the second CPC, thus the number concentrations of the total aerosol and the non-volatile aerosol fraction is measured. The Sky OPC measures the size distribution in the rage theoretically up to 32 μ m. Because of the inlet cut off diameter of D50=3 μ m we are using the 16 channel mode in the range of 250 nm - 2.5 μ m at 1 Hz resolution. In this presentation the IAGOS Aerosol package is characterized for pressure levels relevant for the planned application, down to cruising level of 150 hPa including the inlet system. In our aerosol lab we have tested the system against standard instrumentation with different aerosol test substances in a long duration test. Particle losses are characterized for the inlet system. In addition first results for airborne measurements are shown from a first field campaign.

  8. Pulsed supersonic molecular beam for characterization of chemically active metal-organic complexes at surfaces

    NASA Astrophysics Data System (ADS)

    Lear, Amanda M.

    Metal-organic coordination networks (MOCNs) at surfaces consist of a complex of organic ligands bound to an atomic metal center. The MOCNs, when chosen appropriately, can form highly-ordered arrays at surfaces. Ultra-high vacuum surface studies allow control of surface composition and provide 2D growth restrictions, which lead to under-coordinated metal centers. These systems provide an opportunity to tailor the chemical function of the metal centers due to the steric restrictions imposed by the surface. Tuning the adsorption/desorption energy at a metal center and developing a cooperative environment for catalysis are the key scientific questions that motivate the construction of a molecular beam surface analysis system. Characterization of the created systems can be performed utilizing a pulsed supersonic molecular beam (PSMB) in unison with a quadrupole mass spectrometer. A PSMB allows for the highly controlled delivery of reactants with well-defined energy to a given platform making it possible to elucidate detailed chemical tuning information. In this thesis, a summary of prior theoretical molecular beam derivations is provided. Design considerations and an overview of the construction procedure for the current molecular beam apparatus, including initial characterization experiments, are presented. By impinging an Ar beam on a Ag(111) surface, the location of the specular angle (˜65°) and rough sample perimeter coordinates were determined. Additionally, surface analysis experiments, mainly Auger Electron Spectroscopy (AES), were performed to investigate the oxidation of epitaxial graphene on the SiC(0001) surface utilizing an oxygen cracking method. The AES experiments are described in detail and highlight the challenges that were faced when several different graphene samples were used for the oxygen adsorption/desorption experiments.

  9. First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash.

    PubMed

    Fahmy, Inas Farouk; Taha, Omnia; El-Ashry, Abdel Nasser

    2015-06-01

    This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.

  10. Phenotypic and molecular characterization of intrauterine fetal growth restriction in interspecies sheep pregnancy.

    PubMed

    Chávez-García, A; Vázquez-Martínez, E R; Murcia, C; Rodríguez, A; Cerbón, M; Mejía, O

    2015-10-01

    Interspecies pregnancies between closely related species are usually performed in livestock to obtain improved and enriched offspring. Indeed, different hybrids have been obtained for research purposes since many years ago, and the maternal-fetal interactions have been studied as a possible strategy for species preservation. The aim of this study was to characterize by physiological and molecular approaches the interspecies pregnancy between bighorn sheep () and domestic sheep (). Hybrids were obtained by artificial insemination; the blood pressure and protein urine levels were measured during the last two-thirds of gestation. After parturition, offspring and placentas were weighed and measured and cotyledons were counted and weighed and their surface area determined. Plasma samples were obtained between wk 8 and 21 of gestation to assess progesterone (P4), vascular endothelial growth factor (VEGF), and placental growth factor (PlGF) levels and cell-free RNA was isolated during the same period to assess hypoxia-inducible factor-1 α (α) gene expression. Hybrid and normal pregnancies were analyzed using physiological and molecular parameters during the last two-thirds of gestation (wk 8-21). The results show that during the measurement period, ewes with a hybrid pregnancy presented normal blood pressure and no alteration in urinary protein content. However, compared with sheep with a normal pregnancy, those with a hybrid pregnancy had a decrease in fetal and placental growth as well as in the cotyledonary surface area. Furthermore, in the hybrid group, there was placental insufficiency, characterized by a decrease in P4 production, as well as indications of endothelial dysfunction, characterized an increase in plasma levels of VEGF and PlGF as well as in plasma gene expression of α. Overall, the results indicate that hybrids of and presented intrauterine growth restriction, essentially due to altered endothelial function and chronic placental insufficiency

  11. Screening and ranking of POPs for global half-life: QSAR approaches for prioritization based on molecular structure.

    PubMed

    Gramatica, Paola; Papa, Ester

    2007-04-15

    Persistence in the environment is an important criterion in prioritizing hazardous chemicals and in identifying new persistent organic pollutants (POPs). Degradation half-life in various compartments is among the more commonly used criteria for studying environmental persistence, but the limited availability of experimental data or reliable estimates is a serious problem. Available half-life data for degradation in air, water, sediment, and soil, for a set of 250 organic POP-type chemicals, were combined in a multivariate approach by principal component analysis to obtain a ranking of the studied organic pollutants according to their relative overall half-life. A global half-life index (GHLI) applicable for POP screening purposes is proposed. The reliability of this index was verified in comparison with multimedia model results. This global index was then modeled as a cumulative end-point using a QSAR approach based on few theoretical molecular descriptors, and a simple and robust regression model externally validated for its predictive ability was derived. The application of this model could allow a fast preliminary identification and prioritization of not yet known POPs, just from the knowledge of their molecular structure. This model can be applied a priori also in the chemical design of safer and alternative non-POP compounds.

  12. Molecular characterization of low molecular weight dissolved organic matter in water reclamation processes using Orbitrap mass spectrometry.

    PubMed

    Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

    2016-09-01

    Reclaimed water has recently become an important water source for urban use, but the composition of dissolved organic matter (DOM) in reclaimed water has rarely been characterized at the compound level because of its complexity. In this study, the transformation and changes in composition of low molecular weight DOM in water reclamation processes, where secondary effluent of the municipal wastewater treatment plant was further treated by biofiltration, ozonation and chlorination, were investigated by "unknown" screening analysis using Orbitrap mass spectrometry (Orbitrap MS). The intense ions were detected over an m/z range from 100 to 450. In total, 2412 formulae with various heteroatoms were assigned, and formulae with carbon (C), hydrogen (H) and oxygen (O) only and C, H, O and sulfur (S) were the most abundant species. During biofiltration, CHO-only compounds with relatively high hydrogen to carbon (H/C) ratio or with saturated structure were preferentially removed, while CHOS compounds were mostly removed. Ozonation induced the greatest changes in DOM composition. CHOS compounds were mostly decreased after ozonation while ozone selectively removed CHO compounds with relatively unsaturated structure and produced compounds that were more saturated and with a higher degree of oxidation. After chlorination, 168 chlorine-containing formulae, chlorinated disinfection by-products (DBPs), were additionally detected. Candidate DBP precursors were determined by tracking chlorinated DBPs formed via electrophilic substitution, half of which were generated during the ozonation. PMID:27235773

  13. Molecular characterization of low molecular weight dissolved organic matter in water reclamation processes using Orbitrap mass spectrometry.

    PubMed

    Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

    2016-09-01

    Reclaimed water has recently become an important water source for urban use, but the composition of dissolved organic matter (DOM) in reclaimed water has rarely been characterized at the compound level because of its complexity. In this study, the transformation and changes in composition of low molecular weight DOM in water reclamation processes, where secondary effluent of the municipal wastewater treatment plant was further treated by biofiltration, ozonation and chlorination, were investigated by "unknown" screening analysis using Orbitrap mass spectrometry (Orbitrap MS). The intense ions were detected over an m/z range from 100 to 450. In total, 2412 formulae with various heteroatoms were assigned, and formulae with carbon (C), hydrogen (H) and oxygen (O) only and C, H, O and sulfur (S) were the most abundant species. During biofiltration, CHO-only compounds with relatively high hydrogen to carbon (H/C) ratio or with saturated structure were preferentially removed, while CHOS compounds were mostly removed. Ozonation induced the greatest changes in DOM composition. CHOS compounds were mostly decreased after ozonation while ozone selectively removed CHO compounds with relatively unsaturated structure and produced compounds that were more saturated and with a higher degree of oxidation. After chlorination, 168 chlorine-containing formulae, chlorinated disinfection by-products (DBPs), were additionally detected. Candidate DBP precursors were determined by tracking chlorinated DBPs formed via electrophilic substitution, half of which were generated during the ozonation.

  14. Characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy

    SciTech Connect

    Lo, Ikai; Pang, Wen-Yuan; Hsu, Yu-Chi; Hsieh, Chia-Ho; Shih, Cheng-Hung; Chou, Mitch M. C.; Chen, Wen-Yen; Hsu, Tzu-Min; Hsu, Gary Z. L.

    2013-06-15

    The characterization of GaN microstructures grown by plasma-assisted molecular beam epitaxy on LiAlO{sub 2} substrate was studied by cathodoluminescence and photoluminescence measurements. We demonstrated that the cathodoluminescence from oblique semi-polar surfaces of mushroom-shaped GaN was much brighter than that from top polar surface due to the reduction of polarization field on the oblique semi-polar surfaces. It implies that the oblique semi-polar surface is superior for the light-emitting surface of wurtzite nano-devices.

  15. From the Bottom Up: Dimensional Control and Characterization in Molecular Monolayers†

    PubMed Central

    Claridge, Shelley A.; Liao, Wei-Ssu; Thomas, John C.; Zhao, Yuxi; Cao, Huan; Cheunkar, Sarawut; Serino, Andrew C.; Andrews, Anne M.; Weiss, Paul S.

    2013-01-01

    Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale. PMID:23258565

  16. Molecular characterization of adenovirus circulating in Central and South America during the 2006–2008 period

    PubMed Central

    García, Josefina; Sovero, Merly; Laguna‐Torres, Victor Alberto; Gomez, Jorge; Chicaiza, Wilson; Barrantes, Melvin; Sanchez, Felix; Jimenez, Mirna; Comach, Guillermo; De Rivera, Ivette L.; Agudo, Roberto; Arango, Ana E.; Barboza, Alma; Aguayo, Nicolas; Kochel, Tadeusz J.

    2009-01-01

    Background  Human Adenoviruses are recognized pathogens, causing a broad spectrum of diseases. Serotype identification is critical for epidemiological surveillance, detection of new strains and understanding of HAdvs pathogenesis. Little data is available about HAdvs subtypes in Latin America. Methods  In this study, we have molecularly characterized 213 adenoviruses collected from ILI presenting patients, during 2006‐08, in Central and South America. Results  Our results indicate that 161(76%) adenoviruses belong to subgroup C, 45 (21%) to subgroup B and 7 (3%) to subtype E4. PMID:19903214

  17. Characterizing regulated reservoirs dynamics in regional to global scale hydrologic models

    NASA Astrophysics Data System (ADS)

    Beighley, E.; Yoon, Y.; Lee, H.; Pavelsky, T.; Allen, G. H.

    2015-12-01

    Lakes and reservoirs are widely used for water supply and flood control resulting in regulated release of outflows that are nonconcurrent with inflows. In hydrologic modeling applications, accounting for the regulated behavior of reservoirs distributed throughout a river system poses a significant challenge because detailed reservoir operation rules or strategies can be difficult or not possible to obtain. Building on this problem, this study addresses the science questions: Can we model reservoir water storage changes and outlet discharges based on satellite measurements of river water surface elevation and inundated area, and How does repeat cycle, mission duration and measurement uncertainty impact our ability to characterize reservoir behavior? A modeling framework suitable for regional to global applications and based on the forthcoming Surface Water and Ocean Topography (SWOT) satellite mission is presented. Although our framework can be combined with data assimilation techniques for real-time flood forecasting, our goal is to represent reservoir storage patterns in large-scale hydrologic models for simulating: (i) impacts of future climate and/or land cover conditions on water resources, and (ii) synthetic storm events (e.g., 100-yr flood) or event catalogs for flood hazard and risk assessments. In-situ and remotely sensed reservoir dynamics are presented for select locations in the Mississippi River Basin and used in the Hillslope River Routing (HRR) hydrologic model to simulate downstream flow dynamics.

  18. Distinctive features of plant organs characterized by global analysis of gene expression in Arabidopsis.

    PubMed

    Obayashi, Takeshi; Okegawa, Takashi; Sasaki-Sekimoto, Yuko; Shimada, Hiroshi; Masuda, Tatsuru; Asamizu, Erika; Nakamura, Yasukazu; Shibata, Daisuke; Tabata, Satoshi; Takamiya, Ken-ichiro; Ohta, Hiroyuki

    2004-02-29

    The distinctive features of plant organs are primarily determined by organ-specific gene expression. We analyzed the expression specificity of 8809 genes in 7 organs of Arabidopsis using a cDNA macroarray system. Using relative expression (RE) values between organs, many known and unknown genes specifically expressed in each organ were identified. We also analyzed the organ specificity of various gene groups using the GRE (group relative expression) value, the average of the REs of all genes in a group. Consequently, we found that many gene groups even ribosomal protein genes, have strong organ-specific expression. Clustering of the expression profiles revealed that the 8809 genes were classified into 9 major categories. Although 3451 genes were clustered into the largest category, which showed constitutive gene expression, 266 and 1005 genes were found to be root- and silique-specific genes, respectively. By this clustering, particular gene groups which showed multi-organ-specific expression profiles, such as bud-flower-specific, stem-silique-specific or bud-flower-root-specific profiles, could be effectively identified. From these results, major features of plant organs could be characterized by their distinct profiles of global gene expression. These data of organ-specific gene expression are available at our web site: Arabidopsis thaliana Tissue-Specific Expression Database, ATTED (http://www.atted.bio.titech.ac.jp/).

  19. Characterization, phase solubility and molecular modeling of α-cyclodextrin/pyrimethamine inclusion complex

    NASA Astrophysics Data System (ADS)

    Araujo, Marcia Valeria Gaspar de; Macedo, Osmir F. L.; Nascimento, Cristiane da Cunha; Conegero, Leila Souza; Barreto, Ledjane Silva; Almeida, Luis Eduardo; Costa, Nivan Bezerra da; Gimenez, Iara F.

    2009-02-01

    An inclusion complex between the dihydrofolate reductase inhibitor pyrimethamine (PYR) and α-cyclodextrin (α-CD) was prepared and characterized. From the phase-solubility diagram, a linear increase of PYR solubility was verified as a function of α-CD concentration, suggesting the formation of a soluble complex. A 1:1 host-guest stoichiometry can be proposed according to the Job's plot, obtained from the difference of PYR fluorescence intensity in the presence and absence of α-CD. Differential scanning calorimetry (DSC) measurements provided additional evidences of complexation such as the absence of the endothermic peak assigned to the melting of the drug. The inclusion mode characterized by two-dimensional 1H NMR spectroscopy (ROESY) involves penetration of the p-chlorophenyl ring into the α-CD cavity, in agreement to the orientation optimized by molecular modeling methods.

  20. Molecular and functional characterization of endophytic fungi from traditional medicinal plants.

    PubMed

    Bhagat, Jyoti; Kaur, Amarjeet; Sharma, Madhunika; Saxena, A K; Chadha, B S

    2012-03-01

    This study reports the isolation of 63 endophytic fungal isolates from two traditional medicinal plants, Ocimum sanctum and Sapindus detergens from different locations of Amritsar, India. The functional characterization of the fungi for their ability to produce anti bacterial and anti cancer agent was carried out. Sixteen strains were characterized at molecular level by sequencing the amplified ITSI-5.8-ITSII region of rDNA. The phylogenetic tree resolved the endophytic fungi into different clades. The fungal endophytes belonging to order Pleosporales (Alternaria sp., Phoma sojicola and Exserohilum sp.) were functionally versatile as they produced diverse biomolecules including antibacterial agent active against Mycobacterium smegmatis, as well as cytotoxic activity against different human cancer cell lines of lung, ovary, breast, prostrate, neuroblastoma and colon. PMID:22805817

  1. Phenotypic and Molecular Characterization of Leptospira interrogans Isolated from Canis familiaris in Southern Brazil.

    PubMed

    Jorge, Sérgio; Monte, Leonardo G; De Oliveira, Natasha R; Collares, Thais F; Roloff, Bárbara C; Gomes, Charles K; Hartwig, Daiane D; Dellagostin, Odir A; Hartleben, Cláudia P

    2015-10-01

    Leptospirosis is a zoonotic disease caused by pathogenic spirochetes from the genus Leptospira, which includes 20 species and more than 300 serovars. Canines are important hosts of pathogenic leptospires and can transmit the pathogen to humans via infected urine. Here, we report the phenotypic and molecular characterization of Leptospira interrogans isolated from Canis familiaris in Southern Brazil. The isolated strain was characterized by variable-number tandem-repeats analysis as L. interrogans, serogroup Icterohaemorrhagiae. In addition, the isolate was recognized by antibodies from human and canine serum samples previously tested by microscopic agglutination test. Ultimately, the expression of membrane-associated antigens (LipL32 and leptospiral immunoglobulin-like proteins) from pathogenic leptospires using monoclonal antibodies was detected by indirect immunofluorescence assay. In conclusion, identification of new strains of Leptospira can help in the diagnosis and control of leptospirosis. PMID:26100241

  2. Molecular characterization of the first leptospires isolated from goats in Brazil

    PubMed Central

    Lilenbaum, Walter; Kremer, Frederico; Ristow, Paula; Dellagostin, Odir; Bourhy, Pascale; Hartskeerl, Rudy; Vasconcellos, Silvio

    2014-01-01

    Two Leptospira sp. isolates were obtained by the first time from goats in Brazil and characterized by sequencing rrs, rpoB and secY genes, PFGE and typing with monoclonal antibodies. Both isolates are identical and belong to Leptospira santarosai. Analysis of the rrs and the rpoB genes sequences revealed 100% identity between the goat isolates and the Bananal reference strain. When secY sequences of the two isolates were compared to each other, it was observed that they had identical sequences. However, when compared to that of the Bananal reference strain, there were 15 mismatches along the 549 bp secY sequence. In conclusion, molecular methods are increasingly useful for the characterization of leptospires and allowed to identify those isolates of caprine origin as closely related but not identical to serovar Bananal, and constitute a new type named Carioca. PMID:25763063

  3. Phenotypic and molecular characterization of Malassezia japonica isolated from psoriasis vulgaris patients.

    PubMed

    Honnavar, Prasanna; Chakrabarti, Arunaloke; Dogra, Sunil; Handa, Sanjeev; Rudramurthy, Shivaprakash M

    2015-03-01

    Malassezia species, which are skin colonizers, are being debated as to their pathogenic role in various cutaneous diseases. Species identification of Malassezia is important as particular species have been implicated in or associated with specific diseases. Malassezia japonica, a relatively newly described species, has not been completely characterized owing to the rarity of its isolation. In the present study we describe phenotypic and molecular characterization of six M. japonica strains isolated from patients with psoriasis vulgaris. In contrast to the physiological and biochemical properties of the M. japonica type strain, CBS9348, all our isolates assimilated Tween 20 and showed positive β-glucosidase activity, and the Cremophor EL utilization test was negative. However, the sequences of the D1/D2 region of rDNA, ITS2 and IGS1 regions of all our isolates clustered with the type strain of M. japonica. PMID:25587082

  4. Investigation of the impact of annealing on global molecular mobility in glasses: optimization for stabilization of amorphous pharmaceuticals.

    PubMed

    Luthra, Suman A; Hodge, Ian M; Pikal, Michael J

    2008-09-01

    The purpose of this research was to investigate the effect of annealing on the molecular mobility in lyophilized glasses using differential scanning calorimetry (DSC) and isothermal microcalorimetry (IMC) techniques. A second objective that emerged was a systematic study of the unusual pre-T(g) thermal events that were observed during DSC warming scans after annealing. Aspartame lyophilized with three different excipients; sucrose, trehalose and poly vinyl pyrrolidone (PVP) was studied. The aim of this work was to quantify the decrease in mobility in amorphous lyophilized aspartame formulations upon systematic postlyophilization annealing. DSC scans of aspartame:sucrose formulation (T(g) = 73 degrees C) showed the presence of a pre-T(g) endotherm which disappeared upon annealing. Aspartame:trehalose (T(g) = 112 degrees C) and aspartame:PVP (T(g) = 100 degrees C) showed a broad exotherm before T(g) and annealing caused appearance of endothermic peaks before T(g). This work also employed IMC to measure the global molecular mobility represented by structural relaxation time (tau(beta)) in both un-annealed and annealed formulations. The effect of annealing on the enthalpy relaxation of lyophilized glasses, as measured by DSC and IMC, was consistent with the behavior predicted using the Tool-Narayanaswamy-Moynihan (TNM) phenomenology (Luthra et al., 2007, in press). The results show that the systems annealed at T(g) -15 degrees C to T(g) -20 degrees C have the lowest molecular mobility.

  5. Molecular Characterization of Community- and Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Isolates in Southern Taiwan.

    PubMed

    Lee, Tai-Min; Yang, Ming-Chang; Yang, Tzu-Feng; Lee, Pei-Ling; Chien, Hsin-I; Hsueh, Jui-Chen; Chang, Shiou-Hui; Hsu, Chao-Hsun; Chien, Shang-Tao

    2015-12-01

    A growing tendency for community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) to be involved in nosocomial infections was reported. The predominance of SCCmec type IV or V CA-MRSA in soft tissue infection has also been indicated in Northern Taiwan. To establish basic information about the molecular characteristics of MRSA in our region, a total of 102 MRSA isolates were collected and characterized by an array of typing methods. Healthcare-associated MRSA (HA-MRSA) were found to be more resistant to levofloxacin (p=0.016) and moxifloxacin (p=0.015) than CA-MRSA. However, no difference was found in each and overall SCCmec type distribution between the two MRSA groups. Type I (8.7% vs. 2.6%) was more frequently found in CA-MRSA, whereas type V was more often observed in HA-MRSA (24.4% vs. 8.7%). No difference was found in the dichotomous group of PVL, SCCmec type IV, V, and IV/V between the two MRSA groups. Twenty-seven distinct spa types were identified; t437 and t1081 were the predominant types in our isolates. Moreover, 12 novel spa types with extremely low global frequency were detected in our isolates. SCCmec type III and IV were the major subtypes in the MRSA we collected. The t1081 clones all belonged to HA-MRSA and mostly to SCCmec type V (71.4%). CA-MRSA t437 clones were mostly SCCmec type IV strains (71.4%), but HA-MRSA t437 clones were predominantly SCCmec type IV (42.1%) and III (36.8%). Our findings support a difference in the molecular characteristics of CA-MRSA and HA-MRSA that may reflect various clonal origins in our isolates.

  6. Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology.

    PubMed

    Tang, Xiaoli; Mu, Xingmin; Shao, Hongbo; Wang, Hongyan; Brestic, Marian

    2015-01-01

    The increasing seriousness of salinization aggravates the food, population and environmental issues. Ameliorating the salt-resistance of plants especially the crops is the most effective measure to solve the worldwide problem. The salinity can cause damage to plants mainly from two aspects: hyperosmotic and hyperionic stresses leading to the restrain of growth and photosynthesis. To the adverse effects, the plants derive corresponding strategies including: ion regulation and compartmentalization, biosynthesis of compatible solutes, induction of antioxidant enzymes and plant hormones. With the development of molecular biology, our understanding of the molecular and physiology knowledge is becoming clearness. The complex signal transduction underlying the salt resistance is being illuminated brighter and clearer. The SOS pathway is the central of the cell signaling in salt stress. The accumulation of the compatible solutes and the activation of the antioxidant system are the effective measures for plants to enhance the salt resistance. How to make full use of our understanding to improve the output of crops is a huge challenge for us, yet the application of the genetic engineering makes this possible. In this review, we will discuss the influence of the salt stress and the response of the plants in detail expecting to provide a particular account for the plant resistance in molecular, physiological and transgenic fields.

  7. Global Studies of Molecular Clouds in the Galaxy, The Magellanic Clouds, and M31

    NASA Technical Reports Server (NTRS)

    Thaddeus, Patrick

    1999-01-01

    Over the course of this grant we used various spacecraft surveys of the Galaxy and M31 in conjunction with our extensive CO spectral line surveys to address central problems in galactic structure and the astrophysics of molecular clouds. These problems included the nature of the molecular ring and its relation to the spiral arms and central bar, the cosmic ray distribution, the origin of the diffuse X-ray background, the distribution and properties of x-ray sources and supernova remnants, and the Galactic stellar mass distribution. For many of these problems, the nearby spiral M31 provided an important complementary perspective. Our CO surveys of GMCs (Galactic Molecular Clouds) were crucial for interpreting Galactic continuum surveys from satellites such as GRO (Gamma Ray Observatory), ROSAT (Roentgen Satellite), IRAS (Infrared Astronomy Satellite), and COBE (Cosmic Background Explorer Satellite) because they provided the missing dimension of velocity or kinematic distance. GMCs are a well-defined and widespread population of objects whose velocities we could readily measure throughout the Galaxy. Through various emission and absorption mechanisms involving their gas, dust, or associated Population I objects, GMCs modulate the galactic emission in virtually every major wavelength band. Furthermore, the visibility. of GMCs at so many wavelengths provided various methods of resolving the kinematic distance ambiguity for these objects in the inner Galaxy. Summaries of our accomplishments in each of the major wavelength bands discussed in our original proposal are given

  8. Characterization of Transport Errors in Chemical Forecasts from a Global Tropospheric Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Bey, I.; Jacob, D. J.; Liu, H.; Yantosca, R. M.; Sachse, G. W.

    2004-01-01

    We propose a new methodology to characterize errors in the representation of transport processes in chemical transport models. We constrain the evaluation of a global three-dimensional chemical transport model (GEOS-CHEM) with an extended dataset of carbon monoxide (CO) concentrations obtained during the Transport and Chemical Evolution over the Pacific (TRACE-P) aircraft campaign. The TRACEP mission took place over the western Pacific, a region frequently impacted by continental outflow associated with different synoptic-scale weather systems (such as cold fronts) and deep convection, and thus provides a valuable dataset. for our analysis. Model simulations using both forecast and assimilated meteorology are examined. Background CO concentrations are computed as a function of latitude and altitude and subsequently subtracted from both the observed and the model datasets to focus on the ability of the model to simulate variability on a synoptic scale. Different sampling strategies (i.e., spatial displacement and smoothing) are applied along the flight tracks to search for systematic model biases. Statistical quantities such as correlation coefficient and centered root-mean-square difference are computed between the simulated and the observed fields and are further inter-compared using Taylor diagrams. We find no systematic bias in the model for the TRACE-P region when we consider the entire dataset (i.e., from the surface to 12 km ). This result indicates that the transport error in our model is globally unbiased, which has important implications for using the model to conduct inverse modeling studies. Using the First-Look assimilated meteorology only provides little improvement of the correlation, in comparison with the forecast meteorology. These general statements can be refined when the entire dataset is divided into different vertical domains, i.e., the lower troposphere (less than 2 km), the middle troposphere (2-6 km), and the upper troposphere (greater than

  9. Molecular characterization of trophic ecology within an island radiation of insect herbivores (Curculionidae: Entiminae: Cratopus).

    PubMed

    Kitson, James J N; Warren, Ben H; Florens, F B Vincent; Baider, Claudia; Strasberg, Dominique; Emerson, Brent C

    2013-11-01

    The phytophagous beetle family Curculionidae is the most species-rich insect family known, with much of this diversity having been attributed to both co-evolution with food plants and host shifts at key points within the early evolutionary history of the group. Less well understood is the extent to which patterns of host use vary within or among related species, largely because of the technical difficulties associated with quantifying this. Here we develop a recently characterized molecular approach to quantify diet within and between two closely related species of weevil occurring primarily within dry forests on the island of Mauritius. Our aim is to quantify dietary variation across populations and assess adaptive and nonadaptive explanations for this and to characterize the nature of a trophic shift within an ecologically distinct population within one of the species. We find that our study species are polyphagous, consuming a much wider range of plants than would be suggested by the literature. Our data suggest that local diet variation is largely explained by food availability, and locally specialist populations consume food plants that are not phylogenetically novel, but do appear to represent a novel preference. Our results demonstrate the power of molecular methods to unambiguously quantify dietary variation across populations of insect herbivores, providing a valuable approach to understanding trophic interactions within and among local plant and insect herbivore communities.

  10. Molecular characterization of fungal communities in non-tilled, cover-cropped upland rice field soils.

    PubMed

    Nishizawa, Tomoyasu; Zhaorigetu; Komatsuzaki, Masakazu; Sato, Yoshinori; Kaneko, Nobuhiro; Ohta, Hiroyuki

    2010-01-01

    This study aimed to characterize soil fungal communities in upland rice fields managed with tillage/non-tillage and winter cover-cropping (hairy vetch and cereal rye) practices, using PCR-based molecular methods. The study plots were maintained as upland fields for 5 years and the soils sampled in the second and fifth years were analyzed using T-RFLP (terminal restriction fragment length polymorphism) profiling and clone libraries with the internal transcribed spacer (ITS) region and domain 1 (D1) of the fungal large-subunit (fLSU) rRNA (D1(fLSU)) as the target DNA sequence. From the 2nd-year-sample, 372 cloned sequences of fungal ITS-D1(fLSU) were obtained and clustered into 80 nonredundant fungal OTUs (operational taxonomic units) in 4 fungal phyla. The T-RFLP profiling was performed with the 2nd- and 5th-year-samples and the major T-RFs (terminal restriction fragments) were identified using a theoretical fragment analysis of the ITS-D1(fLSU) clones. These molecular analyses showed that the fungal community was influenced more strongly by the cover-cropping than tillage practices. Moreover, the non-tilled, cover-cropped soil was characterized by a predominance of Cryptococcus sp. in the phylum Basidiomycota. We provided a genetic database of the fungal ITS-D1(fLSU)s in the differently managed soils of upland rice fields.

  11. Molecular Characterization and Antimicrobial Resistance Profile of Methicillin-Resistant Staphylococcus aureus in Retail Chicken.

    PubMed

    Sallam, Khalid Ibrahim; Abd-Elghany, Samir Mohammed; Elhadidy, Mohamed; Tamura, Tomohiro

    2015-10-01

    The emergence of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) in food-producing animals is of increasing interest, raising questions about the presence of MRSA in food of animal origin and potential sources of transmission to humans via the food chain. In this study, the prevalence, molecular characterization, virulence factors, and antimicrobial susceptibility patterns of MRSA isolates from 200 retail raw chicken samples in Egypt were determined. MRSA was detected by positive amplification of the mecA gene in 38% (76 of 200) of chicken samples analyzed. This represents a potential public health threat in Egypt, as this contamination rate seems to be the highest among other studies reported worldwide. Furthermore, genes encoding α-hemolysin (hla) and staphylococcal enterotoxins (sea, seb, and sec) were detected in all of the 288 MRSA isolates. Nonetheless, none of the strains tested carried tst, the gene encoding toxic shock syndrome toxin 1. Antimicrobial resistance of MRSA isolates was most frequently detected against penicillin (93.4%), ampicillin (88.9%), and cloxacillin (83.3%). These results suggest that retail chicken might be a significant potential source for transmission of multidrug-resistant and toxigenic S. aureus in Egypt. This underlines the need for stricter hygienic measures in chicken production in Egypt to minimize the risk of transmission of these strains to consumers. To the best of our knowledge, this is the first study that reports the isolation and molecular characterization of MRSA in retail chicken samples in Egypt.

  12. Molecular cloning and characterization of a unique type of human papillomavirus from an immune deficient patient.

    PubMed

    Ostrow, R S; Zachow, K R; Thompson, O; Faras, A J

    1984-04-01

    Several papillomas from a single patient who exhibited an unusual immune deficiency syndrome were analyzed for the presence of specific human papillomavirus (HPV) types. Preliminary analysis indicated that the HPV DNA species present in each of these tissues was quite unlike any of the previously characterized HPV types. In order to more rigorously analyze the HPV from this patient we have isolated the HPV DNA by molecularly cloning it into a bacteriophage lambda vector and have constructed a detailed restriction endonuclease map. Comparative hybridization studies using S1 nuclease analyses showed 6% or less nucleotide sequence homology of this viral DNA with HPV types 1, 2, 3, 4, 5, 6, or an HPV-11, molecularly cloned in this laboratory. Moreover, Southern blot analyses under stringent hybridization conditions revealed little, if any, hybridization to HPV types 1, 2, 4, 5, 7, 8, 10, 11, HPV-EV isolated from a patient with epidermodysplasia verruciformis (EV), or 2 previously described HPVs (HPV-P and HPV-PW) related to HPV-3. There was, however, a very weak sequence homology detected with HPV-6 and an extremely weak homology to HPV-3. No filter hybridization was observed with the recently characterized HPVs 9 or -12 to -24. These data accumulatively indicate that the HPV species from this immunosuppressed patient represents a new, hitherto unidentified HPV type. PMID:6323588

  13. Molecular characterization of Babesia vogeli in dogs from Belém, northern Brazil.

    PubMed

    Moraes, P H G; Rufino, C P; Baraúna, A R F; Reis, T; Agnol, L T D; Meneses, A M C; Aguiar, D C F; Nunes, M R T; Gonçalves, E C

    2015-01-01

    Babesiosis is an infectious hemolytic disease that occurs worldwide, and is caused by a protozoan of the Babesia genus (Apicomplexa). Little is known about this genus; therefore, this study conducted a molecular characterization of Babesia spp in naturally infected dogs in northern Brazil. Blood samples were collected from 172 dogs from metropolitan Belém, and screened for Babesia spp using semi-nested polymerase chain reactions. Subsequently, 18S rDNA gene fragments were amplified and sequenced. Alignments of the 27 nucleotide sequences returned fragments measuring 1023 bp in size, which did not include any polymorphic sites (100% identity). This genotype was very similar to the 18S rDNA gene in B. vogeli. This study provides an important molecular characterization of the parasite responsible for canine babesiosis in naturally infected dogs in metropolitan Belém. In addition, the 18S rDNA gene in B. vogeli may represent the most common genotype occurring in South America. PMID:26662431

  14. Functionalized imidazolium and benzimidazolium salts as paraoxonase 1 inhibitors: Synthesis, characterization and molecular docking studies.

    PubMed

    Karataş, Mert Olgun; Uslu, Harun; Alıcı, Bülent; Gökçe, Başak; Gencer, Nahit; Arslan, Oktay; Arslan, N Burcu; Özdemir, Namık

    2016-03-15

    Paraoxonase (PON) is a key enzyme in metabolism of living organisms and decreased activity of PON1 was acknowledged as a risk for atherosclerosis and organophosphate toxicity. The present study describes the synthesis, characterization, PON1 inhibitory properties and molecular docking studies of functionalized imidazolium and benzimidazolium salts (1a-5g). The structures of all compounds were elucidated by IR, NMR, elemental analysis and structures of compounds 2b and 2c were characterized by single-crystal X-ray diffraction. Compound 1c, a coumarin substituted imidazolium salt showed the best inhibitory effect on the activity of PON1 with good IC50 value (6.37 μM). Kinetic investigation was evaluated for this compound and results showed that this compound is competitive inhibitor of PON1 with Ki value of 2.39 μM. Molecular docking studies were also performed for most active compound 1c and one of least active compound 2c in order to determine the probable binding model into active site of PON1 and validation of the experimental results. PMID:26879855

  15. Molecular characterization of trophic ecology within an island radiation of insect herbivores (Curculionidae: Entiminae: Cratopus).

    PubMed

    Kitson, James J N; Warren, Ben H; Florens, F B Vincent; Baider, Claudia; Strasberg, Dominique; Emerson, Brent C

    2013-11-01

    The phytophagous beetle family Curculionidae is the most species-rich insect family known, with much of this diversity having been attributed to both co-evolution with food plants and host shifts at key points within the early evolutionary history of the group. Less well understood is the extent to which patterns of host use vary within or among related species, largely because of the technical difficulties associated with quantifying this. Here we develop a recently characterized molecular approach to quantify diet within and between two closely related species of weevil occurring primarily within dry forests on the island of Mauritius. Our aim is to quantify dietary variation across populations and assess adaptive and nonadaptive explanations for this and to characterize the nature of a trophic shift within an ecologically distinct population within one of the species. We find that our study species are polyphagous, consuming a much wider range of plants than would be suggested by the literature. Our data suggest that local diet variation is largely explained by food availability, and locally specialist populations consume food plants that are not phylogenetically novel, but do appear to represent a novel preference. Our results demonstrate the power of molecular methods to unambiguously quantify dietary variation across populations of insect herbivores, providing a valuable approach to understanding trophic interactions within and among local plant and insect herbivore communities. PMID:24112379

  16. Molecular and histological characterization of bovine papillomavirus in North West Italy.

    PubMed

    Grindatto, Anna; Ferraro, Giuseppina; Varello, Katia; Crescio, Maria Ines; Miceli, Ilaria; Bozzetta, Elena; Goria, Maria; Nappi, Raffaella

    2015-10-22

    Bovine papillomaviruses (BPVs) are group of worldwide-spread DNA virus that infect primarily cattle determining diseases of considerable economic relevance. Recently, research on BPVs, received a great impulse owing to the development of specific biomolecular analysis, mostly based on L1 gene sequencing, that resulted in the identification of new viral types. This work is aimed at the identification and molecular and histopathological characterization of BPVs circulating in North West Italy, one of the main national cattle breeding areas. In this study, 71 bioptic specimens were submitted both to histological examination and to PCR and sequencing analysis. Histopathology revealed various lesion types; however, no connections were demonstrated between involved viral types and histopathological findings. BPV DNA was demonstrated in all the analyzed samples and several viral types were detected. Particularly, molecular investigations revealed a broad diffusion of highly pathogenic BPV1 and 2 Deltapapillomavirus and presence of BPV3 and 9 Xipapillomavirus. Two cases of co-infection were also demonstrated. Phylogenetic analysis revealed presence of different clusters and therefore a noteworthy genetic variety among the analyzed viral types. This study provides information on the main BPVs types in North West Italy and our results demonstrate the complexity of viral epidemiology which is characterized by circulation of multiple viral types even inside single herds. Knowledge of the prevalence and of the variety of BPVs is a milestone for the development of appropriate prophylactic and therapeutic measures. PMID:26315772

  17. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

    PubMed Central

    Burgess, Treena I.

    2015-01-01

    Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

  18. Molecular Characterization of Biomass Burning Aerosols Using High Resolution Mass Spectrometry

    SciTech Connect

    Smith, Jeffrey S.; Laskin, Alexander; Laskin, Julia

    2009-02-13

    Chemical characterizations of atmospheric aerosols is a serious analytical challenge because of the complexity of particulate matter analyte composed of a large number of compounds with a wide range of molecular structures, physico-chemical properties, and reactivity. In this study chemical composition of biomass burning organic aerosol (BBOA) samples is characterized by high resolution electrospray ionization mass spectrometry (ESI/MS). Accurate mass measurement combined with Kendrick analysis allowed us to assign elemental composition for hundreds of compounds in the range of m/z values of 50-1000. ESI/MS spectra of different BBOA samples contain a variety of distinct, sample specific, characteristic peaks that can be used as unique markers for different types of biofuels. Our results indicate that a significant number of high-MW organic compounds in BBOA samples are highly oxidized polar species that can be efficiently detected using ESI/MS but are difficult to observe using the conventional GCMS analysis of aerosol samples. The average O:C ratios obtained for each of the BBOA samples studied in this work are in a strikingly good agreement with the previously reported values obtained using STXM/NEXAFS. The degree of unsaturation of detected organic compounds shows a clear decrease with increase in the molecular weight of the anyalyte molecules. The decrease is particularly pronounced for the samples containing a large number of CH2-based homologous series.

  19. Molecular Characterization and Antimicrobial Resistance Profile of Methicillin-Resistant Staphylococcus aureus in Retail Chicken.

    PubMed

    Sallam, Khalid Ibrahim; Abd-Elghany, Samir Mohammed; Elhadidy, Mohamed; Tamura, Tomohiro

    2015-10-01

    The emergence of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) in food-producing animals is of increasing interest, raising questions about the presence of MRSA in food of animal origin and potential sources of transmission to humans via the food chain. In this study, the prevalence, molecular characterization, virulence factors, and antimicrobial susceptibility patterns of MRSA isolates from 200 retail raw chicken samples in Egypt were determined. MRSA was detected by positive amplification of the mecA gene in 38% (76 of 200) of chicken samples analyzed. This represents a potential public health threat in Egypt, as this contamination rate seems to be the highest among other studies reported worldwide. Furthermore, genes encoding α-hemolysin (hla) and staphylococcal enterotoxins (sea, seb, and sec) were detected in all of the 288 MRSA isolates. Nonetheless, none of the strains tested carried tst, the gene encoding toxic shock syndrome toxin 1. Antimicrobial resistance of MRSA isolates was most frequently detected against penicillin (93.4%), ampicillin (88.9%), and cloxacillin (83.3%). These results suggest that retail chicken might be a significant potential source for transmission of multidrug-resistant and toxigenic S. aureus in Egypt. This underlines the need for stricter hygienic measures in chicken production in Egypt to minimize the risk of transmission of these strains to consumers. To the best of our knowledge, this is the first study that reports the isolation and molecular characterization of MRSA in retail chicken samples in Egypt. PMID:26408138

  20. Synthesis, characterization, and pulsed laser ablation of molecular sieves for thin film applications

    NASA Astrophysics Data System (ADS)

    Munoz, Trinidad, Jr.

    1998-12-01

    Molecular sieves are one class of crystalline low density metal oxides which are made up of one-, two-, and three dimensional pores and/or cages. We have investigated the synthesis and characterization of metal substituted aluminophosphates and all silica molecular sieves for thin film applications. A new copper substituted aluminophosphate, CuAPO-5 has been synthesized and characterized using x-ray powder diffraction, FT-IR spectroscopy and scanning electron microscopy. Electron spin resonance and electron spin echo modulation provided supporting evidence of framework incorporation of Cu(II) ions. Thus, an exciting addition has been added to the family of metal substituted aluminophosphates where substitution of the metal has been demonstrated as framework species. Also presented here is the synthesis and characterization of an iron substituted aluminophosphate, FeAPO-5, and an all silica zeolite, UTD-1 for thin film applications. Pulsed laser ablation has been employed as the technique to generate thin films. Here an excimer laser (KrFsp*, 248 nm) was used to deposit the molecular sieves on a variety of substrates including polished silicon, titanium nitride, and porous stainless steel disks. The crystallinity of the deposited films was enhanced by a post hydrothermal treatment. A vapor phase treatment of the laser deposited FeAPO-5 films has been shown to increase the crystallinity of the film without increasing film thickness. Thin films of the FeAPO-5 molecular sieves were subsequently used as the dielectric phase in capacitive type chemical sensors. The capacitance change of the FeAPO-5 devices to the relative moisture makes them potential humidity sensors. The all silica zeolite UTD-1 thin films were deposited on polished silicon and porous supports. A brief post hydrothermal treatment of the laser deposited films deposited on polished silicon and porous metal supports resulted in oriented film growth lending these films to applications in gas separations

  1. Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays

    PubMed Central

    2013-01-01

    Background Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. Methods Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization. Results The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 102 HAd

  2. Genetic-molecular characterization of backcross generations for sexual conversion in papaya (Carica papaya L.).

    PubMed

    Ramos, H C C; Pereira, M G; Pereira, T N S; Barros, G B A; Ferreguetti, G A

    2014-12-04

    The low number of improved cultivars limits the expansion of the papaya crop, particularly because of the time required for the development of new varieties using classical procedures. Molecular techniques associated with conventional procedures accelerate this process and allow targeted improvements. Thus, we used microsatellite markers to perform genetic-molecular characterization of papaya genotypes obtained from 3 backcross generations to monitor the inbreeding level and parental genome proportion in the evaluated genotypes. Based on the analysis of 20 microsatellite loci, 77 genotypes were evaluated, 25 of each generation of the backcross program as well as the parental genotypes. The markers analyzed were identified in 11 of the 12 linkage groups established for papaya, ranging from 1 to 4 per linkage group. The average values for the inbreeding coefficient were 0.88 (BC1S4), 0.47 (BC2S3), and 0.63 (BC3S2). Genomic analysis revealed average values of the recurrent parent genome of 82.7% in BC3S2, 64.4% in BC1S4, and 63.9% in BC2S3. Neither the inbreeding level nor the genomic proportions completely followed the expected average values. This demonstrates the significance of molecular analysis when examining different genotype values, given the importance of such information for selection processes in breeding programs.

  3. Antipyrine-gamma cyclodextrin inclusion complex: Molecular modeling, preparation, characterization and cytotoxicity studies

    NASA Astrophysics Data System (ADS)

    Gannimani, Ramesh; Perumal, Amanda; Ramesh, Muthusamy; Pillay, Karen; Soliman, Mahmoud E.; Govender, Patrick

    2015-06-01

    Molecular docking, semi-empirical and molecular dynamics studies were conducted for α, β and γ-cyclodextrin-associated inclusion complexes of antipyrine. The results of molecular modeling were systematically analyzed to determine the stability of inclusion complexes. In preliminary computational screening, β and γ-cyclodextrin inclusion complexes of antipyrine were found to be more stable as compared to α-cyclodextrin based on docking score and binding free energies. Further, inclusion complex of antipyrine with γ-cyclodextrin was prepared by freeze drying method. Formation of the inclusion complex was investigated by solid state characterization techniques such as thermogravimetric analysis, differential scanning calorimetry, X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy. The changes observed in decomposition temperature, diffractogram, vibrational frequencies and morphological appearance confirmed the formation of inclusion complex. In addition, results from 1H NMR and 2D NOESY studies supported the inclusion phenomenon. The results obtained from computational studies were found to be in consistent with experimental data to ascertain the encapsulation of antipyrine into γ-cyclodextrin. The inclusion complex was found to be non-toxic toward MDCK-1 cell lines. Thus, this approach may be helpful in the formulation of drug molecules using cyclodextrins.

  4. Synthesis and characterization of montmorillonite clay intercalated with molecular magnetic compounds

    SciTech Connect

    Martins, Marcel G.; Martins, Daniel O.T.A.; Carvalho, Beatriz L.C. de; Mercante, Luiza A.; Soriano, Stéphane; Andruh, Marius; Vieira, Méri D.; Vaz, Maria G.F.

    2015-08-15

    In this work montmorillonite (MMT) clay, whose matrix was modified with an ammonium salt (hexadecyltrimethylammonium bromide – CTAB), was employed as an inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange: a nitronyl nitroxide derivative 2-[4-(N-ethyl)-pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (p-EtRad{sup +}) and two binuclear coordination compounds, [Ni(valpn)Ln]{sup 3+}, where H{sub 2}valpn stands for 1,3-propanediyl-bis(2-iminomethylene-6-methoxy-phenol), and Ln=Gd{sup III}; Dy{sup III}. The pristine MMT and the intercalated materials were characterized by X-ray powder diffraction (XRD), infrared spectroscopy (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and magnetic measurements. The X-ray diffraction data analysis showed an increase of the interlamellar space of the intercalated MMT, indicating the intercalation of the magnetic compounds. Furthermore, the magnetic properties of the hybrid compounds were investigated, showing similar behavior as the pure magnetic guest species. - Graphical abstract: Montmorillonite clay was employed as inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange - Highlights: • Montmorillonite was employed as a host material. • Three molecular magnetic compounds were intercalated through ion exchange. • The compounds were successful intercalated maintaining the layered structure. • The hybrid materials exhibited similar magnetic behavior as the pure magnetic guest.

  5. Molecular characterization and biological response to respiration inhibitors of Pyricularia isolates from ctenanthe and rice plants.

    PubMed

    Paplomatas, Epaminondas J; Pappas, Athanasios C; Syranidou, Elene

    2005-07-01

    The molecular profile and the biological response of isolates of Pyricularia oryzae Cavara obtained from ctenanthe to two strobilurins (azoxystrobin, kresoxim-methyl) and the phenylpyridinamine fungicide fluazinam were characterized, and compared with isolates from rice plants. Five different isozymes (alpha-esterase, lactate, malate, isocitrate and sorbitol dehydrogenases) and five random decamer primers for RAPD-PCR were used to generate molecular markers. Using unweighted pair-group with arithmetic average analysis, ctenanthe isolates were found to form a separate group distinct from that of the rice isolates for both sets of markers. Amplified polymorphic sequences of mitochondrial cytochrome b that were digested with Fnu4HI or StyI revealed no differences among Pyricularia isolates at amino acid positions 143 or 129 which confer resistance to strobilurins in several fungi. In absence of the alternative respiration inhibitor salicylhydroxamic acid (SHAM) the three fungicides showed inferior and variable efficacy, with a trend toward the rice isolate being less sensitive. The addition of SHAM enhanced the effectiveness of all fungicides against isolates regardless of their origin. Appressorium formation was the most vulnerable target of action of the respiration inhibitors and azoxystrobin the most effective. This is the first report of a comparison between the molecular profiles and sensitivities to respiration inhibitors for Pyricularia oryzae isolates from a non-gramineous host and from rice. PMID:15739234

  6. Synthesis and characterization of a new microporous cesium silicotitanate (SNL-B) molecular sieve

    SciTech Connect

    NYMAN,MAY D.; GU,B.X.; WANG,L.M.; EWING,R.C.; NENOFF,TINA M.

    2000-03-20

    Ongoing hydrothermal Cs-Ti-Si-O-H{sub 2}O phase investigations has produced several new ternary phases including a novel microporous Cs-silicotitanate molecular sieve, SNL-B with the approximate formula of Cs{sub 3}TiSi{sub 3}O{sub 9.5}{center_dot}3H{sub 2}O. SNL-B is only the second molecular sieve Cs-silicotitanate phase reported to have been synthesized by hydrothermal methods. Crystallites are very small (0.1 x 2 microns) with a blade-like morphology. SNL-B is confirmed to be a 3-dimensional molecular sieve by a variety of characterization techniques (N{sub 2} adsorption, ion exchange, water adsorption/desorption, solid state CP-MAS NMR). SNL-B is able to desorb and adsorb water from its pores while retaining its crystal structure and exchanges Cs cations readily. Additional techniques were used to describe fundamental properties (powder X-ray diffraction, FTIR, {sup 29}Si and {sup 133}/Cs MAS NMR, DTA, SEM/EDS, ion selectivity, and radiation stability). The phase relationships of metastable SNL-B to other hydrothermally synthesized Cs-Ti-Si-O-H{sub 2}O phases are discussed, particularly its relationship to a Cs-silicotitanate analogue of pharmacosiderite, and a novel condensed phase, a polymorph of Cs{sub 2}TiSi{sub 6}O{sub 15}(SNL-A).

  7. Molecular Characterization Reveals Diverse and Unknown Malaria Vectors in the Western Kenyan Highlands.

    PubMed

    St Laurent, Brandyce; Cooke, Mary; Krishnankutty, Sindhu M; Asih, Puji; Mueller, John D; Kahindi, Samuel; Ayoma, Elizabeth; Oriango, Robin M; Thumloup, Julie; Drakeley, Chris; Cox, Jonathan; Collins, Frank H; Lobo, Neil F; Stevenson, Jennifer C

    2016-02-01

    The success of mosquito-based malaria control is dependent upon susceptible bionomic traits in local malaria vectors. It is crucial to have accurate and reliable methods to determine mosquito species composition in areas subject to malaria. An unexpectedly diverse set of Anopheles species was collected in the western Kenyan highlands, including unidentified and potentially new species carrying the malaria parasite Plasmodium falciparum. This study identified 2,340 anopheline specimens using both ribosomal DNA internal transcribed spacer region 2 and mitochondrial DNA cytochrome oxidase subunit 1 loci. Seventeen distinct sequence groups were identified. Of these, only eight could be molecularly identified through comparison to published and voucher sequences. Of the unidentified species, four were found to carry P. falciparum by circumsporozoite enzyme-linked immunosorbent assay and polymerase chain reaction, the most abundant of which had infection rates comparable to a primary vector in the area, Anopheles funestus. High-quality adult specimens of these unidentified species could not be matched to museum voucher specimens or conclusively identified using multiple keys, suggesting that they may have not been previously described. These unidentified vectors were captured outdoors. Diverse and unknown species have been incriminated in malaria transmission in the western Kenya highlands using molecular identification of unusual morphological variants of field specimens. This study demonstrates the value of using molecular methods to compliment vector identifications and highlights the need for accurate characterization of mosquito species and their associated behaviors for effective malaria control. PMID:26787150

  8. Construction and characterization of an infectious molecular clone of Koala retrovirus.

    PubMed

    Shojima, Takayuki; Hoshino, Shigeki; Abe, Masumi; Yasuda, Jiro; Shogen, Hiroko; Kobayashi, Takeshi; Miyazawa, Takayuki

    2013-05-01

    Koala retrovirus (KoRV) is a gammaretrovirus that is currently endogenizing into koalas. Studies on KoRV infection have been hampered by the lack of a replication-competent molecular clone. In this study, we constructed an infectious molecular clone, termed plasmid pKoRV522, of a KoRV isolate (strain Aki) from a koala reared in a Japanese zoo. The virus KoRV522, derived from pKoRV522, grew efficiently in human embryonic kidney (HEK293T) cells, attaining 10(6) focus-forming units/ml. Several mutations in the Gag (L domain) and Env regions reported to be involved in reduction in viral infection/production in vitro are found in pKoRV522, yet KoRV522 replicated well, suggesting that any effects of these mutations are limited. Indeed, a reporter virus pseudotyped with pKoRV522 Env was found to infect human, feline, and mink cell lines efficiently. Analyses of KoRV L-domain mutants showed that an additional PPXY sequence, PPPY, in Gag plays a critical role in KoRV budding. Altogether, our results demonstrate the construction and characterization of the first infectious molecular clone of KoRV. The infectious clone reported here will be useful for elucidating the mechanism of endogenization of the virus in koalas and screening for antiretroviral drugs for KoRV-infected koalas.

  9. Electrical transport characterization of benzenedithiol and methylbenzenethiol molecular junctions with PEDOT:PSS interlayer electrodes

    NASA Astrophysics Data System (ADS)

    Jeong, Inho; Song, Hyunwook

    2016-08-01

    We have fabricated and characterized molecular electronic devices using benzene-based molecular monolayers and PEDOT:PSS (3,4-ethylenedioxythiophene) interlayer electrodes. In particular, we compared the electrical characteristics of two different benzenethiol molecules, 4-methylbenzenethiol (MBT) and 1,4-benzenedithiol (BDT), which have the same backbone structure but different top-end groups. From statistically representative data, we observed that the current density of the MBT devices was greater than that of the BDT devices by a factor of ˜4. The difference in current density between the two molecular electronic devices was attributed to the difference in the contact properties between the MBT and BDT molecules with the PEDOT:PSS interlayer electrodes. We also found an increase in the current density with increasing temperature within the range of 300 - 400 K, which could be caused by changes in the interfacial properties of the PEDOT:PSS-molecule contact and by removal of residual solvent or water from the interface.

  10. Isolation and characterization of low molecular weight glycosaminoglycans from marine mollusc Amussium pleuronectus (linne) using chromatography.

    PubMed

    Saravanan, R; Shanmugam, A

    2010-03-01

    The glycosaminoglycan (GAG) heparin is a polyanionic sulfated polysaccharide most recognized for its anticoagulant activity. In the present study, the GAGs were extracted from bivalve mollusc Amussium pleuronectus. The crude GAGs were fractionated by ion-exchange (DEAE-cellulose and Amberlite IRA-900 & 120) chromatography. The recovered active fractions (as determined by metachromatic assay) were confirmed by agarose gel electrophoresis and the active fractions were purified in Sephadex G-100 column. Fractionated and purified GAG molecular weight was determined through gradient polyacrylamide gel electrophoresis. The structural characterization of low molecular weight GAG was analyzed by Fourier transform infrared spectroscopy. The activated partial thromboplastin time of purified GAG is 95 IU/mg and has molecular weight 6,500-7,500 Da. The disaccharide compositional analysis on the GAG sample was sulfated like porcine intestinal mucosal heparan sulfate, and it contains equivalent amount of uronic acid and hexosamine. The results of this study suggest that the GAG from A. pleuronectus could be an alternative source of heparin.

  11. Molecular characterization and biological response to respiration inhibitors of Pyricularia isolates from ctenanthe and rice plants.

    PubMed

    Paplomatas, Epaminondas J; Pappas, Athanasios C; Syranidou, Elene

    2005-07-01

    The molecular profile and the biological response of isolates of Pyricularia oryzae Cavara obtained from ctenanthe to two strobilurins (azoxystrobin, kresoxim-methyl) and the phenylpyridinamine fungicide fluazinam were characterized, and compared with isolates from rice plants. Five different isozymes (alpha-esterase, lactate, malate, isocitrate and sorbitol dehydrogenases) and five random decamer primers for RAPD-PCR were used to generate molecular markers. Using unweighted pair-group with arithmetic average analysis, ctenanthe isolates were found to form a separate group distinct from that of the rice isolates for both sets of markers. Amplified polymorphic sequences of mitochondrial cytochrome b that were digested with Fnu4HI or StyI revealed no differences among Pyricularia isolates at amino acid positions 143 or 129 which confer resistance to strobilurins in several fungi. In absence of the alternative respiration inhibitor salicylhydroxamic acid (SHAM) the three fungicides showed inferior and variable efficacy, with a trend toward the rice isolate being less sensitive. The addition of SHAM enhanced the effectiveness of all fungicides against isolates regardless of their origin. Appressorium formation was the most vulnerable target of action of the respiration inhibitors and azoxystrobin the most effective. This is the first report of a comparison between the molecular profiles and sensitivities to respiration inhibitors for Pyricularia oryzae isolates from a non-gramineous host and from rice.

  12. Molecular characterization of Echinococcus granulosus in a hyperendemic European focus, the Republic of Moldova.

    PubMed

    Umhang, Gérald; Chihai, Oleg; Boué, Franck

    2014-12-01

    Cystic echinococcosis is a zoonosis caused by the tapeworm Echinococcus granulosus sensu lato. The lifecycle of the parasite is mainly domestic, requiring dogs as definitive hosts and livestock species as intermediate hosts. Although human cystic echinococcosis is a high public health priority in the Republic of Moldova, the rare animal data available concerns only infection in cattle. A preliminary slaughterhouse survey was conducted to assess prevalence and perform the first molecular characterization of E. granulosus sensu lato in sheep and cattle. For the survey, 40 sheep and 19 cattle were inspected. Very high prevalence in sheep (82.5%) and in cattle (78.9%) was found. Molecular analyses identified genotypes G1 and G3 of E. granulosus sensu stricto in all the liver and lung samples. Based on the concatenated sequences of cox1 + nad3 (701 bp), 23 different haplotypes were obtained. Mixed infections by different haplotypes/genotypes were frequently identified in both sheep and cattle. The relatively high (20.0%) cyst fertility observed in cattle argues for the potential contribution of cattle to the lifecycle of E. granulosus sensu stricto, unlike previous observations in Europe. The hyperendemic situation of Moldova can be explained by a high majority of animals slaughtered at home usually without veterinary inspection. Further extensive slaughterhouse surveys with molecular identification also involving pigs and goats are needed to obtain a better overview of the epidemiological situation of E. granulosus sensu lato in this hyperendemic focus in the Republic of Moldova.

  13. Molecular weight distribution characterization of hydrophobe-modified hydroxyethyl cellulose by size-exclusion chromatography.

    PubMed

    Li, Yongfu; Meunier, David M; Partain, Emmett M

    2014-09-12

    Size-exclusion chromatography (SEC) of hydrophobe-modified hydroxyethyl cellulose (HmHEC) is challenging because polymer chains are not isolated in solution due to association of hydrophobic groups and hydrophobic interaction with column packing materials. An approach to neutralize these hydrophobic interactions was developed by adding β-cyclodextrin (β-CD) to the aqueous eluent. SEC mass recovery, especially for the higher molecular weight chains, increased with increasing concentration of β-CD in the eluent. A β-CD concentration of 0.75wt% in the eluent was determined to be optimal for the HmHEC polymers studied. These conditions enabled precise determinations of apparent molecular weight distributions exhibiting less than 2% relative standard deviation in the measured weight-average molecular weight (MW) for five injections on three studied samples and showed no significant differences in MW determined on two different days. The developed technology was shown to be very robust for characterizing HmHEC having MW from 500kg/mol to 2000kg/mol, and it can be potentially applied to other hydrophobe-modified polymers.

  14. Application of different molecular techniques for characterization of catalase-positive cocci isolated from sucuk.

    PubMed

    Kesmen, Zülal; Yarimcam, Burcu; Aslan, Hakiye; Ozbekar, Esra; Yetim, Hasan

    2014-02-01

    This study was carried out for the characterization and discrimination of the indigenous Gram positive, catalase-positive cocci (GCC) population in sucuk, a traditional Turkish dry-fermented sausage. Sucuk samples, produced by the traditional method without starter culture were collected from 8 local producers in Kayseri/Turkey and a total of 116 GCC isolates were identified by using different molecular techniques. Two different molecular fingerprinting methods; namely, randomly amplified polymorphic DNA-PCR (RAPD-PCR) and repetitive extragenic palindrome-PCR (rep-PCR), were used for the clustering of isolates and identification at species level was carried out by full length sequencing of 16S rDNA. Combining the results obtained from molecular fingerprinting and 16S rDNA sequencing showed that the dominant GCC species isolated from the sucuk samples was Staphylococcus saprophyticus followed by Staphylococcus succinus and Staphylococcus equorum belonging to the Staphylococcus genus. Real-time PCR DNA melting curve analysis and high-resolution melting (HRM) analysis targeting the V1 + V3 regions of 16S rDNA were also applied for the discrimination of isolates belonging to different species. It was observed statistically different Tm values and species-specific HRM profiles for all except 2 species (S. saprophyticus and Staphylococcus xylosus) that have high 16S rDNA sequence similarity. The combination of rep-PCR and/or PCR-RAPD with 16S rRNA gene sequencing was an efficient approach for the characterization and identification of the GCC population in spontaneously fermented sucuk. On the other hand, intercalating dye assays were found to be a simple and very promising technique for the differentiation of the GCC population at species level.

  15. Molecular identification and characterization of Anaplasma platys and Ehrlichia canis in dogs in Mexico.

    PubMed

    Almazán, Consuelo; González-Álvarez, Vicente H; Fernández de Mera, Isabel G; Cabezas-Cruz, Alejandro; Rodríguez-Martínez, Rafael; de la Fuente, José

    2016-03-01

    The tick-borne pathogens Ehrlichia canis and Anaplasma platys are the causative agents of canine monocytic ehrlichiosis (CME) and canine cyclic thrombocytopenia (CCT). Although molecular evidence of E. canis has been shown, phylogenetic analysis of this pathogen has not been performed and A. platys has not been identified in Mexico, where the tick vector Rhipicephalus sanguineus sensu lato (s.l.) is common. The aim of this research was to screen, identify and characterize E. canis and A. platys by PCR and phylogenetic analysis in dogs from La Comarca Lagunera, a region formed by three municipalities, Torreon, Gomez-Palacio and Lerdo, in the Northern states of Coahuila and Durango, Mexico. Blood samples and five engorged R. sanguineus s.l. ticks per animal were collected from 43 females and 57 male dogs presented to veterinary clinics or lived in the dog shelter from La Comarca Lagunera. All the sampled dogs were apparently healthy and PCR for Anaplasma 16S rRNA, Ehrlichia 16S rRNA, and E. canis trp36 were performed. PCR products were sequenced and used for phylogenetic analysis. PCR products were successfully amplified in 31% of the samples using primers for Anaplasma 16S rRNA, while 10% and 4% amplified products using primers for Ehrlichia 16S rRNA and E. canis trp36 respectively. Subsequent sequencing and phylogenetic analyses of these products showed that three samples corresponded to A. platys and four to E. canis. Based on the analysis of trp36 we confirmed that the E. canis strains isolated from Mexico belong to a conservative clade of E. canis and are closely related to strains from USA. In conclusion, this is the first molecular identification of A. platys and the first molecular characterization and phylogenetic study of both A. platys and E. canis in dogs in Mexico. PMID:26615872

  16. Application of different molecular techniques for characterization of catalase-positive cocci isolated from sucuk.

    PubMed

    Kesmen, Zülal; Yarimcam, Burcu; Aslan, Hakiye; Ozbekar, Esra; Yetim, Hasan

    2014-02-01

    This study was carried out for the characterization and discrimination of the indigenous Gram positive, catalase-positive cocci (GCC) population in sucuk, a traditional Turkish dry-fermented sausage. Sucuk samples, produced by the traditional method without starter culture were collected from 8 local producers in Kayseri/Turkey and a total of 116 GCC isolates were identified by using different molecular techniques. Two different molecular fingerprinting methods; namely, randomly amplified polymorphic DNA-PCR (RAPD-PCR) and repetitive extragenic palindrome-PCR (rep-PCR), were used for the clustering of isolates and identification at species level was carried out by full length sequencing of 16S rDNA. Combining the results obtained from molecular fingerprinting and 16S rDNA sequencing showed that the dominant GCC species isolated from the sucuk samples was Staphylococcus saprophyticus followed by Staphylococcus succinus and Staphylococcus equorum belonging to the Staphylococcus genus. Real-time PCR DNA melting curve analysis and high-resolution melting (HRM) analysis targeting the V1 + V3 regions of 16S rDNA were also applied for the discrimination of isolates belonging to different species. It was observed statistically different Tm values and species-specific HRM profiles for all except 2 species (S. saprophyticus and Staphylococcus xylosus) that have high 16S rDNA sequence similarity. The combination of rep-PCR and/or PCR-RAPD with 16S rRNA gene sequencing was an efficient approach for the characterization and identification of the GCC population in spontaneously fermented sucuk. On the other hand, intercalating dye assays were found to be a simple and very promising technique for the differentiation of the GCC population at species level. PMID:24410408

  17. Molecular Characterization of UpaB and UpaC, Two New Autotransporter Proteins of Uropathogenic Escherichia coli CFT073

    PubMed Central

    Allsopp, Luke P.; Beloin, Christophe; Ulett, Glen C.; Valle, Jaione; Totsika, Makrina; Sherlock, Orla; Ghigo, Jean-Marc

    2012-01-01

    Uropathogenic Escherichia coli (UPEC) is the primary cause of urinary tract infection (UTI) in the developed world. The major factors associated with virulence of UPEC are fimbrial adhesins, which mediate specific attachment to host receptors and trigger innate host responses. Another group of adhesins is represented by the autotransporter (AT) subgroup of proteins. The genome-sequenced prototype UPEC strain CFT073 contains 11 putative AT-encoding genes. In this study, we have performed a detailed molecular characterization of two closely related AT adhesins from CFT073: UpaB (c0426) and UpaC (c0478). PCR screening revealed that the upaB and upaC AT-encoding genes are common in E. coli. The upaB and upaC genes were cloned and characterized in a recombinant E. coli K-12 strain background. This revealed that they encode proteins located at the cell surface but possess different functional properties: UpaB mediates adherence to several ECM proteins, while UpaC expression is associated with increased biofilm formation. In CFT073, upaB is expressed while upaC is transcriptionally repressed by the global regulator H-NS. In competitive colonization experiments employing the mouse UTI model, CFT073 significantly outcompeted its upaB (but not upaC) isogenic mutant strain in the bladder. This attenuated phenotype was also observed in single-challenge experiments, where deletion of the upaB gene in CFT073 significantly reduced early colonization of the bladder. PMID:21930758

  18. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 7 - Pathogenesis and Molecular Biology.

    PubMed

    Robinson, L; Knight-Jones, T J D; Charleston, B; Rodriguez, L L; Gay, C G; Sumption, K J; Vosloo, W

    2016-06-01

    We assessed research knowledge gaps in the fields of FMDV (foot-and-mouth disease virus) pathogenesis and molecular biology by performing a literature review (2011-15) and collecting research updates (2014) from 33 institutes from across the world. Findings were used to identify priority areas for future research. There have been important advances in FMDV pathogenesis; FMDV remains in lymph nodes of many recovered animals that otherwise do not appear persistently infected, even in species previously not associated with the carrier state. Whether virus retention helps maintain host immunity and/or virus survival is not known. Studies of FMDV pathogenesis in wildlife have provided insights into disease epidemiology, in endemic and epidemic settings. Many aspects of FMDV infection and virus entry remain unknown; however, at the cellular level, we know that expression level and availability of integrins (that permit viral entry), rate of clearance of infected cells and strength of anti-viral type I IFN (interferon) response are key determinants of tissue tropism. Extending findings to improved understanding of transmission requires a standardized approach and adoption of natural routes of infection during experimental study. There has been recognition of the importance of autophagosomes for FMDV entry into the cytoplasm following cell surface receptor binding, and that distinct internal cellular membranes are exploited for viral replication and immune evasion. New roles for viral proteins in blocking type I IFN production and downstream signalling have been identified facilitating research in anti-viral therapeutics. We know more about how infection affects cell protein expression, and research into molecular determinants of capsid stability has aided the development of stable vaccines. We have an expanding knowledge of viral and host molecular determinates of virulence and infectiousness, and of how phylogenetics may be used to estimate vaccine match and strain

  19. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 7 - Pathogenesis and Molecular Biology.

    PubMed

    Robinson, L; Knight-Jones, T J D; Charleston, B; Rodriguez, L L; Gay, C G; Sumption, K J; Vosloo, W

    2016-06-01

    We assessed research knowledge gaps in the fields of FMDV (foot-and-mouth disease virus) pathogenesis and molecular biology by performing a literature review (2011-15) and collecting research updates (2014) from 33 institutes from across the world. Findings were used to identify priority areas for future research. There have been important advances in FMDV pathogenesis; FMDV remains in lymph nodes of many recovered animals that otherwise do not appear persistently infected, even in species previously not associated with the carrier state. Whether virus retention helps maintain host immunity and/or virus survival is not known. Studies of FMDV pathogenesis in wildlife have provided insights into disease epidemiology, in endemic and epidemic settings. Many aspects of FMDV infection and virus entry remain unknown; however, at the cellular level, we know that expression level and availability of integrins (that permit viral entry), rate of clearance of infected cells and strength of anti-viral type I IFN (interferon) response are key determinants of tissue tropism. Extending findings to improved understanding of transmission requires a standardized approach and adoption of natural routes of infection during experimental study. There has been recognition of the importance of autophagosomes for FMDV entry into the cytoplasm following cell surface receptor binding, and that distinct internal cellular membranes are exploited for viral replication and immune evasion. New roles for viral proteins in blocking type I IFN production and downstream signalling have been identified facilitating research in anti-viral therapeutics. We know more about how infection affects cell protein expression, and research into molecular determinants of capsid stability has aided the development of stable vaccines. We have an expanding knowledge of viral and host molecular determinates of virulence and infectiousness, and of how phylogenetics may be used to estimate vaccine match and strain

  20. Characterization factors for terrestrial acidification at the global scale: a systematic analysis of spatial variability and uncertainty.

    PubMed

    Roy, Pierre-Olivier; Azevedo, Ligia B; Margni, Manuele; van Zelm, Rosalie; Deschênes, Louise; Huijbregts, Mark A J

    2014-12-01

    Characterization factors (CFs) are used in life cycle assessment (LCA) to quantify the potential impact per unit of emission. CFs are obtained from a characterization model which assess the environmental mechanisms along the cause-effect chain linking an emission to its potential damage on a given area of protection, such as loss in ecosystem quality. Up to now, CFs for acidifying emissions did not cover the global scale and were only representative of their characterization model geographical scope. Consequently, current LCA practices implicitly assume that all emissions from a global supply chain occur within the continent referring to the characterization method geographical scope. This paper provides worldwide 2°×2.5° spatially-explicit CFs, representing the change in relative loss of terrestrial vascular plant species due to an emission change of nitrogen oxides (NOx), ammonia (NH3) and sulfur dioxide (SO2). We found that spatial variability in the CFs is much larger compared to statistical uncertainty (six orders of magnitude vs. two orders of magnitude). Spatial variability is mainly caused by the atmospheric fate factor and soil sensitivity factor, while the ecological effect factor is the dominant contributor to the statistical uncertainty. The CFs provided in our study allow the worldwide spatially explicit evaluation of life cycle impacts related to acidifying emissions. This opens the door to evaluate regional life cycle emissions of different products in a global economy.

  1. Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle.

    PubMed

    Maalcke, Wouter J; Reimann, Joachim; de Vries, Simon; Butt, Julea N; Dietl, Andreas; Kip, Nardy; Mersdorf, Ulrike; Barends, Thomas R M; Jetten, Mike S M; Keltjens, Jan T; Kartal, Boran

    2016-08-12

    Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms. PMID:27317665

  2. Molecular and biochemical characterizations of a new low-temperature active mannanase.

    PubMed

    Zhang, Rui; Zhou, Junpei; Gao, Yajie; Guan, Yaping; Li, Junjun; Tang, Xianghua; Xu, Bo; Ding, Junmei; Huang, Zunxi

    2015-11-01

    A mannanase-coding gene was cloned from Sphingobacterium sp. GN25 isolated from the feces of Grus nigricollis. The gene encodes a 371-residue polypeptide (ManAGN25) showing less than 74 % identity with a number of hypothetical proteins and putative glucanases and mannanases. Before experiment's performance, ManAGN25 was predicted to be a low-temperature active mannanase based on the molecular characterization, including (1) ManAGN25 shared the highest identity of 41.1 % with the experimentally verified low-temperature active mannanase (ManAJB13) from Sphingomonas sp. JB13; (2) compared with their mesophilic and thermophilic counterparts, ManAGN25 and ManAJB13 had increased number of amino acid residues around their catalytic sites; (3) these increased number of amino acid residues built longer loops, more α-helices, and larger total accessible surface area and packing volume. Then the experiments of biochemical characterization verified that the purified recombinant ManAGN25 is a low-temperature active mannanase: the enzyme showed apparently optimal activity at 35-40 °C and retained 78.2, 44.8, and 15.0 % of its maximum activity when assayed at 30, 20, and 10 °C, respectively; the half-life of the enzyme was approximately 60 min at 37 °C; the enzyme presented a K m of 4.2 mg/ml and a k cat of 0.4/s in McIlvaine buffer (pH 7.0) at 35 °C using locust bean gum as the substrate; and the activation energy for hydrolysis of locust bean gum by the enzyme was 36.0 kJ/mol. This study is the first to report the molecular and biochemical characterizations of a mannanase from a strain. PMID:25868895

  3. Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences.

    PubMed

    Amor, Nabil; Farjallah, Sarra; Salem, Mohamed; Lamine, Dia Mamadou; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

    2011-10-01

    Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n=60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene. Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries.

  4. Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues.

    PubMed

    Almeida, Tânia; Menéndez, Esther; Capote, Tiago; Ribeiro, Teresa; Santos, Conceição; Gonçalves, Sónia

    2013-01-15

    The molecular processes associated with cork development in Quercus suber L. are poorly understood. A previous molecular approach identified a list of genes potentially important for cork formation and differentiation, providing a new basis for further molecular studies. This report is the first molecular characterization of one of these candidate genes, QsMYB1, coding for an R2R3-MYB transcription factor. The R2R3-MYB gene sub-family has been described as being involved in the phenylpropanoid and lignin pathways, both involved in cork biosynthesis. The results showed that the expression of QsMYB1 is putatively mediated by an alternative splicing (AS) mechanism that originates two different transcripts (QsMYB1.1 and QsMYB1.2), differing only in the 5'-untranslated region, due to retention of the first intron in one of the variants. Moreover, within the retained intron, a simple sequence repeat (SSR) was identified. The upstream regulatory region of QsMYB1 was extended by a genome walking approach, which allowed the identification of the putative gene promoter region. The relative expression pattern of QsMYB1 transcripts determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR) revealed that both transcripts were up-regulated in cork tissues; the detected expression was several times higher in newly formed cork harvested from trees producing virgin, second or reproduction cork when compared with wood. Moreover, the expression analysis of QsMYB1 in several Q. suber organs showed very low expression in young branches and roots, whereas in leaves, immature acorns or male flowers, no expression was detected. These preliminary results suggest that QsMYB1 may be related to secondary growth and, in particular, with the cork biosynthesis process with a possible alternative splicing mechanism associated with its regulatory function.

  5. Clinical and Molecular Characterization of Patients with Mucopolysaccharidosis Type I in an Algerian Series

    PubMed Central

    Tebani, Abdellah; Zanoutene-Cheriet, Lahouaria; Adjtoutah, Zoubir; Abily-Donval, Lenaig; Brasse-Lagnel, Carole; Laquerrière, Annie; Marret, Stephane; Chalabi Benabdellah, Abla; Bekri, Soumeya

    2016-01-01

    Mucopolysaccharidoses (MPS’s) represent a subgroup of lysosomal storage diseases related to a deficiency of enzymes that catalyze glycosaminoglycans degradation. Mucopolysaccharidosis type I (MPS I) is a rare autosomal recessive disorder caused by a deficiency of α-l-iduronidase encoded by the IDUA gene. Partially degraded heparan sulfate and dermatan sulfate accumulate progressively and lead to multiorgan dysfunction and damage. The aim of this study is to describe the clinical, biochemical, and molecular characteristics of 13 Algerian patients from 11 distinct families. MPS I diagnosis was confirmed by molecular study of the patients’ IDUA gene. Clinical features at the diagnosis and during the follow-up are reported. Eighty-four percent of the studied patients presented with a mild clinical phenotype. Molecular study of the IDUA gene allowed the characterization of four pathological variations at the homozygous or compound heterozygote status: IDUA NM_00203.4:c.1598C>G-p.(Pro533Arg) in 21/26 alleles, IDUA NM_00203.4:c.532G>A-p.(Glu178Lys) in 2/26 alleles, IDUA NM_00203.4:c.501C>G-p.(Tyr167*) in 2/26 alleles, and IDUA NM_00203. 4: c.1743C>G-p.(Tyr581*) in 1/26 alleles. This molecular study unveils the predominance of p.(Pro533Arg) variation in our MPS I patients. In this series, the occurrence of some clinical features linked to the Scheie syndrome is consistent with the literature, such as systematic valvulopathies, corneal opacity, and umbilical hernia; however, storage signs, facial dysmorphic features, and hepatomegaly were more frequent in our series. Screening measures for these debilitating diseases in highly consanguineous at-risk populations must be considered a priority health problem. PMID:27196898

  6. Global assessment of molecularly identified Anisakis Dujardin, 1845 (Nematoda: Anisakidae) in their teleost intermediate hosts.

    PubMed

    Kuhn, Thomas; Hailer, Frank; Palm, Harry W; Klimpel, Sven

    2013-05-01

    Here, we present the ITS ribosomal DNA (rDNA) sequence data on 330 larvae of nematodes of the genus Anisakis Dujardin, 1845 collected from 26 different bony fish species from 21 sampling locations and different climatic zones. New host records are provided for Anisakis simplex (Rudolphi, 1809) sensu stricto (s.s.) and A. pegreffli Campana-Rouget et Biocca, 1955 from Anoplopoma fimbria (Pallas) (Santa Barbara, East Pacific), A. typica (Diesing, 1860) from Caesio cuning (Bloch), Lepturacanthus savala (Cuvier) and Katsuwonus pelamis (Linnaeus) (Indonesia, West Pacific), A. simplex s.s. from Cololabis saira (Brevoort) (Hawaii, Central Pacific), A. simplex C of Nascetti et al. (1986) from Sebastolobus alascanus Bean (Santa Barbara, East Pacific) and A. physeteris Baylis, 1923 from Synaphobranchus kaupii Johnson (Namibia, East Atlantic). Comparison with host records from 60 previous molecular studies of Anisakis species reveals the teleost host range so far recorded for the genus. Perciform (57 species) and gadiform (21) fishes were the most frequently infected orders, followed by pleuronectiforms (15) and scorpaeniforms (15). Most commonly infected fish families were Scombridae (12), Gadidae (10), Carangidae (8) and Clupeidae (7), with Merluccius merluccius (Linnaeus) alone harbouring eight Anisakis species. Different intermediate host compositions implicate differing life cycles for the so far molecularly identified Anisakis sibling species. PMID:23724731

  7. Pyrolysis-Molecular Beam Mass Spectrometry to Characterize Soil Organic Matter Composition in Chemically Isolated Fractions from Differing Land Uses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Questions concerning the role of soil organic matter (SOM) in soil fertility, ecosystem functioning and global change requires knowledge of the controls on SOM stabilization and their interactions. Pyrolysis molecular beam mass spectrometry (py-MBMS) provides a powerful and rapid means of characteri...

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

    PubMed

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

    2014-12-01

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

  9. Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran, 2014-2015.

    PubMed

    Najafi, Hamideh; Langeroudi, Arash Ghalyanchi; Hashemzadeh, Masoud; Karimi, Vahid; Madadgar, Omid; Ghafouri, Seyed Ali; Maghsoudlo, Hossein; Farahani, Reza Khaltabadi

    2016-01-01

    Infectious bronchitis (IB) is a viral avian disease with economic importance in the world, including Iran. S1 gene sequencing has been used for molecular epidemiological studies and genotypic characterization of infectious bronchitis virus (IBV). A total of 118 IBV isolates were obtained from tissue samples from chickens with clinically suspected IB from Iranian broiler farms (eight provinces, 200 samples). The isolates were confirmed by real-time polymerase chain reaction (PCR) and characterized by sequencing the spike glycoprotein gene. The isolates formed six distinct phylogenetic groups (IS/1494/06 [Var2] like, 4/91-like, IS/720-like, QX-like, IR-1 and Mass-like) that were related to variants isolated in the region. The most frequently detected viruses were of the Var2-like (IS/1494/06-like) genotype, with an overall prevalence of 34 %. Twenty-one percent of the isolates formed a cluster together with the 4/91 IBV type, 10 % were of the QX genotype, and 8 % were of the IS/720 genotype. In addition, 4 % and 3 % of the isolates belonged to the Massachusetts and IR-1 genotype, respectively. For the first time, we have isolated and characterized IBV variants from broiler farms in different provinces of Iran. This study demonstrates a constant evolution of IBV in Iran, demonstrating the need for continuous monitoring and development of new vaccines based on indigenous viruses.

  10. Morphological and molecular characterization of Fusarium spp pathogenic to pecan tree in Brazil.

    PubMed

    Lazarotto, M; Milanesi, P M; Muniz, M F B; Reiniger, L R S; Beltrame, R; Harakava, R; Blume, E

    2014-11-11

    The occurrence of Fusarium spp associated with pecan tree (Carya illinoinensis) diseases in Brazil has been observed in recent laboratory analyses in Rio Grande do Sul State. Thus, in this study, we i) obtained Fusarium isolates from plants with disease symptoms; ii) tested the pathogenicity of these Fusarium isolates to pecan; iii) characterized and grouped Fusarium isolates that were pathogenic to the pecan tree based on morphological characteristics; iv) identified Fusarium spp to the species complex level through TEF-1α sequencing; and v) compared the identification methods used in the study. Fifteen isolates collected from the inflorescences, roots, and seeds of symptomatic plants (leaf necrosis or root rot) were used for pathogenicity tests. Morphological characterization was conducted using only pathogenic isolates, for a total of 11 isolates, based on the mycelial growth rate, sporulation, colony pigmentation, and conidial length and width variables. Pathogenic isolates were grouped based on morphological characteristics, and molecular characterization was performed by sequencing TEF-1α genes. Pathogenic isolates belonging to the Fusarium chlamydosporum species complex, Fusarium graminearum species complex, Fusarium proliferatum, and Fusarium oxysporum were identified based on the TEF-1α region. Morphological characteristics were used to effectively differentiate isolates and group the isolates according to genetic similarity, particularly conidial width, which emerged as a key morphological descriptor in this study.

  11. 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

  12. Morphological and molecular characterization of Fusarium spp pathogenic to pecan tree in Brazil.

    PubMed

    Lazarotto, M; Milanesi, P M; Muniz, M F B; Reiniger, L R S; Beltrame, R; Harakava, R; Blume, E

    2014-01-01

    The occurrence of Fusarium spp associated with pecan tree (Carya illinoinensis) diseases in Brazil has been observed in recent laboratory analyses in Rio Grande do Sul State. Thus, in this study, we i) obtained Fusarium isolates from plants with disease symptoms; ii) tested the pathogenicity of these Fusarium isolates to pecan; iii) characterized and grouped Fusarium isolates that were pathogenic to the pecan tree based on morphological characteristics; iv) identified Fusarium spp to the species complex level through TEF-1α sequencing; and v) compared the identification methods used in the study. Fifteen isolates collected from the inflorescences, roots, and seeds of symptomatic plants (leaf necrosis or root rot) were used for pathogenicity tests. Morphological characterization was conducted using only pathogenic isolates, for a total of 11 isolates, based on the mycelial growth rate, sporulation, colony pigmentation, and conidial length and width variables. Pathogenic isolates were grouped based on morphological characteristics, and molecular characterization was performed by sequencing TEF-1α genes. Pathogenic isolates belonging to the Fusarium chlamydosporum species complex, Fusarium graminearum species complex, Fusarium proliferatum, and Fusarium oxysporum were identified based on the TEF-1α region. Morphological characteristics were used to effectively differentiate isolates and group the isolates according to genetic similarity, particularly conidial width, which emerged as a key morphological descriptor in this study. PMID:25501150

  13. Molecular Characterization of Circulating Plasma Cells in Patients with Active Systemic Lupus Erythematosus

    PubMed Central

    Lugar, Patricia L.; Love, Cassandra; Grammer, Amrie C.; Dave, Sandeep S.; Lipsky, Peter E.

    2012-01-01

    Systemic lupus erythematosus (SLE) is a generalized autoimmune disease characterized by abnormal B cell activation and the occurrence of increased frequencies of circulating plasma cells (PC). The molecular characteristics and nature of circulating PC and B cells in SLE have not been completely characterized. Microarray analysis of gene expression was used to characterize circulating PC in subjects with active SLE. Flow cytometry was used to sort PC and comparator B cell populations from active SLE blood, normal blood and normal tonsil. The gene expression profiles of the sorted B cell populations were then compared. SLE PC exhibited a similar gene expression signature as tonsil PC. The differences in gene expression between SLE PC and normal tonsil PC and tonsil plasmablasts (PB) suggest a mature Ig secreting cell phenotype in the former population. Despite this, SLE PC differed in expression of about half the genes from previously published gene expression profiles of normal bone marrow PC, indicating that these cells had not achieved a fully mature status. Abnormal expression of several genes, including CXCR4 and S1P1, suggests a mechanism for the persistence of SLE PC in the circulation. All SLE B cell populations revealed an interferon (IFN) gene signature previously only reported in unseparated SLE peripheral blood mononuclear cells. These data indicate that SLE PC are a unique population of Ig secreting cells with a gene expression profile indicative of a mature, but not fully differentiated phenotype. PMID:23028528

  14. Molecular characterization of circulating plasma cells in patients with active systemic lupus erythematosus.

    PubMed

    Lugar, Patricia L; Love, Cassandra; Grammer, Amrie C; Dave, Sandeep S; Lipsky, Peter E

    2012-01-01

    Systemic lupus erythematosus (SLE) is a generalized autoimmune disease characterized by abnormal B cell activation and the occurrence of increased frequencies of circulating plasma cells (PC). The molecular characteristics and nature of circulating PC and B cells in SLE have not been completely characterized. Microarray analysis of gene expression was used to characterize circulating PC in subjects with active SLE. Flow cytometry was used to sort PC and comparator B cell populations from active SLE blood, normal blood and normal tonsil. The gene expression profiles of the sorted B cell populations were then compared. SLE PC exhibited a similar gene expression signature as tonsil PC. The differences in gene expression between SLE PC and normal tonsil PC and tonsil plasmablasts (PB) suggest a mature Ig secreting cell phenotype in the former population. Despite this, SLE PC differed in expression of about half the genes from previously published gene expression profiles of normal bone marrow PC, indicating that these cells had not achieved a fully mature status. Abnormal expression of several genes, including CXCR4 and S1P(1), suggests a mechanism for the persistence of SLE PC in the circulation. All SLE B cell populations revealed an interferon (IFN) gene signature previously only reported in unseparated SLE peripheral blood mononuclear cells. These data indicate that SLE PC are a unique population of Ig secreting cells with a gene expression profile indicative of a mature, but not fully differentiated phenotype.

  15. Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.

    PubMed

    Brown, J K

    2000-11-01

    Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a

  16. Communication: Global minimum search of Ag{sub 10}{sup +} with molecular beam optical spectroscopy

    SciTech Connect

    Shayeghi, A. Schäfer, R.; Johnston, R. L.

    2014-11-14

    The present study is focused on the optical properties of the Ag{sub 10}{sup +} cluster in the photon energy range ℏω = 1.9–4.4 eV. Absorption spectra are recorded by longitudinal molecular beam depletion spectroscopy and compared to optical response calculations using time-dependent density functional theory. Several cluster isomers obtained by the new pool-based parallel implementation of the Birmingham Cluster Genetic Algorithm, coupled with density functional theory, are used in excited state calculations. The experimental observations, together with additional simulations of ion mobilities for the several geometries found within this work using different models, clearly identify the ground state isomer of Ag{sub 10}{sup +} to be composed of two orthogonal interpenetrating pentagonal bipyramids, having overall D{sub 2d} symmetry.

  17. Bipolaris sorokiniana, a cereal pathogen of global concern: cytological and molecular approaches towards better controldouble dagger.

    PubMed

    Kumar, Jagdish; Schäfer, Patrick; Hückelhoven, Ralph; Langen, Gregor; Baltruschat, Helmut; Stein, Elke; Nagarajan, Subramaniam; Kogel, Karl-Heinz

    2002-07-01

    Summary Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is the causal agent of common root rot, leaf spot disease, seedling blight, head blight, and black point of wheat and barley. The fungus is one of the most serious foliar disease constraints for both crops in warmer growing areas and causes significant yield losses. High temperature and high relative humidity favour the outbreak of the disease, in particular in South Asia's intensive 'irrigated wheat-rice' production systems. In this article, we review the taxonomy and worldwide distribution, as well as strategies to counteract the disease as an emerging threat to cereal production systems. We also review the current understanding of the cytological and molecular aspects of the interaction of the fungus with its cereal hosts, which makes B. sorokiniana a model organism for studying plant defence responses to hemibiotrophic pathogens. The contrasting roles of cell death and H(2)O(2) generation in plant defence during biotrophic and necrotrophic fungal growth phases are discussed.

  18. A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches.

    PubMed

    Che, Yanli; Wang, Dong; Shi, Yan; Du, Xiaohong; Zhao, Yongquan; Lo, Nathan; Wang, Zongqing

    2016-05-01

    Cryptocercus is a genus of sub-social wood-feeding cockroaches that represents the sister group to the eusocial termites. We generated mitochondrial (12S+16S rRNA, COII), nuclear (28S rRNA) and Blattbacterium endosymbiont (16S+23S rRNA) sequence data for 8 new Chinese species, and combined these with previously available data to undertake the most extensive analysis of phylogenetic relationships within the genus to date. As expected, phylogenetic relationships among Blattabacterium strains were found to be congruent with those of their hosts. Three major clades were found to exist in Asian populations, one representing taxa from the Hengduan mountains in Southwestern China, a second including taxa from Russia, Korea, Northeastern China, and Yunnan in the Hengduan Mountains, and a third including taxa from the Qinling Mountains and Daba Mountains in Central China. A molecular dating analysis using 7 termite fossils to calibrate the molecular clock indicated that the divergence of American and Asian Cryptocercus occurred 55.09Ma (41.55-72.28Ma 95% CI), and that the radiations of American and Asian taxa occurred 28.48Ma (20.83-37.95Ma 95% CI) and 20.97Ma (15.78-27.21Ma 95% CI) respectively. Reconstruction of ancestral geographic distributions using S-DIVA suggested Cryptocercus was originally distributed across both continents, as opposed to ancestral migration of Cryptocercus from one continent to the other. The last common ancestor of Asian Cryptocercus was inferred to have existed in Central China. An examination of male chromosome numbers in Asian Cryptocercus showed that diploid numbers vary from 2n=15 to 2n=41, and indicates the presence of eight new species. Our study represents the most comprehensive phylogenetic and biogeographic study yet performed for this important group of cockroaches.

  19. A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches.

    PubMed

    Che, Yanli; Wang, Dong; Shi, Yan; Du, Xiaohong; Zhao, Yongquan; Lo, Nathan; Wang, Zongqing

    2016-05-01

    Cryptocercus is a genus of sub-social wood-feeding cockroaches that represents the sister group to the eusocial termites. We generated mitochondrial (12S+16S rRNA, COII), nuclear (28S rRNA) and Blattbacterium endosymbiont (16S+23S rRNA) sequence data for 8 new Chinese species, and combined these with previously available data to undertake the most extensive analysis of phylogenetic relationships within the genus to date. As expected, phylogenetic relationships among Blattabacterium strains were found to be congruent with those of their hosts. Three major clades were found to exist in Asian populations, one representing taxa from the Hengduan mountains in Southwestern China, a second including taxa from Russia, Korea, Northeastern China, and Yunnan in the Hengduan Mountains, and a third including taxa from the Qinling Mountains and Daba Mountains in Central China. A molecular dating analysis using 7 termite fossils to calibrate the molecular clock indicated that the divergence of American and Asian Cryptocercus occurred 55.09Ma (41.55-72.28Ma 95% CI), and that the radiations of American and Asian taxa occurred 28.48Ma (20.83-37.95Ma 95% CI) and 20.97Ma (15.78-27.21Ma 95% CI) respectively. Reconstruction of ancestral geographic distributions using S-DIVA suggested Cryptocercus was originally distributed across both continents, as opposed to ancestral migration of Cryptocercus from one continent to the other. The last common ancestor of Asian Cryptocercus was inferred to have existed in Central China. An examination of male chromosome numbers in Asian Cryptocercus showed that diploid numbers vary from 2n=15 to 2n=41, and indicates the presence of eight new species. Our study represents the most comprehensive phylogenetic and biogeographic study yet performed for this important group of cockroaches. PMID:26876638

  20. Global characterization and monitoring of forest cover using Landsat data: opportunities and challanges

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The compilation of global Landsat data-sets and the ever-lowering costs of computing now make it feasible to monitor the Earth’s land cover at Landsat resolutions of 30 m. In this article, we describe the methods to create global products of forest cover and cover change at Landsat resolutions. Neve...

  1. Molecular characterization of a ranavirus isolated from largemouth bass Micropterus salmoides.

    PubMed

    Mao, J; Wang, J; Chinchar, G D; Chinchar, V G

    1999-07-30

    An iridovirus, isolated from largemouth bass Micropterus salmoides following a die-off among adult fish and provisionally designated largemouth bass virus (LMBV), was characterized by analysis of viral protein synthesis in infected cells, viral DNA restriction fragment length polymorphisms (RFLP), and sequence determination of the major capsid protein and viral DNA methyltransferase genes. All 3 approaches yielded results consistent with the suggestion that LMBV was a member of the genus Ranavirus. Moreover, LMBV was nearly identical to 2 isolates from Southeast Asia which had been previously detected in imported ornamental fish. It remains to be determined whether infection of largemouth bass resulted from exposure to an imported virus, or whether the presence of similar viruses in southeast Asia and the southeastern United States indicates that iridovirus species are not geographically limited as suggested earlier, but rather globally distributed.

  2. Molecular phylogeography of canine distemper virus: Geographic origin and global spreading.

    PubMed

    Panzera, Yanina; Sarute, Nicolás; Iraola, Gregorio; Hernández, Martín; Pérez, Ruben

    2015-11-01

    Canine distemper virus (CDV) (Paramyxoviridae-Morbillivirus) is a worldwide spread virus causing a fatal systemic disease in a broad range of carnivore hosts. In this study we performed Bayesian inferences using 208 full-length hemagglutinin gene nucleotide sequences isolated in 16 countries during 37 years (1975-2011). The estimated time to the most recent common ancestor suggested that current CDV strains emerged in the United States in the 1880s. This ancestor diversified through time into two ancestral clades, the current America 1 lineage that recently spread to Asia, and other ancestral clade that diversified and spread worldwide to originate the remaining eight lineages characterized to date. The spreading of CDV was characterized by several migratory events with posterior local differentiation, and expansion of the virus host range. A significant genetic flow between domestic and wildlife hosts is displayed; being domestic hosts the main viral reservoirs worldwide. This study is an extensive and integrative description of spatio/temporal population dynamics of CDV lineages that provides a novel evolutionary paradigm about the origin and dissemination of the current strains of the virus.

  3. Ectomycorrhizal fungi increase soil carbon storage: molecular signatures of mycorrhizal competition driving soil C storage at global scale

    NASA Astrophysics Data System (ADS)

    Averill, C.; Barry, B. K.; Hawkes, C.

    2015-12-01

    Soil carbon storage and decay is regulated by the activity of free-living decomposer microbes, which can be limited by nitrogen availability. Many plants associate with symbiotic ectomycorrhizal fungi on their roots, which produce nitrogen-degrading enzymes and may be able to compete with free-living decomposers for soil organic nitrogen. By doing so, ectomycorrhizal fungi may able to induce nitrogen limitation and reduce activity of free-living microbial decomposition by mining soil organic nitrogen. The implication is that ectomycorrhizal-dominated systems should have increased soil carbon storage relative to non-ectomycorrhizal systems, which has been confirmed at a global scale. To investigate these effects, we analyzed 364 globally distributed observations of soil fungal communities using 454 sequencing of the ITS region, along with soil C and N concentrations, climate and chemical data. We assigned operational taxonomic units using the QIIME pipeline and UNITE fungal database and assigned fungal reads as ectomycorrhizal or non-mycorrhizal based on current taxonomic knowledge. We tested for associations between ectomycorrhizal abundance, climate, and soil carbon and nitrogen. Sites with greater soil carbon had quantitatively more ectomycorrhizal fungi within the soil microbial community based on fungal sequence abundance, after accounting for soil nitrogen availability. This is consistent with our hypothesis that ectomycorrhizal fungi induce nitrogen-limitation of free-living decomposers and thereby increase soil carbon storage. The strength of the mycorrhizal effect increased non-linearly with ectomycorrhizal abundance: the greater the abundance, the greater the effect size. Mean annual temperature, potential evapotranspiration, soil moisture and soil pH were also significant predictors in the final AIC selected model. This analysis suggests that molecular data on soil microbial communities can be used to make quantitative biogeochemical predictions. The

  4. Molecular Characterization of a Novel Bovine Viral Diarrhea Virus Isolate SD-15

    PubMed Central

    Zhu, Lisai; Lu, Haibing; Cao, Yufeng; Gai, Xiaochun; Guo, Changming; Liu, Yajing; Liu, Jiaxu; Wang, Xinping

    2016-01-01

    As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China. SD-15 was revealed to be a noncytopathic BVDV, and has a complete genomic sequence of 12,285 nucleotides that contains a large open reading frame encoding 3900 amino acids. Alignment analysis showed that SD-15 has 93.8% nucleotide sequence identity with BVDV ZM-95 isolate, a previous BVDV strain isolated from pigs manifesting clinical signs and lesions resembling to classical swine fever. Phylogenetic analysis clustered SD-15 to a BVDV-1m subgenotype. Analysis of the deduced amino acid sequence of glycoproteins revealed that E2 has several highly conserved and variable regions within BVDV-1 genotypes. An additional N-glycosylation site (240NTT) was revealed exclusively in SD-15-encoded E2 in addition to four potential glycosylation sites (Asn-X-Ser/Thr) shared by all BVDV-1 genotypes. Furthermore, unique amino acid and linear epitope mutations were revealed in SD-15-encoded Erns glycoprotein compared with known BVDV-1 genotype. In conclusion, we have isolated a noncytopathic BVDV-1m strain that is associated with a disease characterized by high morbidity and mortality, revealed the complete genome sequence of the first BVDV-1m virus originated from cattle, and found a unique glycosylation site in E2 and a linear epitope mutation in Erns encoded by SD-15 strain. Those results will broaden the current understanding of BVDV infection and lay a basis for future investigation on SD-15-related pathogenesis. PMID:27764206

  5. Rapid Characterization of Molecular Chemistry, Nutrient Make-Up and Microlocation of Internal Seed Tissue

    SciTech Connect

    Yu,P.; Block, H.; Niu, Z.; Doiron, K.

    2007-01-01

    Wheat differs from corn in biodegradation kinetics and fermentation characteristics. Wheat exhibits a relatively high rate (23% h{sup 01}) and extent (78% DM) of biodegradation, which can lead to metabolic problems such as acidosis and bloat in ruminants. The objective of this study was to rapidly characterize the molecular chemistry of the internal structure of wheat (cv. AC Barrie) and reveal both its structural chemical make-up and nutrient component matrix by analyzing the intensity and spatial distribution of molecular functional groups within the intact seed using advanced synchrotron-powered Fourier transform infrared (FTIR) microspectroscopy. The experiment was performed at the U2B station of the National Synchrotron Light Source at Brookhaven National Laboratory, New York, USA. The wheat tissue was imaged systematically from the pericarp, seed coat, aleurone layer and endosperm under the peaks at {approx}1732 (carbonyl C{double_bond}O ester), 1515 (aromatic compound of lignin), 1650 (amide I), 1025 (non-structural CHO), 1550 (amide II), 1246 (cellulosic material), 1160, 1150, 1080, 930, 860 (all CHO), 3350 (OH and NH stretching), 2928 (CH{sub 2} stretching band) and 2885 cm{sup -1} (CH{sub 3} stretching band). Hierarchical cluster analysis and principal component analysis were applied to analyze the molecular FTIR spectra obtained from the different inherent structures within the intact wheat tissues. The results showed that, with synchrotron-powered FTIR microspectroscopy, images of the molecular chemistry of wheat could be generated at an ultra-spatial resolution. The features of aromatic lignin, structural and non-structural carbohydrates, as well as nutrient make-up and interactions in the seeds, could be revealed. Both principal component analysis and hierarchical cluster analysis methods are conclusive in showing that they can discriminate and classify the different inherent structures within the seed tissue. The wheat exhibited distinguishable

  6. Global analysis of triacylglycerols including oxidized molecular species by reverse-phase high resolution LC/ESI-QTOF MS/MS.

    PubMed

    Ikeda, Kazutaka; Oike, Yuichi; Shimizu, Takao; Taguchi, Ryo

    2009-09-01

    Recently, global analysis of triacylglycerols (TAGs) has become increasingly important in studies of abnormality of lipid metabolism in metabolic syndrome. TAGs consist of various molecular species, caused by their three fatty acyl chains with a large variety of carbon chain lengths and degrees of unsaturation. Therefore, most previously reported methods have been insufficient in global detection of TAGs including their structural isomers and TAGs with oxidized or odd number acyl carbon chain. Here we report an effective method for global analysis of TAG molecular species from complex lipid mixtures of mouse liver and white adipose tissue (WAT) using reverse-phased high resolution liquid chromatography (LC) coupled with electrospray ionization (ESI)-quadrapole/time of flight hybrid mass spectrometer (QTOF-MS). For effective profiling of TAG molecular species, sensitive two-dimensional (2D) maps were constructed and individual structures were correctly identified by the elution profile and MS/MS. As a result, TAGs including their structural isomers and TAGs with an odd number acyl carbon chain were separated and detected effectively on the 2D map as compared with conventional high performance LC. It was also found that our 2D profiling method was useful in searching characteristic molecular species globally. In mouse WAT, novel oxidized TAGs, which were mainly formed by hydroperoxidation of one of their linoleic acyl chains, were effectively detected in comparison with TAG molecular species of mouse liver.

  7. Molecular Characterization of Microbial Communities in a JP-5 Fuel Contaminated Soil

    SciTech Connect

    Barcelona, M.J.; Chang, Y.-J.; Gan, Y.D.; Macnaughton, S.J.; Peacock, A.; Stephen, J.R.; White, D.C.

    1999-04-19

    In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and saturated-soils were taken from cores within, up- and down-gradient of the contaminant plume. Significant differences in biomass and proportion of Gram negative bacteria were found inside and outside the plume. Sequence analysis of DGGE bands from within the spill site suggested dominance by a limited number of phylogenetically diverse bacteria. Used in tandem with pollutant quantification, these molecular techniques should facilitate significant improvements over current assessment procedures for determination of remediation end points.

  8. Molecular characterization of neurally expressing genes in the para sodium channel gene cluster of Drosophila

    SciTech Connect

    Hong, Chang-Sook; Ganetzky, B.

    1996-03-01

    To elucidate the mechanisms regulating expression of para, which encodes the major class of sodium channels in the Drosophila nervous system, we have tried to locate upstream cis-acting regulatory elements by mapping the transcriptional start site and analyzing the region immediately upstream of para in region 14D of the polytene chromosomes. From these studies, we have discovered that the region contains a cluster of neurally expressing genes. Here we report the molecular characterization of the genomic organization of the 14D region and the genes within this region, which are: calnexin (Cnx), actin related protein 14D (Arp14D), calcineurin A 14D (CnnA14D), and chromosome associated protein (Cap). The tight clustering of these genes, their neuronal expression patterns, and their potential functions related to expression, modulation, or regulation of sodium channels raise the possibility that these genes represent a functionally related group sharing some coordinate regulatory mechanism. 76 refs., 11 figs.

  9. Characterizing molecular motion in H2O and H3O+ with dynamical instability statistics

    NASA Astrophysics Data System (ADS)

    Green, Jason R.; Hofer, Thomas S.; Berry, R. Stephen; Wales, David J.

    2011-11-01

    Sets of finite-time Lyapunov exponents characterize the stability and instability of classically chaotic dynamical trajectories. Here we show that their sample distributions can contain subpopulations identifying different types of dynamics. In small isolated molecules these dynamics correspond to distinct elementary motions, such as isomerizations. Exponents are calculated from constant total energy molecular dynamics simulations of H2O and H3O+, modelled with a classical, reactive, all-atom potential. Over a range of total energy, exponent distributions for these systems reveal that phase space exploration is more chaotic near saddles corresponding to isomerization and less chaotic near potential energy minima. This finding contrasts with previous results for Lennard-Jones clusters, and is explained in terms of the potential energy landscape.

  10. Molecular Characterization of Neurally Expressing Genes in the Para Sodium Channel Gene Cluster of Drosophila

    PubMed Central

    Hong, C. S.; Ganetzky, B.

    1996-01-01

    To elucidate the mechanisms regulating expression of para, which encodes the major class of sodium channels in the Drosophila nervous system, we have tried to locate upstream cis-acting regulatory elements by mapping the transcriptional start site and analyzing the region immediately upstream of para in region 14D of the polytene chromosomes. From these studies, we have discovered that the region contains a cluster of neurally expressing genes. Here we report the molecular characterization of the genomic organization of the 14D region and the genes within this region, which are: calnexin (Cnx), actin related protein 14D (Arp14D), calcineurin A 14D (CnnA14D), and chromosome associated protein (Cap). The tight clustering of these genes, their neuronal expression patterns, and their potential functions related to expression, modulation, or regulation of sodium channels raise the possibility that these genes represent a functionally related group sharing some coordinate regulatory mechanism. PMID:8849894

  11. Molecular and antigenic characterization of rabies viruses from Iran identifies variants with distinct epidemiological origins.

    PubMed

    Nadin-Davis, S A; Simani, S; Armstrong, J; Fayaz, A; Wandeler, A I

    2003-08-01

    A molecular epidemiological study of 48 recent rabies isolates recovered from cases reported throughout Iran identified three distinct viral variants, the evolutionary origins of which were identified by phylogenetic comparison with rabies viruses originating from Europe and Asia. Members of group 1 (15 isolates) were recovered from the northern half of the country only, while those of group 2 (31 isolates) were widely dispersed; both groups clustered within the widely disseminated cosmopolitan lineage. The two isolates of group 3 were detected in the northeastern tip of the country only and belonged to the Arctic strain. Rapid variant discrimination tools, employing restriction fragment length polymorphisms applied to amplified fragments of the viral genome, were devised whilst antigenic characterization of representative viruses identified a small panel of monoclonal antibodies that were also discriminatory. The future application of such methods should provide valuable epidemiological information on rabies incidence in Iran. PMID:12948379

  12. Cryptosporidiosis in broiler chickens in Zhejiang Province, China: molecular characterization of oocysts detected in fecal samples.

    PubMed

    Wang, Lengmei; Xue, Xue; Li, Jianqiu; Zhou, Qianjin; Yu, Yingchao; Du, Aifang

    2014-01-01

    Cryptosporidium is one of the most important parasites in poultry, and this pathogen can infect more than 30 avian species. The present study investigated the infection rate of Cryptosporidium among broiler chicken flocks. A total of 385 fecal samples from broiler chickens in 7 regions of Zhejiang Province collected from November 2010 to January 2012 were examined by microscopy. Thirty-eight (10%) samples were positive for Cryptosporidium infection, and 3 genotypes (Cryptosporidium baileyi, Cryptosporidium meleagridis, and avian genotype II) were identified by PCR and sequencing. A phylogenetic tree of the isolates was analyzed. These results suggest that cryptosporidiosis is widespread in poultry in Zhejiang Province, and is a potential threat to public health as well as the economy. This is the first report about the infection rate and molecular characterization of Cryptosporidium in broiler chickens in Zhejiang. PMID:25075975

  13. Allelic diversity and molecular characterization of puroindoline genes in five diploid species of the Aegilops genus.

    PubMed

    Cuesta, Susana; Guzmán, Carlos; Alvarez, Juan B

    2013-11-01

    Grain hardness is an important quality trait in wheat. This trait is related to the variation in, and the presence of, puroindolines (PINA and PINB). This variation can be increased by the allelic polymorphism present in the Aegilops species that are related to wheat. This study evaluated allelic Pina and Pinb gene variability in five diploid species of the Aegilops genus, along with the molecular characterization of the main allelic variants found in each species. This polymorphism resulted in 16 alleles for the Pina gene and 24 alleles for the Pinb gene, of which 10 and 17, respectively, were novel. Diverse mutations were detected in the deduced mature proteins of these alleles, which could influence the hardness characteristics of these proteins. This study shows that the diploid species of the Aegilops genus could be a good source of genetic variability for both Pina and Pinb genes, which could be used in breeding programmes to extend the range of different textures in wheat.

  14. Morphological and molecular characterization of Pratylenchus lentis n. sp. (Nematoda: Pratylenchidae) from Sicily

    PubMed Central

    De Luca, F.; Handoo, Z. A.; Di Vito, M.

    2008-01-01

    Pratylenchus lentis n. sp. parasitizing roots of lentil in Sicily, Italy, is described and illustrated. The new species is characterized by a relatively high lip region with three annuli, mean stylet length of 16 μm, with anteriorly flattened knobs, cylindrical body with a relatively anterior vulva, large and ovoid spermatheca full of sperm, plump tail with truncate, irregularly annulated terminus, and by the presence of males. Molecular ITS-RFLP and sequencing analyses of the new species showed clear differences from other most morphologically similar species, such as P. thornei and P. mediterraneus. Preliminary host range tests revealed that chickpea, pea, faba bean and durum wheat are good hosts of P. lentis n. sp., whereas common bean, alfalfa and barley are less robust hosts and tomato, bell pepper, eggplant, melon and sunflower are poor hosts for the nematode. PMID:19440258

  15. Cryptosporidiosis in broiler chickens in Zhejiang Province, China: molecular characterization of oocysts detected in fecal samples.

    PubMed

    Wang, Lengmei; Xue, Xue; Li, Jianqiu; Zhou, Qianjin; Yu, Yingchao; Du, Aifang

    2014-01-01

    Cryptosporidium is one of the most important parasites in poultry, and this pathogen can infect more than 30 avian species. The present study investigated the infection rate of Cryptosporidium among broiler chicken flocks. A total of 385 fecal samples from broiler chickens in 7 regions of Zhejiang Province collected from November 2010 to January 2012 were examined by microscopy. Thirty-eight (10%) samples were positive for Cryptosporidium infection, and 3 genotypes (Cryptosporidium baileyi, Cryptosporidium meleagridis, and avian genotype II) were identified by PCR and sequencing. A phylogenetic tree of the isolates was analyzed. These results suggest that cryptosporidiosis is widespread in poultry in Zhejiang Province, and is a potential threat to public health as well as the economy. This is the first report about the infection rate and molecular characterization of Cryptosporidium in broiler chickens in Zhejiang.

  16. Detailed molecular characterization of castor oil ethoxylates by liquid chromatography multistage mass spectrometry.

    PubMed

    Nasioudis, Andreas; van Velde, Jan W; Heeren, Ron M A; van den Brink, Oscar F

    2011-10-01

    The molecular characterization of castor oil ethoxylates (CASEOs) was studied by reverse-phase liquid chromatography (RPLC) mass spectrometry (MS) and multistage mass spectrometry (MS(n)). The developed RPLC method allowed the separation of the various CASEO components, and especially, the baseline separation of multiple nominal isobars (same nominal mass) and isomers (same exact mass). MS and MS(n) were used for the determination and structure elucidation of various structures and for the discrimination of the isobars and isomers. Different ionization techniques and adduct ions were also tested for optimization of the MS detection and the MS(n) fragmentation. A unique fragmentation pathway of ricinoleic acid is proposed, which can be used as a marker of the polymerization process and the topology of ethoxylation in the CASEO. In addition, characteristic neutral losses of ricinoleic acid reveal its (terminal or internal) position in the molecule.

  17. Characterization of atomic and molecular impurity sources and transport at the tokamak edge

    SciTech Connect

    Klepper, C.C.; Hogan, J.T.; Hess, W.R.; Guilhem, D.

    1993-12-31

    The characterization of impurity sources in the tokamak edge is challenging because of the highly localized nature of impurity generation. Detailed, spatially resolved, diagnostic information is needed, and three-dimensional (3-D) modeling is required for interpretation. There is also a need for a more extensive atomic and molecular data base for the conditions encountered in this region. The availability of new measurements of photon efficiencies for some relevant hydrocarbon molecules for plasma conditions typical for the tokamak edge and the development of a 3-D Monte Carlo impurities code have enabled the successful modeling of spatially resolved measurements in the vicinity of the pump limiter neutralizer plate and near the inner wall of Tore Supra.

  18. Notes for developing a molecular test for the full characterization of circulating tumor cells

    PubMed Central

    Rossi, Elisabetta; Facchinetti, Antonella

    2015-01-01

    The proved association between the circulating tumor cell (CTC) levels and the patients’ survival parameters has been growing interest to investigate the molecular profile of these neoplastic cells among which hide out precursors capable of initiating a new distant metastatic lesion. The full characterization of the tumor cells in peripheral blood of cancer patients is expected to be of help for understanding and (prospectively) for counteracting the metastatic process. The major hitch that is hampering the successful gaining of this result is the lack of a consensus onto standard operating procedures (SOPs) for performing what we generally define as the “liquid biopsy”. Here we review the more recent acquisitions in the analysis of CTCs and tumor related nucleic acids, looking to the main open questions that are hampering their definitive employ in the routine clinical practice. PMID:26543333

  19. Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents

    NASA Astrophysics Data System (ADS)

    Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang

    2013-05-01

    Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

  20. Molecular Characterization of Nitrogen Containing Organic Compounds in Biomass Burning Aerosols Using High Resolution Mass Spectrometry

    SciTech Connect

    Laskin, Alexander; Smith, Jeffrey S.; Laskin, Julia

    2009-05-13

    Although nitrogen-containing organic compounds (NOC) are important components of atmospheric aerosols, little is known about their chemical compositions. Here we present detailed characterization of the NOC constituents of biomass burning aerosol (BBA) samples using high resolution electrospray ionization mass spectrometry (ESI/MS). Accurate mass measurements combined with MS/MS fragmentation experiments of selected ions were used to assign molecular structures to individual NOC species. Our results indicate that N-heterocyclic alkaloid compounds - species naturally produced by plants and living organisms - comprise a substantial fraction of NOC in BBA samples collected from test burns of five biomass fuels. High abundance of alkaloids in test burns of ponderosa pine - a widespread tree in the western U.S. areas frequently affected by large scale fires - suggests that N-heterocyclic alkaloids in BBA can play a significant role in dry and wet deposition of fixed nitrogen in this region.

  1. Proteomics, metabolomics, and protein interactomics in the characterization of the molecular features of major depressive disorder.

    PubMed

    Martins-de-Souza, Daniel

    2014-03-01

    Omics technologies emerged as complementary strategies to genomics in the attempt to understand human illnesses. In general, proteomics technologies emerged earlier than those of metabolomics for major depressive disorder (MDD) research, but both are driven by the identification of proteins and/or metabolites that can delineate a comprehensive characterization of MDD's molecular mechanisms, as well as lead to the identification of biomarker candidates of all types-prognosis, diagnosis, treatment, and patient stratification. Also, one can explore protein and metabolite interactomes in order to pinpoint additional molecules associated with the disease that had not been picked up initially. Here, results and methodological aspects of MDD research using proteomics, metabolomics, and protein interactomics are reviewed, focusing on human samples.

  2. Molecular and biological characterization of corchorus mottle virus, a new begomovirus from Brazil.

    PubMed

    Blawid, Rosana; Fontenele, Rafaela S; Lacorte, Cristiano; Ribeiro, Simone G

    2013-12-01

    A begomovirus infecting Orinoco jute (Corchorus hirtus) from Brazil was characterized. Molecular analysis revealed a bipartite genomic organization, which is typical of the New World begomoviruses. Sequence analysis and phylogenetic data showed that both genomic components have the closest relationship with abutilon mosaic Brazil virus, with an identity of 87.3 % for DNA-A, indicating that this virus is a member of a new begomovirus species for which the name "Corchorus mottle virus" (CoMoV) is proposed. Sida rhombifolia plants inoculated by biolistics with an infectious clone of CoMoV showed systemic vein chlorosis, mottling and leaf deformation symptoms, while Nicotiana benthamiana and tomato plants had symptomless infection. CoMoV is the first corchorus-infecting begomovirus reported in Brazil. PMID:23812656

  3. Molecular characterization of three Zika flaviviruses obtained from sylvatic mosquitoes in the Central African Republic.

    PubMed

    Berthet, Nicolas; Nakouné, Emmanuel; Kamgang, Basile; Selekon, Benjamin; Descorps-Declère, Stéphane; Gessain, Antoine; Manuguerra, Jean-Claude; Kazanji, Mirdad

    2014-12-01

    Zika virus (ZIKV) is an emerging pathogen belonging to the Spondweni serocomplex within the genus Flavivirus. It has been isolated from several mosquito species. Two lineages of ZIKV have been defined by polyprotein homology. Using high-throughput sequencing, we obtained and characterized three complete genomes of ZIKV isolated between 1976 and 1980 in the Central African Republic. The three viruses were isolated from two species of mosquito, Aedes africanus and Ae. opok. Two sequences from Ae. africanus had 99.9% nucleotide sequence identity and 100% amino acid identity, whereas the complete genome obtained from Ae. opok had 98.3% nucleotide identity and 99.4% amino acid identity with the other two genomes. Phylogenetic analysis based on the amino acid sequence of the polyprotein showed that the three ZIKV strains clustered together but diverged from all other ZIKV strains. Our molecular data suggest that a different subtype of West African ZIKV strains circulated in Aedes species in Central Africa.

  4. The attractive recombinant phytase from Bacillus licheniformis: biochemical and molecular characterization.

    PubMed

    Borgi, Mohamed Ali; Khila, Mouna; Boudebbouze, Samira; Aghajari, Nushin; Szukala, Florette; Pons, Nicolas; Maguin, Emmanuelle; Rhimi, Moez

    2014-07-01

    The phyL gene encoding phytase from the industrial strain Bacillus licheniformis ATCC 14580 (PhyL) was cloned, sequenced, and overexpressed in Escherichia coli. Biochemical characterization demonstrated that the recombinant enzyme has an apparent molecular weight of nearly 42 kDa. Interestingly, this enzyme was optimally active at 70-75 °C and pH 6.5-7.0. This enzyme is distinguishable by the fact that it preserved more than 40 % of its activity at wide range of temperatures from 4 to 85 °C. This new phytase displayed also a high specific activity of 316 U/mg. For its maximal activity and thermostability, this biocatalyst required only 0.6 mM of Ca(2+) ion and exhibited high catalytic efficiency of 8.3 s(-1) μM(-1) towards phytic acid. PMID:24337251

  5. Molecular identification and characterization of peptide: N-glycanase from Schizosaccharomyces pombe

    SciTech Connect

    Xin Fengxue; Wang Shengjun; Song Lei; Liang Quanfeng; Qi Qingsheng

    2008-04-18

    Peptide:N-glycanase (PNGase) is an enzyme responsible for deglycosylation of misfolded glycoproteins in so-called endoplasmic reticulum-associated degradation (ERAD) system. In this study, we reported the molecular identification and characterization of SpPNGase (Schizosaccharomyces pombe PNGase). Enzymatic analysis revealed that SpPNGase deglycosylated the misfolded glycoproteins and distinguished native and denatured high-mannose glycoproteins in vitro. The deglycosylation activity was lost with the addition of chelating agent EDTA and was not restored by re-addition of metal ions. By construction of deletion mutant, we confirmed that N-terminal {alpha}-helix of SpPNGase was responsible for the protein-protein interaction. Combining the results from ternary structure prediction and dendrogram analysis, we suggested that the N-terminal {alpha}-helices of PNGase are derived from evolutionary motif/peptide fusion.

  6. Isolation and Molecular Characterization of Acanthamoeba Strains from Dental Units in Costa Rica.

    PubMed

    Retana-Moreira, Lissette; Abrahams-Sandí, Elizabeth; Castro-Artavia, Esteban; Fernández-Sánchez, Ana; Castro-Castillo, Alfredo; Reyes-Batlle, María; Lorenzo-Morales, Jacob

    2015-01-01

    Free-living amoebae are protozoa widely distributed in nature, which can be found in a variety of environments. Four genera are recognized as causal agents of infections in humans and animals: Acanthamoeba, Naegleria, Balamuthia, and Sappinia. In this study, the presence of Acanthamoeba in dental units was determined and the isolates obtained were molecularly characterized; osmotolerance and thermotolerance assays were also performed to evaluate multiplication under these conditions, frequently associated with pathogenicity. The morphological analysis and partial sequencing of the 18S rDNA gene revealed the presence of Acanthamoeba genotype T4 in 14% of the units sampled. Osmotolerance and thermotolerance tests were positive for more than 80% of the isolates. Up to date, this is the first study that reports the detection, identification, and genotyping of Acanthamoeba isolated from dental units in Costa Rica and even in Latin-America. Further assays to determine the potential pathogenicity of these Acanthamoeba isolates are underway.

  7. Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

    PubMed

    Condamine, Fabien L; Clapham, Matthew E; Kergoat, Gael J

    2016-01-18

    Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

  8. Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

    PubMed Central

    Condamine, Fabien L.; Clapham, Matthew E.; Kergoat, Gael J.

    2016-01-01

    Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders. PMID:26778170

  9. Feasibility of a workflow for the molecular characterization of single cells by next generation sequencing.

    PubMed

    Salvianti, Francesca; Rotunno, Giada; Galardi, Francesca; De Luca, Francesca; Pestrin, Marta; Vannucchi, Alessandro Maria; Di Leo, Angelo; Pazzagli, Mario; Pinzani, Pamela

    2015-09-01

    The purpose of the study was to explore the feasibility of a protocol for the isolation and molecular characterization of single circulating tumor cells (CTCs) from cancer patients using a single-cell next generation sequencing (NGS) approach. To reach this goal we used as a model an artificial sample obtained by spiking a breast cancer cell line (MDA-MB-231) into the blood of a healthy donor. Tumor cells were enriched and enumerated by CellSearch(®) and subsequently isolated by DEPArray™ to obtain single or pooled pure samples to be submitted to the analysis of the mutational status of multiple genes involved in cancer. Upon whole genome amplification, samples were analysed by NGS on the Ion Torrent PGM™ system (Life Technologies) using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies), designed to investigate genomic "hot spot" regions of 50 oncogenes and tumor suppressor genes. We successfully sequenced five single cells, a pool of 5 cells and DNA from a cellular pellet of the same cell line with a mean depth of the sequencing reaction ranging from 1581 to 3479 reads. We found 27 sequence variants in 18 genes, 15 of which already reported in the COSMIC or dbSNP databases. We confirmed the presence of two somatic mutations, in the BRAF and TP53 gene, which had been already reported for this cells line, but also found new mutations and single nucleotide polymorphisms. Three variants were common to all the analysed samples, while 18 were present only in a single cell suggesting a high heterogeneity within the same cell line. This paper presents an optimized workflow for the molecular characterization of multiple genes in single cells by NGS. The described pipeline can be easily transferred to the study of single CTCs from oncologic patients. PMID:27077040

  10. Development and application of molecular biomarkers for characterizing Caribbean Yellow Band Disease in Orbicella faveolata

    PubMed Central

    Goodner, Kylia; Ross, James; Poole, Angela Z.; Stepp, Elizabeth; Stuart, Christopher H.; Wilbanks, Cydney; Weil, Ernesto

    2015-01-01

    Molecular stress responses associated with coral diseases represent an under-studied area of cnidarian transcriptome investigations. Caribbean Yellow Band Disease (CYBD) is considered a disease of Symbiodinium within the tissues of the coral host Orbicella faveolata. There is a paucity of diagnostic tools to assist in the early detection and characterization of coral diseases. The validity of a diagnostic test is determined by its ability to distinguish host organisms that have the disease from those that do not. The ability to detect and identify disease-affected tissue before visible signs of the disease are evident would then be a useful diagnostic tool for monitoring and managing disease outbreaks. Representational Difference Analysis (RDA) was utilized to isolate differentially expressed genes in O. faveolata exhibiting CYBD. Preliminary screening of RDA products identified a small number of genes of interest (GOI) which included an early growth response factor and ubiquitin ligase from the coral host as well as cytochrome oxidase from the algal symbiont. To further characterize the specificity of response, quantitative real-time PCR (qPCR) was utilized to compare the expression profiles of these GOIs within diseased tissues (visible lesions), tissues that precede visible lesions by 2–4 cm (transition area), and tissues from healthy-looking colonies with no signs of disease. Results show there are distinctive differences in the expression profiles of these three GOIs within each tissue examined. Collectively, this small suite of GOIs can provide a molecular “finger print” which is capable of differentiating between infected and uninfected colonies on reefs where CYBD is known to occur. PMID:26557440

  11. Peroxiredoxin 6 from the Antarctic emerald rockcod: molecular characterization of its response to warming.

    PubMed

    Tolomeo, A M; Carraro, A; Bakiu, R; Toppo, S; Place, S P; Ferro, D; Santovito, G

    2016-01-01

    In the present study, we describe the purification and molecular characterization of two peroxiredoxins (Prdxs), referred to as Prdx6A and Prdx6B, from Trematomus bernacchii, a teleost widely distributed in many areas of Antarctica, that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with Prdx6 orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase and phospholipase activities of these enzymes. Phylogenetic analyses suggest the appearance of the two prdx6 genes through a duplication event before the speciation that led to the differentiation of fish families and that the evolution of the two gene variants seems to proceed together with the evolution of fish orders and families. The temporal expression of Prdx6 mRNA in response to short-term thermal stress showed a general upregulation of prdx6b and inhibition of prdx6a, suggesting that the latter is the variant most affected by temperature increase. The variations of mRNA accumulation are more conspicuous in heart than the liver, probably related to behavioral changes of the specimens in response to elevated temperature. These data, together with the peculiar differences between the molecular structures of the two Prdx6s in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges. PMID:26433650

  12. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin.

    PubMed

    Khan, Naima A; Engle, Mark; Dungan, Barry; Holguin, F Omar; Xu, Pei; Carroll, Kenneth C

    2016-04-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production. PMID:26802271

  13. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin.

    PubMed

    Khan, Naima A; Engle, Mark; Dungan, Barry; Holguin, F Omar; Xu, Pei; Carroll, Kenneth C

    2016-04-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production.

  14. Molecular characterization of Hepatozoon spp. infection in endangered Indian wild felids and canids.

    PubMed

    Pawar, Rahul Mohanchandra; Poornachandar, Anantula; Srinivas, Pasham; Rao, Kancharapu Ramachandra; Lakshmikantan, Uthandaraman; Shivaji, Sisinthy

    2012-05-25

    Hepatozoon species are parasites that infect a wide variety of domestic and wild animals. The objective of this study was to perform the molecular detection and characterization of Hepatozoon spp. in Asiatic lion, Indian tiger, Indian leopard, Indian wild dog, Indian domestic dog and cat based on partial 18S rRNA gene sequences from Hepatozoon spp. in the naturally infected animals. Hepatozoon spp. could be detected in blood samples of 5 out of 9 Asiatic lions, 2 out of 5 Indian tigers, 2 out of 4 Indian leopards and 2 out of 2 Indian wild dogs and, 2 out of 4 domestic cats and 2 out of 3 domestic dog samples by PCR. Sequencing of PCR amplicon and BLAST analysis of partial 18S rRNA gene sequences indicated that the Hepatozoon spp. in Asiatic lion, Bengal tiger, Indian leopard and domestic cat was Hepatozoon felis (98-99% similarity) and in the Indian wild and domestic dog the phylogenetic neighbour was Hepatozoon canis (97-100% similarity). Presence of H. felis and H. canis in both domestic and wild animals suggested that they are not host specific and the same parasite causes infection in domestic and wild felids and canids in India and from different parts of the world. To our knowledge, this is the first report on detection and molecular characterization of H. felis infection in Asiatic lions, Indian tigers, Indian leopards and H. canis in Indian wild dog. Hepatozoon spp. may be a potential pathogen and an opportunistic parasite in immuno-compromised animals and could thus represent a threat to endangered Indian wild felids and canids.

  15. Molecular cloning, purification, and serological characterization of MPT63, a novel antigen secreted by Mycobacterium tuberculosis.

    PubMed Central

    Manca, C; Lyashchenko, K; Wiker, H G; Usai, D; Colangeli, R; Gennaro, M L

    1997-01-01

    Proteins that are actively secreted by Mycobacterium tuberculosis generate immune responses in the infected host. This has prompted the characterization of protein components of mycobacterial culture filtrates to develop subunit vaccines and immunodiagnostic reagents. Fractionation of filtrates of M. tuberculosis cultures has yielded an abundant protein called MPT63, which has an apparent molecular mass of 18 kDa. We report the molecular cloning and nucleotide sequence of the mpt63 gene, purification of recombinant MPT63 antigen from Escherichia coli cells, and serological characterization of MPT63. Nucleotide sequence analysis of mpt63 identified an open reading frame encoding a protein of 159 amino acids (aa) consisting of a 29-aa secretion signal peptide and a 130-aa mature MPT63 protein. Recombinant MPT63 protein, purified from E. coli cells, and native MPT63, purified from M. tuberculosis culture filtrates, were indistinguishable in serological assays. Thus, the recombinant protein constitutes a valuable reagent for immunological studies. MPT63 evoked humoral immune responses in guinea pigs infected with virulent M. tuberculosis by the aerosol route. The mpt63 gene is found only in species of the M. tuberculosis complex, as shown by DNA hybridization experiments. Moreover, polyclonal antibody against MPT63 does not cross-react with proteins of a common environmental mycobacterial species, Mycobacterium avium. The absence of cross-reactive epitopes makes MPT63 an attractive candidate as an M. tuberculosis complex-specific diagnostic reagent. In particular, evaluation of MPT63 as an M. tuberculosis complex-specific reagent for diagnostic skin testing is under way. PMID:8975887

  16. Occurrence and molecular characterization of Cryptosporidium and Giardia in captive wild ruminants in Belgium.

    PubMed

    Geurden, Thomas; Goossens, Els; Levecke, Bruno; Vercammen, Francis; Vercruysse, Jozef; Claerebout, Edwin

    2009-03-01

    Both Cryptosporidium and Giardia are frequently found in the stool of domestic ruminants, especially young animals. Wild ruminants are also host to these protozoa, but the prevalence of these parasites in both free-ranging and captive nondomesticated ruminants needs to be further investigated. Moreover, the role of wild ruminants serving as reservoirs for these zoonotic parasites remains unclear. Therefore, a cross-sectional survey was conducted to estimate the occurrence of Cryptosporidium and Giardia in captive wild ruminants younger than 6 mo and to determine the potential of these animals to serve as reservoirs for these zoonotic parasites. A total of 67 captive wild ruminants belonging to 21 different animal species at the Antwerp Zoo (Belgium), along with 82 American bison (Bison bison) on a commercial breeding farm, were sampled for the detection of Cryptosporidium and Giardia, using a commercial immunofluoresence assay (Merifluor Cryptosporidium/Giardia IFA). The Cryptosporidium prevalence was 7.5% in the Antwerp Zoo animals and 3.7% in the bison from the breeding farm. All but two of the Cryptosporidium-positive animals were younger than 1 mo of age. Molecular characterization by amplification of the 70-kDa heat-shock protein and the 18S ribosomal DNA gene identified Cryptosporidium parvum in four animals of the Antwerp Zoo. The prevalence of Giardia was 8.9% in the Antwerp Zoo animals and 23.2% in the bison calves. Most Giardia-positive animals were older than 1 mo of age. Molecular characterization on the beta-giardin gene and the triose phosphate isomerase gene identified Giardia duodenalis assemblage A in the Antwerp Zoo and both G. duodenalis assemblage A and assemblage E in the bison calves. These findings indicate that both protozoan parasites are prevalent in captive wild ruminants and that these animals can serve as a potential reservoir for zoonotic transmission.

  17. Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

    PubMed

    Paramo, Teresa; East, Alexandra; Garzón, Diana; Ulmschneider, Martin B; Bond, Peter J

    2014-05-13

    Protein cavities and tunnels are critical in determining phenomena such as ligand binding, molecular transport, and enzyme catalysis. Molecular dynamics (MD) simulations enable the exploration of the flexibility and conformational plasticity of protein cavities, extending the information available from static experimental structures relevant to, for example, drug design. Here, we present a new tool (trj_cavity) implemented within the GROMACS ( www.gromacs.org ) framework for the rapid identification and characterization of cavities detected within MD trajectories. trj_cavity is optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, for example, protein channels. Its novel grid-based algorithm performs an efficient neighbor search whose calculation time is linear with system size, and a comparison of performance with other widely used cavity analysis programs reveals an orders-of-magnitude improvement in the computational cost. To demonstrate its potential for revealing novel mechanistic insights, trj_cavity has been used to analyze long-time scale simulation trajectories for three diverse protein cavity systems. This has helped to reveal, respectively, the lipid binding mechanism in the deep hydrophobic cavity of a soluble mite-allergen protein, Der p 2; a means for shuttling carbohydrates between the surface-exposed substrate-binding and catalytic pockets of a multidomain, membrane-proximal pullulanase, PulA; and the structural basis for selectivity in the transmembrane pore of a voltage-gated sodium channel (NavMs), embedded within a lipid bilayer environment. trj_cavity is available for download under an open-source license ( http://sourceforge.net/projects/trjcavity ). A simplified, GROMACS-independent version may also be compiled. PMID:26580540

  18. Development and application of molecular biomarkers for characterizing Caribbean Yellow Band Disease in Orbicella faveolata.

    PubMed

    Morgan, Michael; Goodner, Kylia; Ross, James; Poole, Angela Z; Stepp, Elizabeth; Stuart, Christopher H; Wilbanks, Cydney; Weil, Ernesto

    2015-01-01

    Molecular stress responses associated with coral diseases represent an under-studied area of cnidarian transcriptome investigations. Caribbean Yellow Band Disease (CYBD) is considered a disease of Symbiodinium within the tissues of the coral host Orbicella faveolata. There is a paucity of diagnostic tools to assist in the early detection and characterization of coral diseases. The validity of a diagnostic test is determined by its ability to distinguish host organisms that have the disease from those that do not. The ability to detect and identify disease-affected tissue before visible signs of the disease are evident would then be a useful diagnostic tool for monitoring and managing disease outbreaks. Representational Difference Analysis (RDA) was utilized to isolate differentially expressed genes in O. faveolata exhibiting CYBD. Preliminary screening of RDA products identified a small number of genes of interest (GOI) which included an early growth response factor and ubiquitin ligase from the coral host as well as cytochrome oxidase from the algal symbiont. To further characterize the specificity of response, quantitative real-time PCR (qPCR) was utilized to compare the expression profiles of these GOIs within diseased tissues (visible lesions), tissues that precede visible lesions by 2-4 cm (transition area), and tissues from healthy-looking colonies with no signs of disease. Results show there are distinctive differences in the expression profiles of these three GOIs within each tissue examined. Collectively, this small suite of GOIs can provide a molecular "finger print" which is capable of differentiating between infected and uninfected colonies on reefs where CYBD is known to occur.

  19. Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

    NASA Technical Reports Server (NTRS)

    Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

    2001-01-01

    The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

  20. Peroxiredoxin 6 from the Antarctic emerald rockcod: molecular characterization of its response to warming.

    PubMed

    Tolomeo, A M; Carraro, A; Bakiu, R; Toppo, S; Place, S P; Ferro, D; Santovito, G

    2016-01-01

    In the present study, we describe the purification and molecular characterization of two peroxiredoxins (Prdxs), referred to as Prdx6A and Prdx6B, from Trematomus bernacchii, a teleost widely distributed in many areas of Antarctica, that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with Prdx6 orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase and phospholipase activities of these enzymes. Phylogenetic analyses suggest the appearance of the two prdx6 genes through a duplication event before the speciation that led to the differentiation of fish families and that the evolution of the two gene variants seems to proceed together with the evolution of fish orders and families. The temporal expression of Prdx6 mRNA in response to short-term thermal stress showed a general upregulation of prdx6b and inhibition of prdx6a, suggesting that the latter is the variant most affected by temperature increase. The variations of mRNA accumulation are more conspicuous in heart than the liver, probably related to behavioral changes of the specimens in response to elevated temperature. These data, together with the peculiar differences between the molecular structures of the two Prdx6s in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges.

  1. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin

    USGS Publications Warehouse

    Khan, Naima A.; Engle, Mark A.; Dungan, Barry; Holguin, F. Omar; Xu, Pei; Carroll, Kenneth C.

    2016-01-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production.

  2. Feasibility of a workflow for the molecular characterization of single cells by next generation sequencing

    PubMed Central

    Salvianti, Francesca; Rotunno, Giada; Galardi, Francesca; De Luca, Francesca; Pestrin, Marta; Vannucchi, Alessandro Maria; Di Leo, Angelo; Pazzagli, Mario; Pinzani, Pamela

    2015-01-01

    The purpose of the study was to explore the feasibility of a protocol for the isolation and molecular characterization of single circulating tumor cells (CTCs) from cancer patients using a single-cell next generation sequencing (NGS) approach. To reach this goal we used as a model an artificial sample obtained by spiking a breast cancer cell line (MDA-MB-231) into the blood of a healthy donor. Tumor cells were enriched and enumerated by CellSearch® and subsequently isolated by DEPArray™ to obtain single or pooled pure samples to be submitted to the analysis of the mutational status of multiple genes involved in cancer. Upon whole genome amplification, samples were analysed by NGS on the Ion Torrent PGM™ system (Life Technologies) using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies), designed to investigate genomic “hot spot” regions of 50 oncogenes and tumor suppressor genes. We successfully sequenced five single cells, a pool of 5 cells and DNA from a cellular pellet of the same cell line with a mean depth of the sequencing reaction ranging from 1581 to 3479 reads. We found 27 sequence variants in 18 genes, 15 of which already reported in the COSMIC or dbSNP databases. We confirmed the presence of two somatic mutations, in the BRAF and TP53 gene, which had been already reported for this cells line, but also found new mutations and single nucleotide polymorphisms. Three variants were common to all the analysed samples, while 18 were present only in a single cell suggesting a high heterogeneity within the same cell line. This paper presents an optimized workflow for the molecular characterization of multiple genes in single cells by NGS. The described pipeline can be easily transferred to the study of single CTCs from oncologic patients. PMID:27077040

  3. Molecular characterization and expression analysis of IκB from Haliotis discus discus.

    PubMed

    Kasthuri, Saranya Revathy; Whang, Ilson; Navaneethaiyer, Umasuthan; Lim, Bong-Soo; Choi, Cheol Young; Lee, Jehee

    2013-06-01

    Innate immune system relies on the recognition of pathogen associated molecular patterns present in the microbes by the pattern recognition receptors leading to the activation of signaling cascade and subsequent synthesis of cytokines. NF-κB is a major stimulus activated transcription factor, which regulates the expression of a diverse array of genes. IκB is an inhibitor of NF-κB, retaining NF-κB in an inactive state in the cytoplasm. In this study, we have reported the characterization of first abalone IκB (HdIκB). The cDNA possessed an ORF of 1200 bp coding for a protein of 400 amino acids with molecular mass of 45 kDa and isoelectric point of 4.7. HdIκB protein possessed a conserved phosphorylation site (58)DSGIFS(63) in the N-terminal region, six ankyrin repeats, and a PEST sequence in the C-terminal region. A casein kinase II phosphorylation site could also be observed in the PEST sequence. Constitutive expression of HdIκB revealed its physiological significance since NF-κB is known to be activated by various stimuli. Elevated expression of HdIκB transcripts could be observed in abalones challenged with various mitogens and live microbes. This novel characterization of abalone IκB would further be a positive approach in the affirmation of evolutionary conservation and significance of this protein as a repressor/inhibitor of a pleiotropic transcription factor like NF-κB.

  4. Molecular and serotyping characterization of shiga toxogenic Escherichia coli associated with food collected from Saudi Arabia

    PubMed Central

    Al-Zogibi, Onizan G.; Mohamed, Moussa I.; Hessain, Ashgan M.; El-Jakee, Jakeen K.; Kabli, Saleh A.

    2015-01-01

    Shiga toxin-producing Escherichia coli (STEC) strains are considered as one of the major food-borne disease agents in humans worldwide. STEC strains, also called verotoxin-producing E. coli strains. The objectives of the present study were serotyping and molecular characterization of shiga toxigenic E. coli associated with raw meat and milk samples collected from Riyadh, Saudi Arabia. A total of 540 milk samples were collected from 5 dairy farms and 150 raw meat samples were collected from different abattoirs located in Riyadh, Saudi Arabia. E. coli were recovered from 86 milk samples (15.93%), serotyping of E. coli isolates revealed, 26 (4.81%) strains O157: H7, 23 (4.26%) strains O111, 20 (3.70%) strains O113: H21, 10 (1.85%) strains O22: H8 and 7 (1.3%) strains O172: H21. Meanwhile, 17 (11.33%) strains of E. coli were recovered from raw meat samples, serotyping of E. coli isolates revealed, 6 (4%) strains O157: H7, 5 (3.33%) strains O111 and 4 (2.67%) strains O174: H2 and only two (1.33%) strains were identified as O22: H8. Shiga toxin2 was detected in 58 (67.44%) serotypes of E. coli recovered from milk samples and 16 (94.12%) serotypes of E. coli recovered from meat samples, while intimin gene was detected in 38 (44.186%) serotypes of E. coli recovered from milk samples and in 10 (58.82%) serotypes of E. coli recovered from meat samples. The results of this study revealed the efficiency of combination between serotyping and molecular typing of E. coli isolates recovered from food of animal origin for rapid detection and characterization of STEC. PMID:26150750

  5. Molecular characterization of Hepatozoon spp. infection in endangered Indian wild felids and canids.

    PubMed

    Pawar, Rahul Mohanchandra; Poornachandar, Anantula; Srinivas, Pasham; Rao, Kancharapu Ramachandra; Lakshmikantan, Uthandaraman; Shivaji, Sisinthy

    2012-05-25

    Hepatozoon species are parasites that infect a wide variety of domestic and wild animals. The objective of this study was to perform the molecular detection and characterization of Hepatozoon spp. in Asiatic lion, Indian tiger, Indian leopard, Indian wild dog, Indian domestic dog and cat based on partial 18S rRNA gene sequences from Hepatozoon spp. in the naturally infected animals. Hepatozoon spp. could be detected in blood samples of 5 out of 9 Asiatic lions, 2 out of 5 Indian tigers, 2 out of 4 Indian leopards and 2 out of 2 Indian wild dogs and, 2 out of 4 domestic cats and 2 out of 3 domestic dog samples by PCR. Sequencing of PCR amplicon and BLAST analysis of partial 18S rRNA gene sequences indicated that the Hepatozoon spp. in Asiatic lion, Bengal tiger, Indian leopard and domestic cat was Hepatozoon felis (98-99% similarity) and in the Indian wild and domestic dog the phylogenetic neighbour was Hepatozoon canis (97-100% similarity). Presence of H. felis and H. canis in both domestic and wild animals suggested that they are not host specific and the same parasite causes infection in domestic and wild felids and canids in India and from different parts of the world. To our knowledge, this is the first report on detection and molecular characterization of H. felis infection in Asiatic lions, Indian tigers, Indian leopards and H. canis in Indian wild dog. Hepatozoon spp. may be a potential pathogen and an opportunistic parasite in immuno-compromised animals and could thus represent a threat to endangered Indian wild felids and canids. PMID:22154254

  6. Molecular characterization and genetic diversity of insecticidal crystal protein genes in native Bacillus thuringiensis isolates.

    PubMed

    Mahadeva Swamy, H M; Asokan, R; Mahmood, Riaz; Nagesha, S N

    2013-04-01

    The Western Ghats of Karnataka natural ecosystem are among the most diverse and is one of the eight hottest hotspots of biological diversity in the world, that runs along the western part of India through four states including Karnataka. Bacillus thuringiensis (Bt) strains were isolated from soils of Western Ghats of Karnataka and characterized by molecular and analytical methods as a result of which 28 new Bt-like isolates were identified. Bt strains were isolated from soil samples using sodium acetate selection method. The morphology of crystals was studied using light and phase contrast microscopy. Isolates were further characterized for insecticidal cry gene by PCR, composition of toxins in bacterial crystals by SDS-PAGE cloning, sequencing and evaluation of toxicity was done. As a result 28 new Bt-like isolates were identified. Majority of the isolates showed the presence of a 55 kDa protein bands on SDS-PAGE while the rest showed 130, 73, 34, and 25 kDa bands. PCR analysis revealed predominance of Coleopteran-active cry genes in these isolates. The variations in the nucleotide sequences, crystal morphology, and mass of crystal protein(s) purified from the Bt isolates revealed genetic and molecular diversity. Three strains containing Coleopteran-active cry genes showed higher activity against larvae Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) than B. thuringiensis subsp. Morrisoni. Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production.

  7. Molecular characterization of Mycobacterium bovis isolates from patients with tuberculosis in Baja California, Mexico.

    PubMed

    Laniado-Laborín, Rafael; Muñiz-Salazar, Raquel; García-Ortiz, Rosa Alejandra; Vargas-Ojeda, Adriana Carolina; Villa-Rosas, Cecilia; Oceguera-Palao, Lorena

    2014-10-01

    The incidence of tuberculosis (TB) from Mycobacterium bovis in humans is likely to be underestimated and in some cases even ignored in most developing countries. This may be due to the difficulty of differentiating TB caused by either Mycobacteriumtuberculosis or M. bovis. Our objectives were to determine the prevalence of M. bovis human disease among the patients referred for study to the Tuberculosis Laboratory of the Tijuana General Hospital in Baja California, Mexico and to characterize molecularly the clinical isolates using 8 loci of MIRU-VNTR. A cross-sectional analysis of all culture-proven cases of tuberculosis was conducted during the period from January 1, 2011 through June 30, 2013. Clinical isolates that exhibited resistance to pyrazinamide (Z) were submitted for molecular analysis. A total of 2699 clinical samples were cultured during the study period and 600 (22%) that tested positive were processed for drug susceptibility for first line drugs. Sixty-four (10.7%) of the tested isolates tested were resistant to Z, and 27 (4.5%) of those were subsequently identified molecularly as M. bovis. Three of the M. bovis isolates were polyresistant to Z, isoniazid (H), ethambutol (E) and rifampicin (R) (Z+H+E, Z+E and Z+R); the rest were only resistant only to Z. VNTR typing, based on the 8 VNTR loci commonly tested for M.bovis, detected 12 allelic profiles (genotypes). The real burden of M. bovis cases among the total reported human tuberculosis cases can only be known from especially designed studies in which, during a specific period, all specimens submitted to tuberculosis diagnosis in one or more laboratories are cultured on the appropriate media and the isolated mycobacteria are analyzed to differentiate M. bovis from M. tuberculosis and other Mycobacterium species.

  8. Molecular and biochemical characterization of rice pectin methylesterase inhibitors (OsPMEIs).

    PubMed

    Nguyen, Hong Phuong; Jeong, Ho Young; Kim, Hun; Kim, Young Chang; Lee, Chanhui

    2016-04-01

    Cell wall modifications such as partial degradation and depolymerization by cell wall hydrolases are normal cellular processes and are required for the functionalities of different cell types. Pectin, one of the major cell wall polysaccharides, is predominantly found in primary cell walls and middle lamellae and is subjected to in muro modification, primarily by cell wall-localized pectin methylesterases (PMEs). Molecular biochemical studies have demonstrated that enzymatic activities of PMEs are governed by multiple pectin methylesterase inhibitors (PMEIs), which consequently control the pectin methylesterification status. Although a few studies in Arabidopsis have shown the importance of this PMEI-mediated regulation in the biophysical properties of cell walls, little is known about the molecular physiological functions of rice PMEIs. We found 49 members of the PMEI family in the rice genome. Analysis of their transcript levels by quantitative real-time PCR and meta expression analysis showed that they are regulated spatially and temporally, as well as in response to diverse stresses. Quantification of cell wall-bound methylesters indicated that the degree of pectin methylesterification is developmentally regulated; in particular, higher PMEI activities were detected in cell wall proteins prepared from young leaves. Furthermore, an activity assay demonstrated that two recombinant OsPMEI proteins (OsPMEI8 and 12) were able to inhibit the enzymatic activity of a commercial PME protein. Subcellular localization indicated that OsPMEI8 is targeted to the middle lamella and OsPMEI12 is localized in the plasma membrane and nucleus. Taken together, our findings provide the first molecular and biochemical evidence for functional characterization of PMEIs in rice growth and development.

  9. Molecular cloning and characterization of a group II chaperonin delta-subunit from soybean.

    PubMed

    Nong, Van Hai; Arahira, Masaomi; Phan, Van Chi; Kim, Chan-Shick; Zhang, Deyu; Udaka, Kyoko; Fukazawa, Chikafusa

    2002-08-01

    Molecular characterization of plant group II chaperonin (CCT, c-cpn, or TriC) still remains elusive. By PCR-based cloning techniques using soybeans, we have made a successful attempt to clone a delta-subunit homologue of CCT (CCTdelta). This subunit is responsible for the binding of an in vivo substrate, alpha-actin, by assisting the correct folding of the cytoskeletal protein in mouse, and the occurrence of the subunit homologue in plant CCT was unclear. As the cloning strategy, a putative amino acid segment, NH(2)-Gly-Gly-Gly-Ala-Pro-Glu-COOH, which is tightly conserved in all known animal and yeast CCTdelta subunits, was chosen for designing a degenerate primer of the PCR-cloning. The resultant 1881-bp cDNA was found to have an open-reading frame of 533 amino acids with a calculated molecular mass of 57,677 Da and to share about 58-65% identity overall at the amino acid level with the corresponding subunits known to date. Using antibodies raised against Escherichia coli-produced soybean insoluble CCTdelta as a monitoring tool, we purified soybean CCT from the extract of its immature seeds. STEM images demonstrated that the molecular shape of soybean CCT is a double eight-membered ring, which resembles the known group II chaperonins. The CCT also reactivated a denatured firefly luciferase with a significant, but limited level of the native enzymic activity in an in vitro system. Northern blot analysis showed that soybean CCTdelta gene, which is intronless and composed of a small family, was only expressed at a very early stage of seed development of soybean.

  10. Applied Protein and Molecular Techniques for Characterization of B Cell Neoplasms in Horses

    PubMed Central

    Badial, Peres R.; Tallmadge, Rebecca L.; Miller, Steven; Stokol, Tracy; Richards, Kristy; Borges, Alexandre S.

    2015-01-01

    Mature B cell neoplasms cover a spectrum of diseases involving lymphoid tissues (lymphoma) or blood (leukemia), with an overlap between these two presentations. Previous studies describing equine lymphoid neoplasias have not included analyses of clonality using molecular techniques. The objective of this study was to use molecular techniques to advance the classification of B cell lymphoproliferative diseases in five adult equine patients with a rare condition of monoclonal gammopathy, B cell leukemia, and concurrent lymphadenopathy (lymphoma/leukemia). The B cell neoplasms were phenotypically characterized by gene and cell surface molecule expression, secreted immunoglobulin (Ig) isotype concentrations, Ig heavy-chain variable (IGHV) region domain sequencing, and spectratyping. All five patients had hyperglobulinemia due to IgG1 or IgG4/7 monoclonal gammopathy. Peripheral blood leukocyte immunophenotyping revealed high proportions of IgG1- or IgG4/7-positive cells and relative T cell lymphopenia. Most leukemic cells lacked the surface B cell markers CD19 and CD21. IGHG1 or IGHG4/7 gene expression was consistent with surface protein expression, and secreted isotype and Ig spectratyping revealed one dominant monoclonal peak. The mRNA expression of the B cell-associated developmental genes EBF1, PAX5, and CD19 was high compared to that of the plasma cell-associated marker CD38. Sequence analysis of the IGHV domain of leukemic cells revealed mutated Igs. In conclusion, the protein and molecular techniques used in this study identified neoplastic cells compatible with a developmental transition between B cell and plasma cell stages, and they can be used for the classification of equine B cell lymphoproliferative disease. PMID:26311245

  11. The Importance of Accurate Atomic and Molecular Line-lists for Characterizing Exoplanetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Madhusudhan, Nikku; Freedman, R.; Tennyson, J.

    2013-06-01

    Recent advancements in exoplanet observations are placing unprecedented constraints on the physical and chemical properties of exoplanetary atmospheres. Statistically significant constraints have been placed on the abundances of atomic and molecular species, elemental abundance ratios, temperature profiles, energy circulation, presence of hazes/clouds, and non-equilibrium chemistry, in several exoplanetary atmospheres, including gas giants, ice giants, as well as super-Earths, over a wide temperature range. The chemical constraints have also motivated new paradigms for classifying exoplanets and new efforts to constraint their formation conditions. Central to all interpretations of exoplanet spectra, however, is the accuracy of fundamental inputs in the models, primarily, the atomic and molecular opacities, which are derived from laboratory experiments and/or ab initio numerical calculations. In this talk, we will review the state-of-the-art in atomic and molecular line-lists as applied to studies of exoplanetary atmospheres. We will discuss examples where advances in laboratory astrophysics, experimental and computational, have addressed important problems in the area of exoplanetary atmospheres, as well as outstanding questions requiring new experiments and/or theoretical calculations. For example, recent studies are suggesting that high-temperature line-lists of hydrocarbons (CH4, C2H2, HCN, etc.), and several metal hydrides, in addition to refined line-lists of several well-studied molecules, are important to accurately interpret exoplanetary spectra. We will highlight several fundamental questions in the area that require new efforts in laboratory astrophysics. Besides their importance in interpreting observations with current instruments, the refined parameters are also critical in the assessment of future facilities for exoplanet characterization, such as JWST, GMT, etc.

  12. Living Behaviors and Molecular Characterization of Benthic Foraminifera in the Arabian Gulf

    NASA Astrophysics Data System (ADS)

    Arslan, Muhammad; Kaminski, Michael; Khalil, Amjad; Holzmann, Maria

    2016-04-01

    The benthic foraminifera are among the major carbonate producers in modern Arabian Gulf waters and are found living in all marine habitats. They have been recognized as proxies to assess paleoenvironmental changes, however, their biological behaviors in modern environments needs to be further studied. The current study attempts to explain the biology of benthic foraminifera in terms of their living behaviors and molecular characterization, from different regions of the western side of the Arabian Gulf. Accordingly, two major groups of benthic foraminifera, namely rotaliids and miliolids, are examined under laboratory conditions. Results illustrate that the rotaliids are more resistant to environmental changes than miliolids, as their granular reticulopodial network is stronger than among the miliolids, with high cytoplasmic streaming. The pseudopodia extend out from both primary and secondary apertures, and aid the organism in locomotion by attaching to the wall of hard substrate. As a result they drag their whole bodies toward the direction of motion. In rotaliids, the movement rate is high and is attributed to the extension of pseudopodia through all apertures, compared with miliolids in which pseudopodia extend out from the primary aperture only. The innate behavior of both groups was observed as a function of external stimulus, i.e., light, nutrients, and availability of substrate. The observation on average life span reflected that the rotaliids was able to survive longer than miliolids. Molecular analysis reveals the presence of four groups, i.e., Ammonia, Murrayinella, Glabratellina, and Elphidium which support the morphological taxonomy at the genus level. However, BLAST analysis contradicts the species level taxonomy, which challenges the classification based upon hard-shell morphology. Nevertheless, monophyletic clustering is observed among all major groups. The study concludes that the morphological taxonomy needs to be augmented by molecular analysis

  13. Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa.

    PubMed

    Ueno, Hiroki; Matsumoto, Etsuo; Aruga, Daisuke; Kitagawa, Satoshi; Matsumura, Hideo; Hayashida, Nobuaki

    2012-12-01

    Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.

  14. Molecular characterization of the gag gene of caprine arthritis encephalitis virus from goats in the Philippines.

    PubMed

    Padiernos, Ryan Bismark C; Balbin, Michelle M; Parayao, Arman M; Mingala, Claro N

    2015-04-01

    Caprine arthritis encephalitis virus (CAEV) causes caprine arthritis encephalitis syndrome, which is an emerging disease of goats in the Philippines. DNA sequence analysis showed homology of 86-93 % between Philippine CAEV and available CAEV sequences in GenBank. CAEV was detected using nested polymerase chain reaction (PCR), and new sets of primers were designed in order to amplify the gag gene, which is a highly conserved region of the viral genome. In addition, the Philippine CAEV isolate clustered in group B with the prototype caprine lentivirus. Based on amino acid sequence alignments, it is possible that the Philippine CAEV isolate is a new strain of CAEV, but it is also possible that it was already present in the country even before the start of goat importation. Molecular characterization of the CAEV gag gene is important for the development of a detection kit specific for the local strain of CAEV and the establishment of small ruminant lentivirus eradication programs in the Philippines. This study is the first report to describe the molecular characteristics of CAEV circulating in the Philippines.

  15. Molecular Characterization of the Newly Identified Human Parvovirus 4 in the Family Parvoviridae

    PubMed Central

    Lou, Sai; Xu, Baoyan; Huang, Qinfeng; Zhi, Ning; Cheng, Fang; Wong, Susan; Brown, Kevin; Delwart, Eric; Liu, Zhengwen; Qiu, Jianming

    2011-01-01

    Human parvovirus 4 (PARV4) is an emerging human virus, and little is known about the molecular aspects of PARV4 apart from its incomplete genome sequence, which lacks information of the termini. We analyzed the gene expression profile of PARV4 using a nearly full-length HPV4 genome in a replication competent system in 293 cells. We found that PARV4 utilizes two promoters to transcribe non-structural protein- and structural protein-encoding mRNAs, respectively, which were polyadenylated at the right end of the genome. Three major proteins, including the large non-structural protein NS1a, whose mRNA is spliced, and capsid proteins VP1 and VP2, were detected. Additional functional analysis of the NS1a revealed its capability to induce cell cycle arrest at G2/M phase in ex vivo-generated human hematopoietic stem cells. Taken together, our characterization of the molecular features of PARV4 suggests that PARV4 represents a new genus in the family Parvoviridae. PMID:22044541

  16. Molecular characterization of Acidithiobacillus ferrooxidans and A. thiooxidans strains isolated from mine wastes in Brazil.

    PubMed

    Paulino, L C; Bergamo, R F; Garcia, O; de Mello, M P; Manfio, G P; Ottoboni, L M

    2001-10-01

    Nineteen strains of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans, including 12 strains isolated from coal, copper, gold and uranium mines in Brazil, strains isolated from similar sources in other countries and the type strains of the two species were characterized together with the type strain of A. caldus by using a combination of molecular