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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 wild-type measles viruses in Tamil Nadu, India, during 2005-2006: relationship of genotype D8 strains from Tamil Nadu to global strains.

    PubMed

    Duraisamy, Raja; Rota, Paul A; Palani, Gunasekaran; Elango, Varalakshmi; Sambasivam, Mohana; Lowe, Luis; Lopareva, Elena; Ramamurty, Nalini

    2012-02-01

    Molecular characterization of measles viruses is a valuable tool for measuring the effectiveness of measles control and elimination programmes. WHO recommends that virological surveillance be conducted during all phases of measles control to document circulation of indigenous strains and trace future importation. This report describes the genetic characterization of wild type measles viruses from Tamil Nadu, India isolated between January 2005 and January 2006. In the study, 304 suspected measles cases (292 from 56 outbreaks and 12 sporadic cases) were investigated. Blood samples were collected from suspected measles outbreaks and 11 suspected sporadic cases and tested for the presence of measles and rubella specific IgM. Based on serological results, 53 outbreaks were confirmed as measles, 2 as a combination of measles and rubella, and 1 negative for both. Eight sporadic cases were confirmed as measles and one as rubella. Throat swab and urine samples were collected for virus isolation and 28 isolates were obtained. Sequencing and analysis showed that 3 isolates belonged to genotype D4 and 25 to genotype D8. Comparison of the genotype D8 sequences from Tamil Nadu with previously reported genotype D8 sequences from India and abroad showed six distinct clusters with Tamil Nadu strains forming two clusters. This study has established baseline molecular data and is the first report that describes genetic diversity of circulating measles strains in Tamil Nadu, a state in India. D8 has multiple lineages and this has been linked with importation of measles into the USA and UK.

  3. Global phenotypic characterization of bacteria

    PubMed Central

    Bochner, Barry R

    2009-01-01

    The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described. PMID:19054113

  4. A global optimization perspective on molecular clusters.

    PubMed

    Marques, J M C; Pereira, F B; Llanio-Trujillo, J L; Abreu, P E; Albertí, M; Aguilar, A; Pirani, F; Bartolomei, M

    2017-04-28

    Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca(2+) ions with various types of solvents.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

  5. Indentifying the Molecular Origin of Global Warming

    NASA Astrophysics Data System (ADS)

    Bera, P. P.; Lee, T. J.; Francisco, J.

    2009-12-01

    Indentifying the Molecular Origin of Global Warming Partha P. Bera, Joseph S. Francisco and Timothy J. Lee NASA Ames Research Center, Space Science and Astrobiology Division, Moffett Field, California 94035, and Department of Chemistry and Department of Earth and Atmospheric Sciences, Purdue University, West Lafayette, Indiana 47907-1393 Abstract The physical characteristics of greenhouse gases (GHGs) have been investigated to assess which properties are most important in determining the radiative efficiency of a GHG. Chlorofluorcarbons (CFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), hydrofluoroethers, fluoroethers, 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 carbon atom becoming more positive. This leads to a linear increase in the total or integrated X-F 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 and a new design strategy for more environmentally friendly industrial materials from a molecular quantum chemistry perspective will be discussed.

  6. Fabrication and Characterization of Molecular Electronic Devices.

    PubMed

    Kim, Youngsang; Song, Hyunwook

    2015-02-01

    The concept of molecular electronic devices is utilizing single molecules or molecular monolayers as active electronic components. Rapid advances in technology have enabled us to engineer molecular electronic devices with diverse functionalities. This review article emphasizes on experimental aspects of electronic devices made with single molecules or molecular monolayers, with a primary focus on the characterization and manipulation of charge transport.

  7. Molecular characterization of genetically-modified crops: Challenges and strategies.

    PubMed

    Li, Rong; Quan, Sheng; Yan, Xiaofang; Biswas, Sukumar; Zhang, Dabing; Shi, Jianxin

    Molecular characterization lays a foundation for safety assessment and subsequent monitoring of genetically modified (GM) crops. Due to the target-specific nature, conventional polymerase chain reaction (PCR)-based methods cannot comprehensively detect unintended gene insertions, let alone unknown GM events. As more and more new developed GM crops including new plant breeding technology (NPBT) generated crops are in the pipeline for commercialization, alternative -omics approaches, particularly next generation sequencing, have been developed for molecular characterization of authorized or unauthorized GM (UGM) crops. This review summarizes first those methods, addresses their challenges, and discusses possible strategies for molecular characterization of engineered crops generated by NPBT, highlighting needs for a global information-sharing database and cost-effective, accurate and comprehensive molecular characterization approaches.

  8. Modelling the global tropospheric molecular hydrogen cycle

    NASA Astrophysics Data System (ADS)

    Pieterse, G.

    2013-01-01

    Would urban air quality and climate improve if we replaced the fossil fuels by molecular hydrogen (H2) as an energy carrier? A quantitative answer to this question requires a thorough understanding of the current role of H2 in the Earth’s atmosphere. On its own, H2 does not impact climate, as for example carbon dioxide or methane. However, increasing levels of H2 in the stratosphere can lead to increased ozone loss due to the formation of polar stratospheric clouds. Additionally, the atmospheric lifetime of methane could increase because both H2 and methane are removed by photochemical oxidation with the hydroxyl radical. Consequently, the lifetime of the strong greenhouse gas methane could be prolonged. During the last two decades, more and more experimental data have become available to put tighter constraints on the different sources and sinks that contribute to the global H2 cycle. However, the main removal process, dry deposition due to microbial/enzymatic decomposition of H2 in the soils, still has a rather large uncertainty between 40-99 Tg/yr globally. This is a highly uncertain number compared to the estimated overall amount of 136-166 Tg present in the troposphere. The photochemical removal of H2 from the atmosphere is estimated at 14-24 Tg/yr. Together with the estimates for the burden and dry deposition, this implies a tropospheric lifetime of H2 between 1.1-3.1 years. The atmospheric H2 is replenished by emissions from the Earth’s surfaces due to fossil fuel burning (5-25 Tg/yr), biomass burning (7-21 Tg/yr) and nitrogen fixation processes in the oceans (1-11 Tg/yr) and soils (0-11 Tg/yr). H2 is photochemically produced from methane (15-21 Tg/yr) and non-methane hydrocarbons (10-25 Tg/yr) in the atmosphere. These uncertainties suggest that at present, the global hydrogen cycle is poorly understood. However, this statement would do little justice to the scientific quality of most studies so far. The main purpose of the research in this thesis is to

  9. Molecular characterization of opioid receptors

    SciTech Connect

    Howard, A.D.

    1986-01-01

    The aim of this research was to purify and characterize active opioid receptors and elucidate molecular aspects of opioid receptor heterogeneity. Purification to apparent homogeneity of an opioid binding protein from bovine caudate was achieved by solubilization in the non-ionic detergent, digitonin, followed by sequential chromatography on the opiate affinity matrix, ..beta..-naltrexylethylenediamine-CH-Sepharose 4B, and on the lectine affinity matrix, wheat germ agglutinin-agarose. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE) followed by autoradiography revealed that radioiodinated purified receptor gave a single band. Purified receptor preparations showed a specific activity of 12,000-15,000 fmol of opiate bound per mg of protein. Radioiodinated human beta-endorphin (/sup 125/I-beta-end/sub H/) was used as a probe to investigate the ligand binding subunits of mu and delta opioid receptors. /sup 125/I-beta-end/sub H/ was shown to bind to a variety of opioid receptor-containing tissues with high affinity and specificity with preference for mu and delta sites, and with little, if any, binding to kappa sites. Affinity crosslinking techniques were employed to covalently link /sup 125/I-beta-end/sub H/ to opioid receptors, utilizing derivatives of bis-succinimidyl esters that are bifunctional crosslinkers with specificities for amino and sulfhydryl groups. This, and competition experiments with high type-selective ligands, permitted the assignment of two labeled peptides to their receptor types, namely a peptide of M/sub r/ = 65,000 for mu receptors and one of M/sub r/ = 53,000 for delta receptors.

  10. Characterization of global vegetation using AVHRR data

    NASA Astrophysics Data System (ADS)

    Kiang, Richard K.

    1998-03-01

    Increase in the levels of carbon dioxide and other greenhouse gases over the next half-century may result in an increase in global mean temperature. The recent discoveries of possible advance of arctic tree line into the tundra and earlier greening of northern vegetation provide additional warnings that global warming may indeed be occurring. On the Earth surface, land cover and its changes affect the coupling between the biosphere and the atmosphere, and control many important Earth system processes. Satellite remote sensing provides long-term, repeated coverage over extended area and is the essential data source for monitoring climate changes. An Advanced Very-High Resolution Radiometer (AVHRR) Pathfinder dataset from 1987, in 1 degree latitude-longitude resolution, is used in this study. Two reflective channels, two thermal channels, and Normalized Difference Vegetation Index are the input parameters. In conjunction with a global vegetation ground truth, a multi-layer neural network is trained and used for global vegetation characterization. As the same type of vegetation may appear very differently over different parts of the Earth at any given time, global classification is more difficult than local classification. It is shown that a multitemporal approach, in which data from multiple dates are used, may improve the accuracy.

  11. Molecular Characterization of Attenuated Junin Virus Variants.

    DTIC Science & Technology

    1992-07-14

    No. DAMD17-89-Z-9024 Area de Quimica Biologica y Biologia Molecular Facultad de Ciencias Exactas Universidad Nacional de La Plata Calles 47 y 115, 1900...MONITORING ORGANIZATION Area de Quimica Biologica (If applicable) y Biologia Molecular I 6c. ADDRESS (City, State, and ZIPCode) 7b. ADDRESS (City, State...AD-A260 128 AD____ MOLECULAR CHARACTERIZATION OF ATTENUATED JUNIN VIRUS VARIANTS FINAL REPORT VICTOR ROMANOWSKI PABLO D. GHIRINGHELLI CESAR G

  12. Global Characterization of the Ocean Ridge System

    NASA Astrophysics Data System (ADS)

    Gale, A.; Langmuir, C. H.; Dalton, C. A.

    2010-12-01

    The mid-ocean ridge system is a window into the upper mantle, producing over 80% of Earth’s volcanism. Fundamental, first-order questions remain debated and require a reliable global perspective. Such questions include the relative roles of mantle temperature, mantle heterogeneity and spreading rate on mid-ocean ridge basalt (MORB) compositions, and the importance of spreading rate to melting and fractionation processes. To address these issues and provide a common reference for geochemists and geophysicists, we have assembled a comprehensive petrological presentation of global MORB. The data are compiled from PetDB as well as unpublished data. Transforming the raw data into a useful catalog poses several challenges. First, to link each sample with a particular ridge segment requires defining the individual segments of the ridge system. Using the highest resolution bathymetry available, we identified 771 global ridge segments with a total length of 60,864km. For each segment we also generated a digital along-strike depth profile, enabling precise characterization of both mean depth and depth range. Second, as noted in earlier work, different laboratories calibrate their analyses to different standards, which can lead to significant, systematic offsets among analyses. It is therefore important to apply correction factors to the data to make them consistent with one another. Erroneous data and mislocated samples were identified and either eliminated or manually corrected, leading to a total dataset of 11,366 glass and 874 whole-rock analyses that have had interlab correction values carefully applied. These results show that the mean depth of the global ridge system is 2981m, calculated by averaging the segment mean depths, weighted by segment length. Of the 771 ridge segments, 476 have at least one basalt sample within 10km of the ridge axis but only 181 segments have samples from three or more unique locations. Using these data, a far more reliable composition can

  13. Identifying the molecular origin of global warming.

    PubMed

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

    2009-11-12

    We have investigated the physical characteristics of greenhouse gases (GHGs) to assess which properties are most important in determining the efficiency of a GHG. Chlorofluorocarbons (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 X-F bond dipole derivatives for the molecule, which leads to a nonlinear (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.

  14. 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.

  15. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma.

    PubMed

    Fishbein, Lauren; Leshchiner, Ignaty; Walter, Vonn; Danilova, Ludmila; Robertson, A Gordon; Johnson, Amy R; Lichtenberg, Tara M; Murray, Bradley A; Ghayee, Hans K; Else, Tobias; Ling, Shiyun; Jefferys, Stuart R; de Cubas, Aguirre A; Wenz, Brandon; Korpershoek, Esther; Amelio, Antonio L; Makowski, Liza; Rathmell, W Kimryn; Gimenez-Roqueplo, Anne-Paule; Giordano, Thomas J; Asa, Sylvia L; Tischler, Arthur S; Pacak, Karel; Nathanson, Katherine L; Wilkerson, Matthew D

    2017-02-13

    We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight PCC/PGL susceptibility genes. We identified CSDE1 as a somatically mutated driver gene, complementing four known drivers (HRAS, RET, EPAS1, and NF1). We also discovered fusion genes in PCCs/PGLs, involving MAML3, BRAF, NGFR, and NF1. Integrated analysis classified PCCs/PGLs into four molecularly defined groups: a kinase signaling subtype, a pseudohypoxia subtype, a Wnt-altered subtype, driven by MAML3 and CSDE1, and a cortical admixture subtype. Correlates of metastatic PCCs/PGLs included the MAML3 fusion gene. This integrated molecular characterization provides a comprehensive foundation for developing PCC/PGL precision medicine.

  16. 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

    2014-11-27

    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.

  17. Molecular cytogenetic characterization of mammary neuroendocrine carcinoma.

    PubMed

    Xiang, De-Bing; Wei, Bing; Abraham, Susan C; Huo, Lei; Albarracin, Constance T; Zhang, Hong; Babiera, Gildy; Caudle, Abigail S; Akay, Catherine L; Rao, Pulivarthi; Zhao, Yi-Jue; Lu, Xinyan; Wu, Yun

    2014-09-01

    Primary mammary neuroendocrine carcinoma (NEC) is an uncommon entity that accounts for 2% to 5% of breast carcinomas. Recent reports have shown that NEC of the breast is an aggressive subtype of mammary carcinoma that is distinct from invasive ductal carcinoma, not otherwise specified, and have suggested that these tumors have a poorer prognosis than invasive ductal carcinoma, not otherwise specified. In this study, we provide the first cytogenetic characterization of mammary NEC using both conventional G-banding and spectral karyotype on a group of 7 tumors. We identified clonal chromosomal aberrations in 5 (71.4%) cases, with 4 of them showing complex karyotypes. Of these, recurrent numerical aberrations included gain of chromosome 7 (n = 2) and loss of chromosome 15 (n = 2). Recurrent clonal structural chromosomal aberrations involved chromosomes 1 (n = 3), 3 (n = 2), 6q (n = 3), and 17q (n = 3). Of the 4 (57.1%) cases with complex karyotypes, 2 showed evidence of chromothripsis, a phenomenon in which tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. One of these had evidence of chromothripsis involving chromosomes 1, 6, 8, and 15. The other also had evidence of chromosome 8 chromothripsis, making this a recurrent finding shared by both cases. We also found that mammary NEC shared some cytogenetic abnormalities--such as trisomy 7 and 12--with other neuroendocrine tumors in the lung and gastrointestinal tract, suggesting trisomy 7 and 12 as potential common molecular aberrations in neuroendocrine tumors. To our knowledge, this is the first report on molecular cytogenetic characterization of mammary NEC.

  18. 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.

  19. Global Molecular Epidemiology of IMP-Producing Enterobacteriaceae.

    PubMed

    Matsumura, Yasufumi; Peirano, Gisele; Motyl, Mary R; Adams, Mark D; Chen, Liang; Kreiswirth, Barry; DeVinney, Rebekah; Pitout, Johann D D

    2017-04-01

    International data on the molecular epidemiology of Enterobacteriaceae with IMP carbapenemases are lacking. We performed short-read (Illumina) whole-genome sequencing on a global collection of 38 IMP-producing clinical Enterobacteriaceae (2008 to 2014). IMP-producing Enterobacteriaceae (7 varieties within 11 class 1 integrons) were mainly present in the South Pacific and Asia. Specific blaIMP-containing integrons (In809 with blaIMP-4, In722 with blaIMP-6, and In687 with blaIMP-14) were circulating among different bacteria in countries such as Australia, Japan, and Thailand. In1312 with blaIMP-1 was present in Klebsiella pneumoniae from Japan and Citrobacter freundii from Brazil. Klebsiella pneumoniae (n = 22) was the most common species; clonal complex 14 (CC14) from Philippines and Japan was the most common clone and contained In1310 with blaIMP-26 and In1321 with blaIMP-6 The Enterobacter cloacae complex (n = 9) consisted of Enterobacter hormaechei and E. cloacae cluster III. CC78 (from Taiwan) containing In73 with blaIMP-8 was the most common clone among the E. cloacae complex. This study highlights the importance of surveillance programs using the latest molecular techniques for providing insight into the characteristics and global distribution of Enterobacteriaceae with blaIMP genes.

  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. 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

  3. 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

  4. Characterization of molecular recognition in gas sensors

    SciTech Connect

    Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.; Goepel, W.

    1998-08-01

    Molecular recognition is an important topic when searching for new, selective coating materials for chemical sensing. Recently, the general idea of molecular recognition in the gas phase was challenged by Grate et al. However, in earlier thickness-shear mode resonator (TSMR) investigations, convincing evidence was presented for specific recognition of particular analyte target molecules. In this study, the authors systematically investigated coatings previously shown to be highly selective, such as the bucket-like cyclodextrins for chiral recognition, Ni-camphorates for the specific detection of the bases pyridine and DMMP (dimethylmethylphosphonate), and phthalocyanines to specifically detect benzene, toluene, and xylene (BTX).

  5. Molecular characterization of organic electronic films.

    PubMed

    DeLongchamp, Dean M; Kline, R Joseph; Fischer, Daniel A; Richter, Lee J; Toney, Michael F

    2011-01-18

    Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology.

  6. 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.

  7. Advances in molecular imaging for breast cancer detection and characterization

    PubMed Central

    2012-01-01

    Advances in our ability to assay molecular processes, including gene expression, protein expression, and molecular and cellular biochemistry, have fueled advances in our understanding of breast cancer biology and have led to the identification of new treatments for patients with breast cancer. The ability to measure biologic processes without perturbing them in vivo allows the opportunity to better characterize tumor biology and to assess how biologic and cytotoxic therapies alter critical pathways of tumor response and resistance. By accurately characterizing tumor properties and biologic processes, molecular imaging plays an increasing role in breast cancer science, clinical care in diagnosis and staging, assessment of therapeutic targets, and evaluation of responses to therapies. This review describes the current role and potential of molecular imaging modalities for detection and characterization of breast cancer and focuses primarily on radionuclide-based methods. PMID:22423895

  8. 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; Penny, Robert; Gardner, Johanna; Kemkes, Ariane; Mallery, David; Morris, Scott; Shelton, Troy; Shelton, Candace; Curley, Erin; Alexopoulou, Iakovina; Engel, Jay; Bartlett, John; Albert, Monique; Park, Do-Youn; Dhir, Rajiv; Luketich, James; Landreneau, Rodney; Janjigian, Yelena Y.; Kelsen, David P.; Cho, Eunjung; Ladanyi, Marc; Tang, Laura; McCall, Shannon J.; Park, Young S.; Cheong, Jae-Ho; Ajani, Jaffer; Camargo, M. Constanza; Alonso, Shelley; Ayala, Brenda; Jensen, Mark A.; Pihl, Todd; Raman, Rohini; Walton, Jessica; Wan, Yunhu; Demchok, John A.; Eley, Greg; Mills Shaw, Kenna R.; Sheth, Margi; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean Claude; Davidsen, Tanja; Hutter, Carolyn M.; Sofia, Heidi J.; Burton, Robert; Chudamani, Sudha; Liu, Jia

    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

  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. 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.

  11. [Biochemical and molecular characterization of gliadins].

    PubMed

    Qi, P F; Wei, Y M; Yue, Y W; Yan, Z H; Zheng, Y L

    2006-01-01

    Gliadins account for about 40-50% of the total proteins in wheat seeds and play an important role on the nutritional and processing quality of flour. Usually, gliadins could be divided into alpha- (alpha/beta-), gamma- and omega-groups, whereas the low-molecular-weigh (LMW) gliadins were novel seed storage proteins. The low-molecular-weight glutenin subunits (LMW-GSs) were also designated as gliadins in a few literatures. The genes encoding gliadins were mainly located on the short arms of group 6 and group 1 chromosomes, and not evenly distributed. Repetitive sequences covered most of un-coding regions, which attributed greatly to the evolution of wheat genome. Primary structure of each gliadin has been divided into several domains, and the long repetitive domains consisted of peptide motifs. Conserved cysteine residues mainly formed intramolecular disulphide bonds. The rare potential intermolecular disulphide bonds and the long repetitive domains played an important role in the wheat flour quality. There was a general idea that gliadin genes, even prolamin genes, have a common origin and subsequent divergence lead to the gene polymorphism. The gamma-gliadins have been considered to be the most ancient of the wheat prolamin family. Several elements in the 5'-flanking (e.g. CAAT and TATA box) and the 3'-flanking sequences had been detected, which had been shown necessary for the proper expression of gliadins.

  12. Comprehensive molecular characterization of urothelial bladder carcinoma.

    PubMed

    2014-03-20

    Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment of 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 signalling 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 microRNA 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 phosphatidylinositol-3-OH kinase/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 other common cancer studied so far, indicating the future possibility of targeted therapy for chromatin abnormalities.

  13. 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.

  14. 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

  15. Ligament repair: a molecular and immunohistological characterization.

    PubMed

    Roseti, L; Buda, R; Cavallo, C; Desando, G; Facchini, A; Grigolo, B

    2008-01-01

    The anterior cruciate ligament (ACL) is the most commonly injured tissue of the human knee. Its poor ability to regenerate after injury represents a challenge to ligament tissue engineering. An understanding of the molecular composition of the structures used for its repair is essential for clinical assessments and for the implementation of tissue engineering strategies. The objective of this study was to evaluate, both at gene and protein levels, the expression of characteristic molecules in human ACL, patellar, semitendinosus and gracilis tendons and in the ligament reconstructed with patellar or semitendinosus and gracilis tendons. We demonstrated that primary ACL and tendon tissues all express collagen I, II, Sox-9, tenascin-C and aggrecan. Collagen X expression was detected at very low levels or undetectable. Cathepsin B, MMP-1 and MMP-13 were expressed at higher levels in the ACL reconstructed by the two tendons, showing that a remodeling process occurs during "ligamentization". Both our molecular and immunohistochemical evaluations did not reveal significative differences between the tendons and ligaments analyzed. However, ACL reconstructed with semitendinosus and gracilis tendon seems to present a higher expression of collagen type II when compared to that reconstructed with patellar tendon. This study could give a reasonable identification of genetic and protein markers specific to tendon/ligament tissues and be helpful in testing tissue engineering approaches for ACL reconstruction.

  16. From puffs to global Ca2+ signals: How molecular properties shape global signals

    NASA Astrophysics Data System (ADS)

    Skupin, Alexander; Falcke, Martin

    2009-09-01

    The universality of Ca2+ as second messenger in living cells is achieved by a rich spectrum of spatiotemporal cellular concentration dynamics. Ca2+ release from internal storage compartments plays a key role in shaping cytosolic Ca2+ 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 Ca2+ oscillations and its relevance for modeling Ca2+ 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 Ca2+ 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 Ca2+ signaling.

  17. 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

    2016-02-19

    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.

  18. 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

    2016-08-09

    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.

  19. Molecular characterization of the mouse agouti locus.

    PubMed

    Bultman, S J; Michaud, E J; Woychik, R P

    1992-12-24

    The agouti (a) locus acts within the microenvironment of the hair follicle to regulate coat color pigmentation in the mouse. We have characterized a gene encoding a novel 131 amino acid protein that we propose is the one gene associated with the agouti locus. This gene is normally expressed in a manner consistent with a locus function, and, more importantly, its structure and expression are affected by a number of representative alleles in the agouti dominance hierarchy. In addition, we found that the pleiotropic effects associated with the lethal yellow (Ay) mutation, which include pronounced obesity, diabetes, and the development of neoplasms, are accompanied by deregulated overexpression of the agouti gene in numerous tissues of the adult animal.

  20. 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.

  1. Integrated Molecular Characterization of Uterine Carcinosarcoma.

    PubMed

    Cherniack, Andrew D; Shen, Hui; Walter, Vonn; Stewart, Chip; Murray, Bradley A; Bowlby, Reanne; Hu, Xin; Ling, Shiyun; Soslow, Robert A; Broaddus, Russell R; Zuna, Rosemary E; Robertson, Gordon; Laird, Peter W; Kucherlapati, Raju; Mills, Gordon B; Weinstein, John N; Zhang, Jiashan; Akbani, Rehan; Levine, Douglas A

    2017-03-13

    We performed genomic, epigenomic, transcriptomic, and proteomic characterizations of uterine carcinosarcomas (UCSs). Cohort samples had extensive copy-number alterations and highly recurrent somatic mutations. Frequent mutations were found in TP53, PTEN, PIK3CA, PPP2R1A, FBXW7, and KRAS, similar to endometrioid and serous uterine carcinomas. Transcriptome sequencing identified a strong epithelial-to-mesenchymal transition (EMT) gene signature in a subset of cases that was attributable to epigenetic alterations at microRNA promoters. The range of EMT scores in UCS was the largest among all tumor types studied via The Cancer Genome Atlas. UCSs shared proteomic features with gynecologic carcinomas and sarcomas with intermediate EMT features. Multiple somatic mutations and copy-number alterations in genes that are therapeutic targets were identified.

  2. 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.

  3. OT1_dhunter_3: Characterizing Molecular Clouds at Low Metallicity

    NASA Astrophysics Data System (ADS)

    Hunter, D.

    2010-07-01

    Molecular gas is difficult to detect from traditional millimeter CO transitions in dwarf galaxies below a certain metallicity. Yet, there is evidence for lots of molecular H_2 in these galaxies. Fortunately, Photo-dissociation Regions are a better tracer of the molecular material in low metallicity systems. In metal-poor galaxies, PDRs dominate the molecular core where CO is found, and in the current paradigm the PDR grows and the core shrinks as metallicity decreases. Thus, we expect critical differences in the molecular clouds of dwarfs compared to spirals, with the differences becoming more extreme with lower metallicity. Yet, understanding these differences and their consequences to star formation is essential to understanding the processes that drive star formation at low metallicities. Therefore, we propose to observe the PDRs in 5 regions in 5 typical metal-poor dwarf galaxies spanning a range in oxygen abundance. We will use these observations to characterize the molecular gas, examine the correspondence between the molecular clouds and the atomic gas and star formation characteristics, and determine the characteristics of the atomic ISM that are necessary for the formation of these dense molecular clouds. We will also test the molecular cloud structure paradigm as a function of metallicity.

  4. 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

  5. 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.

  6. Molecular characterization of the evolution of phagosomes

    PubMed Central

    Boulais, Jonathan; Trost, Matthias; Landry, Christian R; Dieckmann, Régis; Levy, Emmanuel D; Soldati, Thierry; Michnick, Stephen W; Thibault, Pierre; Desjardins, Michel

    2010-01-01

    Amoeba use phagocytosis to internalize bacteria as a source of nutrients, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in vertebrates, initiate a sustained immune response. By using a large-scale approach to identify and compare the proteome and phosphoproteome of phagosomes isolated from distant organisms, and by comparative analysis over 39 taxa, we identified an ‘ancient' core of phagosomal proteins around which the immune functions of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, compared with the whole cell proteome, has been acquired through gene duplication at a period coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation. PMID:20959821

  7. 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

  8. Global star formation in the L1630 molecular cloud

    NASA Technical Reports Server (NTRS)

    Lada, Elizabeth A.

    1992-01-01

    The first systematic and coordinated surveys for both dense gas and young stellar objects within a single molecular cloud, the L1630 molecular cloud are compared. It is found that (1) star formation in the L1630 molecular cloud occurs almost exclusively within the dense gas; (2) star formation does not occur uniformly throughout the dense gas and is strongly favored in a few very massive dense cores, where efficient conversion of molecular gas into stars has resulted in the production of rich stellar clusters; and (3) high gas densities and high gas mass may be necessary but not sufficient conditions for the formation of star clusters since two of the five most massive dense cores in the cloud have very low levels of star formation activity.

  9. 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.

  10. 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...

  11. Global and local properties used as analyses tools for molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bachlechner, Martina E.; Anderson, Jonas T.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Schiffbauer, Jarrod E.; Burky, Melissa R.; Ducatman, Samuel C.; Guffey, Eric J.; Serrano Ramos2, Fernando

    2006-03-01

    Molecular dynamics simulations have been used to study mechanical failure in realistic interface materials. Averaging over the individual atoms' contributions yields local and global information including displacements, bond angles, strains, stress tensor components, and pair distribution functions. A combined analysis of global and local properties facilitates detailed insight in the mechanisms of failure, which will eventually guide on how to prevent failure of interfaces.

  12. Preliminary molecular characterization of a fowl poxvirus isolate in Grenada.

    PubMed

    Arathy, D S; Tripathy, D N; Sabarinath, G P; Bhaiyat, M I; Chikweto, A; Matthew, V; Sharma, R N

    2010-09-01

    Two 1-mo-old local breed chickens, with gross lesions in the skin of the head region suspected to be fowl poxvirus infection, were submitted to the Diagnostic Laboratory of the School of Veterinary Medicine, Grenada, West Indies. Cutaneous lesions were collected from these birds for virus isolation, histopathologic diagnosis, and molecular analysis. Fowl poxvirus infection was confirmed by virus isolation in chicken embryo and by histopathology. Molecular characterization of the fowl poxvirus was conducted by PCR amplification of selected genomic fragments and by nucleotide sequencing. Integration of reticuloendotheliosis virus fragments into the fowl poxvirus genome was confirmed by PCR and DNA sequencing. This is the first report from the Caribbean region on the preliminary molecular characterization of a fowl poxvirus isolate.

  13. The molecular characterization of von Willebrand disease: good in parts.

    PubMed

    James, P D; Lillicrap, D

    2013-04-01

    Since the cloning of the gene that encodes von Willebrand factor (VWF), 27 years ago, significant progress has been made in our understanding of the molecular basis of the most common inherited bleeding disorder, von Willebrand disease (VWD). The molecular pathology of this condition represents a range of genetic mechanisms, some of which are now very well characterized, and others that are still under investigation. In general, our knowledge of the molecular basis of type 2 and 3 VWD is now well advanced, and in some instances this information is being used to enhance clinical management. In contrast, our understanding of the molecular pathogenesis of the most common form of VWD, type 1 disease, is still at an early stage, with preliminary evidence that this phenotype involves a complex interplay between environmental factors and the influence of genetic variability both within and outside of the VWF locus.

  14. Recent Advances in the Molecular Characterization of Circulating Tumor Cells

    PubMed Central

    Lowes, Lori E.; Allan, Alison L.

    2014-01-01

    Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch® system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a “real-time liquid biopsy” that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing. PMID:24633084

  15. 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

  16. 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.

  17. Global Franck-Condon breakdown: nonresonant molecular photoionization processes

    NASA Astrophysics Data System (ADS)

    Das, Aloke; Hardy, David; Aguilar, Alejandro; Kilcoyne, A. L. D.; Bozek, John D.; Poliakoff, Erwin D.

    2007-06-01

    We report photoelectron spectroscopy results of nonresonant Franck-Condon breakdown in the photoionization of CO and ICN. Most importantly, the deviations occur over a surprisingly wide range of energies. For the case of CO^+(X^2σ^+), the v^ + = 1/v^ + = 0 vibrational branching ratio is found to vary significantly (>50%) over a 200 eV range. While it is well understood that resonances can lead to coupling between photoelectron and molecular vibration, there is little information on nonresonant sources of coupling. It appears that Cooper minima may be responsible for the observations. Moreover, for ICN, the vibrationally resolved deviations from Franck-Condon behavior are vibrationally mode-specific. Studies on alternative molecular targets are planned to see whether they exhibit photoelectron dynamics that are geometry-dependent.

  18. Performance Characterization of Global Address Space Applications: A Case Study with NWChem

    SciTech Connect

    Hammond, Jeffrey R.; Krishnamoorthy, Sriram; Shende, Sameer; Romero, Nichols A.; Malony, Allen D.

    2012-02-01

    The use of global address space languages and one-sided communication for complex applications is gaining attention in the parallel computing community. However, lack of good evaluative methods to observe multiple levels of performance makes it difficult to isolate the cause of performance deficiencies and to understand the fundamental limitations of system and application design for future improvement. NWChem is a popular computational chemistry package which depends on the Global Arrays/ ARMCI suite for partitioned global address space functionality to deliver high-end molecular modeling capabilities. A workload characterization methodology was developed to support NWChem performance engineering on large-scale parallel platforms. The research involved both the integration of performance instrumentation and measurement in the NWChem software, as well as the analysis of one-sided communication performance in the context of NWChem workloads. Scaling studies were conducted for NWChem on Blue Gene/P and on two large-scale clusters using different generation Infiniband interconnects and x86 processors. The performance analysis and results show how subtle changes in the runtime parameters related to the communication subsystem could have significant impact on performance behavior. The tool has successfully identified several algorithmic bottlenecks which are already being tackled by computational chemists to improve NWChem performance.

  19. 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.

  20. Morphological, physiochemical and molecular characterization of Anabaena strains.

    PubMed

    Prasanna, Radha; Kumar, Ramesh; Sood, Anjuli; Prasanna, B M; Singh, P K

    2006-01-01

    A set of 30 Anabaena strains, isolated from diverse geographical regions of India, were characterized using morphological and physiochemical attributes as well as molecular marker profiles. Significant differences were observed among the Anabaena strains with regard to the shape and size of trichomes and individual cells within a filament, besides qualitative and quantitative aspects of phycobiliprotein accumulation and activities of enzymes involved in nitrogen metabolism. Analyses of molecular polymorphisms in a selected set of 13 Anabaena strains, using primers based on repetitive sequences in the genome, led to unambiguous differentiation of the strains as well as understanding of their genetic relationships. Informative morphological, physio-chemical and molecular characters have been identified that could aid in differentiation and utilization of Anabaena strains as bioinoculants or as sources of pigments.

  1. 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

  2. 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.

  3. Rapid detection and simultaneous molecular profile characterization of Acanthamoeba infections.

    PubMed

    Goldschmidt, Pablo; Degorge, Sandrine; Benallaoua, Djida; Batellier, Laurence; Di Cave, David; Chaumeil, Christine

    2012-10-01

    Diagnosis of Acanthamoeba by microscopic examination, culture, and polymerase chain reactions (PCRs) has several limitations (sensitivity, specificity, lack of detection of several strains, cost of testing for discrimination among strains). We developed a new high-resolution melting real-time PCR (HRM) to detect and characterize Acanthamoeba infections. HRM performances were evaluated with strains from the American Type Culture Collection (ATCC) and with 20 corneal scrapings. The DNA extracted from specimens were amplified, detected, and characterized in 1 run using 2 original primers diluted in a solution containing an intercalating dye. Detection and molecular characterization of Acanthamoeba infections could be achieved in less than 2.5 h with a dramatic reduction in cost of reactants (postamplification procedures and radioactive or fluorescent-labeled molecular probes were unnecessary). HRM detection limits were 0.1 cyst/μL or less (including genotypes T5 and T11), and its sensitivity and specificity were higher than other molecular tests. For the tested strains from the ATCC, the HRM drafted 4 different profiles: Type I (genotypes T2 and T4), Type II (T5 and T7), Type III (T8), and Type IV (T1, T3, T6, T9, T11, T12, and T13).

  4. 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.

  5. 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.

  6. 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

  7. An integrative characterization of recurrent molecular aberrations in glioblastoma genomes.

    PubMed

    Sintupisut, Nardnisa; Liu, Pei-Ling; Yeang, Chen-Hsiang

    2013-10-01

    10 CNVs manifested strong negative and positive associations with survival times in brain tumors. By aligning the information of association modules with the established GBM subclasses based on transcription or methylation levels, we found each subclass possessed multiple concurrent molecular aberrations. Furthermore, the joint molecular characteristics derived from 16 association modules had prognostic power not explained away by the strong biomarker of CpG island methylator phenotypes. Functional and survival analyses indicated that immune/inflammatory responses and epithelial-mesenchymal transitions were among the most important determining processes of prognosis. Finally, we demonstrated that certain molecular aberrations uniquely recurred in GBM but were relatively rare in non-GBM glioma cells. These results justify the utility of an integrative analysis on cancer genomes and provide testable characterizations of driver aberration events in GBM.

  8. 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.

  9. Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques

    PubMed Central

    Menendez, M. C.; Palenque, E.; Navarro, M. C.; Nuñez, M. C.; Rebollo, M. J.; Garcia, M. J.

    2001-01-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members. PMID:11724827

  10. Optimization, evaluation, and characterization of molecularly imprinted polymers.

    PubMed

    Spivak, David A

    2005-12-06

    The underlying mechanisms for molecular recognition exhibited by the imprinting effect can be attributed to two processes. The pre-organization of complementary functional groups in the polymer by the template and the formation of a shape-selective cavity that is complementary to the template. However, measurements of binding and selectivity combine all effects contributing to molecular recognition in MIPs into one figure of merit. If the two molecules being compared are not enantiomers, then there are other factors which contribute to differential binding such as size or different partitioning effects due to differences in polarity, hydrophobicity, ionization state or shape and/or conformational effects. The best probe for the imprinting effect is therefore an enantiomeric pair. Therefore, the first section of this article discusses enantioselective optimization of polymerization, the second section will review methods employed for evaluation of MIPs and the last section will cover materials science methods used to characterize the physical properties of MIP materials.

  11. Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics.

    PubMed

    Urano, Kaoru; Maruyama, Kyonoshin; Ogata, Yoshiyuki; Morishita, Yoshihiko; Takeda, Migiwa; Sakurai, Nozomu; Suzuki, Hideyuki; Saito, Kazuki; Shibata, Daisuke; Kobayashi, Masatomo; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

    2009-03-01

    Drought is the major environmental threat to agricultural production and distribution worldwide. Adaptation by plants to dehydration stress is a complex biological process that involves global changes in gene expression and metabolite composition. Here, using one type of functional genomics analysis, metabolomics, we characterized the metabolic phenotypes of Arabidopsis wild-type and a knockout mutant of the NCED3 gene (nc3-2) under dehydration stress. NCED3 plays a role in the dehydration-inducible biosynthesis of abscisic acid (ABA), a phytohormone that is important in the dehydration-stress response in higher plants. Metabolite profiling performed using two types of mass spectrometry (MS) systems, gas chromatography/time-of-flight MS (GC/TOF-MS) and capillary electrophoresis MS (CE-MS), revealed that accumulation of amino acids depended on ABA production, but the level of the oligosaccharide raffinose was regulated by ABA independently under dehydration stress. Metabolic network analysis showed that global metabolite-metabolite correlations occurred in dehydration-increased amino acids in wild-type, and strong correlations with raffinose were reconstructed in nc3-2. An integrated metabolome and transcriptome analysis revealed ABA-dependent transcriptional regulation of the biosynthesis of the branched-chain amino acids, saccharopine, proline and polyamine. This metabolomics analysis revealed new molecular mechanisms of dynamic metabolic networks in response to dehydration stress.

  12. 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

  13. 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...

  14. Molecular characterization of Brazilian isolates of orf virus.

    PubMed

    Mazur, C; Ferreira, I I; Rangel Filho, F B; Galler, R

    2000-05-11

    Outbreaks of an epidermic disease suggesting parapox virus infections have been observed in all major herds of sheep and goats from different geographical areas of Brazil. Clinical samples (dried scabs) were collected and orf virus was isolated and characterized by electron microscopy in previous work. In order to characterize these viruses at the molecular level, a modified methodology for genomic DNA extraction directly from scabs was used and such DNA was used to derive the restriction enzyme digestion patterns for clinical samples from three distinct geographic origins. Pulsed field gel electrophoresis was used to separate restriction enzyme DNA fragments and heterogeneity among isolates from different geographic areas could be observed on stained gels. The HindIII-G DNA fragment from orf-A virus genome was cloned and hybridized to DNA of other orf virus isolates. Further heterogeneity was confirmed by these hybridizations.

  15. Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification.

    PubMed

    Sjödahl, Gottfrid; Eriksson, Pontus; Liedberg, Fredrik; Höglund, Mattias

    2017-02-13

    Global mRNA expression analysis is efficient for phenotypic profiling of tumours and has been used to define molecular subtypes for almost every major tumour type. A key limitation is that most tumours are communities of both tumour and non-tumour cells. This problem is particularly pertinent when analysing advanced invasive tumours, known to induce major changes and responses in both the tumour and the surrounding tissue. To identify bladder cancer tumour-cell phenotypes and compare classification by tumour-cell phenotype with classification by global gene expression analysis, we analysed 307 advanced bladder cancers (cystectomised) both by genome gene expression analysis and by immunohistochemistry using antibodies for 28 proteins. By systematic analysis of gene and protein expression data, focusing on key molecular processes, we describe five tumour-cell phenotypes of advanced urothelial carcinoma; Urothelial-like, Genomically Unstable, Basal/SCC-like, Mesenchymal-like, and Small cell/Neuroendocrine like. We provide molecular pathological definitions for each subtype. Tumours expressing urothelial differentiation factors show inconsistent and abnormal protein expression of terminal differentiation markers, suggesting pseudo-differentiation. Cancers with different tumour-cell phenotypes may co-cluster (converge), and cases with identical tumour-cell phenotypes may cluster apart (diverge) in global mRNA analyses. This divergence/convergence suggests that broad global commonalities related to the invasive process may exist between muscle-invasive tumours regardless of specific tumour-cell phenotype. Hence, there is a systematic disagreement in subtype classification determined by global mRNA profiling and by IHC profiling at the tumour-cell level. We suggest that a combination of molecular pathology (tumour cell phenotype) and global mRNA profiling (context) is required for adequate subtype classification of muscle-invasive bladder cancer.

  16. 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.

  17. Hazelnut Allergens: Molecular Characterization, Detection, and Clinical Relevance.

    PubMed

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

    2016-11-17

    In last few years, special attention has been given to food-induced allergies, in which hazelnut allergy is highlighted. Hazelnut is one of the most commonly consumed tree nuts, being largely used by the food industry in a variety of processed foods. It has been regarded as a food with potential health benefits, but also as a source of allergens capable of inducing mild to severe allergic reactions in sensitized individuals. Considering the great number of reports addressing hazelnut allergens, with an estimated increasing trend, this review intends to assemble all the relevant information available so far on the following main issues: prevalence of tree nut allergy, clinical threshold levels, molecular characterization of hazelnut allergens (Cor a 1, Cor a 2, Cor a 8, Cor a 9, Cor a 10, Cor a 11, Cor a 12, Cor a 14, and Cor a TLP) and their clinical relevance, and methodologies for detection of hazelnut allergens in foods. A comprehensive overview of the current data about the molecular characterization of hazelnut allergens is presented, relating to biochemical classification and biological function with clinical importance. Recent advances in hazelnut allergen detection methodologies are summarized and compared, including all the novel protein-based and DNA-based approaches.

  18. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

    NASA Astrophysics Data System (ADS)

    Zaccai, Giuseppe; Natali, Francesca; Peters, Judith; Řihová, Martina; Zimmerman, Ella; Ollivier, J.; Combet, J.; Maurel, Marie-Christine; Bashan, Anat; Yonath, Ada

    2016-11-01

    Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.

  19. 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.

  20. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

    PubMed Central

    Zaccai, Giuseppe; Natali, Francesca; Peters, Judith; Řihová, Martina; Zimmerman, Ella; Ollivier, J.; Combet, J.; Maurel, Marie-Christine; Bashan, Anat; Yonath, Ada

    2016-01-01

    Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome. PMID:27849042

  1. 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.

  2. MOLECULAR CHARACTERIZATION OF CYP2B6 SUBSTRATES

    PubMed Central

    Ekins, Sean; Iyer, Manisha; Krasowski, Matthew D.; Kharasch, Evan D.

    2008-01-01

    CYP2B6 has not been as fully characterized at the molecular level as other members of the human cytochrome P450 family. As more widely used in vitro probes for characterizing the involvement of this enzyme in the metabolism of xenobiotics have become available, the number of molecules identified as CYP2B6 substrates has increased. In this study we have analyzed the available kinetic data generated by multiple laboratories with human recombinant expressed CYP2B6 and along with calculated molecular properties derived from the ChemSpider database, we have determined the molecular features that appear to be important for CYP2B6 substrates. In addition we have applied 2D and 3D QSAR methods to generate predictive pharmacophore and 2D models. For 28 molecules with Km data, the molecular weight (mean ± SD) is 253.78±74.03, ACD/logP is 2.68±1.51, LogDpH 5.5 is 1.51±1.43, LogDpH 7.4 is 2.02±1.25, hydrogen bond donor (HBD) count is 0.57 ±0.57, hydrogen bond acceptor (HBA) count is 2.57±1.37, rotatable bonds is 3.50±2.71 and total polar surface area (TPSA) is 27.63±19.42. A second set of 15 molecules without Km data possessed similar mean molecular property values. These properties are comparable to those of a set of 21 molecules used in a previous pharmacophore modeling study (Ekins et al., J Pharmacol Exp Ther 288 (1), 21–29, 1999). Only the LogD and HBD values were statistically significantly different between these different datasets. We have shown that CYP2B6 substrates are generally small hydrophobic molecules that are frequently central nervous system active, which may be important for drug discovery research. PMID:18537573

  3. 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.

  4. 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.

  5. Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types.

    PubMed

    Cogliati, Massimo

    2013-01-01

    Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge.

  6. Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types

    PubMed Central

    Cogliati, Massimo

    2013-01-01

    Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge. PMID:24278784

  7. 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...

  8. 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

  9. 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.

  10. Physiological and molecular characterization of atypical isolates of Malassezia furfur.

    PubMed

    González, A; Sierra, R; Cárdenas, M E; Grajales, A; Restrepo, S; Cepero de García, M C; Celis, A

    2009-01-01

    The species constituting the genus Malassezia are considered to be emergent opportunistic yeasts of great importance. Characterized as lipophilic yeasts, they are found in normal human skin flora and sometimes are associated with different dermatological pathologies. We have isolated seven Malassezia species strains that have a different Tween assimilation pattern from the one typically used to differentiate M. furfur, M. sympodialis, and M. slooffiae from other Malassezia species. In order to characterize these isolates of Malassezia spp., we studied their physiological features and conducted morphological and molecular characterization by PCR-restriction fragment length polymorphism and sequencing of the 26S and 5.8S ribosomal DNA-internal transcribed spacer 2 regions in three strains from healthy individuals, four clinical strains, and eight reference strains. The sequence analysis of the ribosomal region was based on the Blastn algorithm and revealed that the sequences of our isolates were homologous to M. furfur sequences. To support these findings, we carried out phylogenetic analyses to establish the relationship of the isolates to M. furfur and other reported species. All of our results confirm that all seven strains are M. furfur; the atypical assimilation of Tween 80 was found to be a new physiological pattern characteristic of some strains isolated in Colombia.

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

    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.

  12. Biochemical and molecular characterization of hazelnut (Corylus avellana) seed lipoxygenases.

    PubMed

    Santino, Angelo; De Paolis, Angelo; Gallo, Antonia; Quarta, Angela; Casey, Rod; Mita, Giovanni

    2003-11-01

    Plant lipoxygenases (LOXs) are a class of dioxygenases which display diverse functions in several physiological processes such as growth, development and response to biotic and abiotic stresses. Even though LOXs have been characterized from several plant species, the physiological role of seed LOXs is still unclear. With the aim to better clarify the occurrence of LOXs and their influence on hazelnut seed quality, we carried out the biochemical and molecular characterization of the main LOX isoforms expressed during seed development. A genomic clone containing a complete LOX gene was isolated and fully characterized. The 9887 bp sequence reported contains an open reading frame of 5334 bp encoding a putative polypeptide of 99 kDa. Semiquantitative RT-PCR carried out from RNAs extracted from seeds at different maturation stages showed that LOXs are mainly expressed at early developmental stages. These results were confirmed by LOX activity assays. Biochemical characterization of the reaction products of the hazelnut LOX indicated that it is a 9-LOX. Two cDNAs were isolated by RT-PCR carried out on total RNA from immature hazelnut seeds. Sequence analysis indicated that the two cDNAs are highly homologous (91.9% degree of identity) and one of these corresponded exactly to the genomic clone. The deduced amino acid sequences of the hazelnut LOXs showed that they are closely related to a previously reported almond LOX (79.5% identity) and, to a lesser extent, to some LOXs involved in plant responses to pathogens (cotton and tobacco LOXs, 75.5 and 74.6% identity, respectively). The physiological role of hazelnut LOXs and their role in influencing seed quality are also discussed.

  13. Isolation and molecular characterization of circulating melanoma cells.

    PubMed

    Luo, Xi; Mitra, Devarati; Sullivan, Ryan J; Wittner, Ben S; Kimura, Anya M; Pan, Shiwei; Hoang, Mai P; Brannigan, Brian W; Lawrence, Donald P; Flaherty, Keith T; Sequist, Lecia V; McMahon, Martin; Bosenberg, Marcus W; Stott, Shannon L; Ting, David T; Ramaswamy, Sridhar; Toner, Mehmet; Fisher, David E; Maheswaran, Shyamala; Haber, Daniel A

    2014-05-08

    Melanoma is an invasive malignancy with a high frequency of blood-borne metastases, but circulating tumor cells (CTCs) have not been readily isolated. We adapted microfluidic CTC capture to a tamoxifen-driven B-RAF/PTEN mouse melanoma model. CTCs were detected in all tumor-bearing mice and rapidly declined after B-RAF inhibitor treatment. CTCs were shed early from localized tumors, and a short course of B-RAF inhibition following surgical resection was sufficient to dramatically suppress distant metastases. The large number of CTCs in melanoma-bearing mice enabled a comparison of RNA-sequencing profiles with matched primary tumors. A mouse melanoma CTC-derived signature correlated with invasiveness and cellular motility in human melanoma. CTCs were detected in smaller numbers in patients with metastatic melanoma and declined with successful B-RAF-targeted therapy. Together, the capture and molecular characterization of CTCs provide insight into the hematogenous spread of melanoma.

  14. 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.

  15. Global characterization of atmospheric hydrology with HDO measurements from Aura

    NASA Astrophysics Data System (ADS)

    Noone, D.; Worden, J.; Bowman, K.

    2005-12-01

    The history of condensation and evaporation processes is captured by the isotopic composition of atmospheric water. While the analysis of the isotopic measurement from a global standpoint provides new insight to the role of the hydrologic cycle in climate, the richness of the measurements lies in the fact that the isotopes are indicative of processes rather than atmospheric state. Isotopic methods have been used extensively in previous studies to understand continental hydrology and specifically estimate recycling of water between the atmosphere and landscapes. Similarly the use of water isotopes in determining the sources of atmospheric water has been endorsed widely based on global model calculations. The isotopic composition of precipitation has been monitored since the 1950 globally, yet the existing vapor isotope datasets are inadequate to allow source estimation at anything but local scales and largely inadequate for examining the hydrology of the troposphere at large. New measurements from the Tropospheric Emission Spectrometer (TES) aboard the NASA Aura spacecraft address this need by providing estimates of vapor H2O and HDO in the lower and mid troposphere. Here, we use over 5000 observations scattered globally from 9 days of nadir observations taken in November 2004 and January 2005. The retrieved HDO and H2O profiles are averaged between 850 hPa and 400 hPa to attain a typical precision is approximately 1%, which translates to an error in HDO delta values of around 15 permil. The data show greater depletion toward the polar regions and is characteristic of preferential removal of heavy nuclides during condensation as water vapor moves pole-ward. These observations are consistent with precipitation measurements that also show a latitudinal gradient. In the extra-tropics we contrast results from cloud free profiles with low humidity (where evaporation from the ocean surface is more dominant) with those having clouds and high humidity (where condensations

  16. 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.

  17. Isolation and molecular characterization of bovine enteroviruses in Egypt.

    PubMed

    Sobhy, N M; Mor, S K; Mohammed, M E M; Bastawecy, I M; Fakhry, H M; Youssef, C R B; Abouzeid, N Z; Goyal, S M

    2015-12-01

    Enteroviruses belong to the Picornaviridae family and infect a wide range of mammals including cattle. Bovine enterovirus (BEV) has recently been reclassified into E and F serotypes. BEV was first isolated in Egypt in 1966 although it has been known in other countries since the 1950s. In this study, BEV-F2 was isolated from calves with severe diarrhea and the isolated viruses were subjected to molecular characterization. Illumina sequencing of one of the isolates revealed the presence of a complete BEV-F genome sequence. The phylogenetic analysis revealed nucleotide substitutions along the genome in comparison with other known strains of BEV-F (HQ663846, AY508697 and DQ092795). Two primer sets were designed from the 3D and 5'NTR regions and used for the examination of the remaining isolates, which were confirmed to be of the BEV-F2 serotype. The availability of the complete genome sequence of this virus adds to the sequence database of the members of Picornaviridae and should be useful in future molecular studies of BEV.

  18. Integrated genomic and molecular characterization of cervical cancer.

    PubMed

    2017-03-16

    Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers.

  19. 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.

  20. Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics.

    PubMed

    Rindler, Tara N; Hinton, Robert B; Salomonis, Nathan; Ware, Stephanie M

    2017-01-18

    Pediatric restrictive cardiomyopathy (RCM) is a genetically heterogeneous heart disease with limited therapeutic options. RCM cases are largely idiopathic; however, even within families with a known genetic cause for cardiomyopathy, there is striking variability in disease severity. Although accumulating evidence implicates both gene expression and alternative splicing in development of dilated cardiomyopathy (DCM), there have been no detailed molecular characterizations of underlying pathways dysregulated in RCM. RNA-Seq on a cohort of pediatric RCM patients compared to other forms of adult cardiomyopathy and controls identified transcriptional differences highly common to the cardiomyopathies, as well as those unique to RCM. Transcripts selectively induced in RCM include many known and novel G-protein coupled receptors linked to calcium handling and contractile regulation. In-depth comparisons of alternative splicing revealed splicing events shared among cardiomyopathy subtypes, as well as those linked solely to RCM. Genes identified with altered alternative splicing implicate RBM20, a DCM splicing factor, as a potential mediator of alternative splicing in RCM. We present the first comprehensive report on molecular pathways dysregulated in pediatric RCM including unique/shared pathways identified compared to other cardiomyopathy subtypes and demonstrate that disruption of alternative splicing patterns in pediatric RCM occurs in the inverse direction as DCM.

  1. Molecular characterization of Rhodococcus equi isolates in equines

    PubMed Central

    Javed, Rabyia; Taku, A. K.; Sharma, R. K.; Badroo, Gulzaar Ahmed

    2017-01-01

    Aim: The aim was to determine the occurrence of Rhodococcus equi in equines and their environment in Jammu (R.S. Pura, Katra), molecular characterization and to determine the antibiotic resistance pattern of R. equi. Materials and Methods: A total of 96 nasopharyngeal swab samples were collected from equines. The organism was isolated on Columbia nalidixic acid agar containing 5% sheep blood as well as on sheep blood agar and was later confirmed by cultural characteristics and biochemical tests. Molecular detection of R. equi isolates was done by 16S rRNA gene amplification followed by virulence associated protein A (Vap A) gene amplification. Antibiogram was performed against five antibiotics, viz., amoxicillin, penicillin G, streptomycin, rifampicin, and methicillin. Results: During the study, 9 R. equi isolates were identified on the basis of cultural and biochemical tests. In the polymerase chain reaction based detection, 3 among the 9 rhodococcal isolates were positive for species-specific 16S rRNA gene and revealed amplicon of 450 bp for confirmation of 16S rRNA gene. None of the sample was found positive for Vap A gene. In antibiogram, R. equi isolates were found sensitive for amoxicillin, while some isolates were also found resistant to the most conventional antibiotic penicillin G. Conclusion: From this study, it was concluded that R. equi infection is prevalent in equines in Jammu region of India and the indiscriminate use of the antibiotics is leading toward the development of resistant strains of R. equi. PMID:28246441

  2. Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics

    PubMed Central

    Rindler, Tara N.; Hinton, Robert B.; Salomonis, Nathan; Ware, Stephanie M.

    2017-01-01

    Pediatric restrictive cardiomyopathy (RCM) is a genetically heterogeneous heart disease with limited therapeutic options. RCM cases are largely idiopathic; however, even within families with a known genetic cause for cardiomyopathy, there is striking variability in disease severity. Although accumulating evidence implicates both gene expression and alternative splicing in development of dilated cardiomyopathy (DCM), there have been no detailed molecular characterizations of underlying pathways dysregulated in RCM. RNA-Seq on a cohort of pediatric RCM patients compared to other forms of adult cardiomyopathy and controls identified transcriptional differences highly common to the cardiomyopathies, as well as those unique to RCM. Transcripts selectively induced in RCM include many known and novel G-protein coupled receptors linked to calcium handling and contractile regulation. In-depth comparisons of alternative splicing revealed splicing events shared among cardiomyopathy subtypes, as well as those linked solely to RCM. Genes identified with altered alternative splicing implicate RBM20, a DCM splicing factor, as a potential mediator of alternative splicing in RCM. We present the first comprehensive report on molecular pathways dysregulated in pediatric RCM including unique/shared pathways identified compared to other cardiomyopathy subtypes and demonstrate that disruption of alternative splicing patterns in pediatric RCM occurs in the inverse direction as DCM. PMID:28098235

  3. Molecular Characterization of Brown Carbon in Biomass Burning Aerosol Particles

    SciTech Connect

    Lin, Peng; Aiona, Paige K.; Li, Ying; Shiraiwa, Manabu; Laskin, Julia; Nizkorodov, Sergey A.; Laskin, Alexander

    2016-11-01

    Emissions from biomass burning are a significant source of brown carbon (BrC) in the atmosphere. In this study, we investigate the molecular composition of freshly-emitted biomass burning organic aerosol (BBOA) samples collected during test burns of selected biomass fuels: sawgrass, peat, ponderosa pine, and black spruce. We characterize individual BrC chromophores present in these samples using high performance liquid chromatography coupled to a photodiode array detector and a high-resolution mass spectrometer. We demonstrate that both the overall BrC absorption and the chemical composition of light-absorbing compounds depend significantly on the type of biomass fuels and burning conditions. Common BrC chromophores in the selected BBOA samples include nitro-aromatics, polycyclic aromatic hydrocarbon derivatives, and polyphenols spanning a wide range of molecular weights, structures, and light absorption properties. A number of biofuel-specific BrC chromophores are observed, indicating that some of them may be used as potential markers of BrC originating from different biomass burning sources. On average, ~50% of the light absorption above 300 nm can be attributed to a limited number of strong BrC chromophores, which may serve as representative light-absorbing species for studying atmospheric processing of BrC aerosol. The absorption coefficients of BBOA are affected by solar photolysis. Specifically, under typical atmospheric conditions, the 300 nm absorbance decays with a half-life of 16 hours. A “molecular corridors” analysis of the BBOA volatility distribution suggests that many BrC compounds in the fresh BBOA have low volatility (<1 g m-1) and will be retained in the particle phase under atmospherically relevant conditions.

  4. 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.

  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. 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...

  7. 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.

  8. 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.

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

    PubMed Central

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

    1992-01-01

    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 mutations which remained uncharacterized by this approach were defined by denaturing gradient gel electrophoresis (DGGE) followed by direct sequence analysis on amplified DNA. We 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 we 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. The results herein presented allowed an expansion of the applicability of prenatal diagnosis by DNA analysis, to all couples at risk for beta-thalassemia in our population. Images Figure 2 PMID:1734721

  10. Molecular cloning and characterization of hagfish estrogen receptors.

    PubMed

    Nishimiya, Osamu; Katsu, Yoshinao; Inagawa, Hiroyuki; Hiramatsu, Naoshi; Todo, Takashi; Hara, Akihiko

    2017-01-01

    One or more distinct forms of the nuclear estrogen receptor (ER) have been isolated from many vertebrates to date. To better understand the molecular evolution of ERs, we cloned and characterized er cDNAs from the inshore hagfish, Eptatretus burgeri, a modern representative of the most primitive vertebrates, the agnathans. Two er cDNAs, er1 and er2, were isolated from the liver of a reproductive female hagfish. A phylogenetic analysis placed hagfish ER1 into a position prior to the divergence of vertebrate ERs. Conversely, hagfish ER2 was placed at the base of the vertebrate ERβ clade. The tissue distribution patterns of both ER subtype mRNAs appeared to be different, suggesting that each subtype has different physiological roles associated with estrogen actions. An estrogen responsive-luciferase reporter assay using mammalian HEK293 cells was used to functionally characterize these hagfish ERs. Both ER proteins displayed estrogen-dependent activation of transcription. These results clearly demonstrate that the hagfish has two functional ER subtypes.

  11. 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.

  12. 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

  13. 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.

  14. Molecular characterization of the effects of Y-27632.

    PubMed

    Darenfed, Hassina; Dayanandan, Bama; Zhang, Tong; Hsieh, Sidney H-K; Fournier, Alyson E; Mandato, Craig A

    2007-02-01

    Many key cellular functions, such as cell motility and cellular differentiation are mediated by Rho-associated protein kinases (ROCKs). Numerous studies have been conducted to examine the ROCK signal transduction pathways involved in these motile and contractile events with the aid of pharmacological inhibitors such as Y-27632. However the molecular mechanism of action of Y-27632 has not been fully defined. To assess the relative contribution of these Rho effectors to the effects of Y-27632, we compared the cytoskeletal phenotype, wound healing and neurite outgrowth in cells treated with Y-27632 or subjected to knockdown with ROCK-I, ROCK-II or PRK-2- specific siRNAs. Reduction of ROCK-I enhances the formation of thin actin-rich membrane extensions, a phenotype that closely resembles the effect of Y-27632. Knockdown of ROCK II or PRK-2, leads to the formation of disc-like extensions and thick actin bundles, respectively. The effect of ROCK-I knockdown also mimicked the effect of Y-27632 on wound closer rates. ROCK-I knockdown and Y-27632 enhanced wound closure rates, while ROCK-II and PRK-2 were not appreciably different from control cells. In neurite outgrowth assays, knockdown of ROCK-I, ROCK-II or PRK-2 enhances neurite lengths, however no individual knockdown stimulated neurite outgrowth as robustly as Y-27632. We conclude that several kinases contribute to the global effect of Y-27632 on cellular responses.

  15. 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.

  16. 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

  17. Integration of Molecular Pathology, Epidemiology, and Social Science for Global Precision Medicine

    PubMed Central

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

    2015-01-01

    Summary 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. PMID:26636627

  18. 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.

  19. Molecular cloning, purification and characterization of Brugia malayi phosphoglycerate kinase.

    PubMed

    Kumar, Ranjeet; Doharey, Pawan Kumar; Saxena, Jitendra Kumar; Rathaur, Sushma

    2017-04-01

    Phosphoglycerate kinase (PGK) is a glycolytic enzyme present in many parasites. It has been reported as a candidate molecule for drug and vaccine developments. In the present study, a full-length cDNA encoding the Brugia malayi 3-phosphoglycerate kinase (BmPGK) with an open reading frame of 1.3 kb was isolated and PCR amplified and cloned. The exact size of the BmPGK's ORF is 1377 bps. The BmPGK gene was subcloned into pET-28a (+) expression vector, the expressed enzyme was purified by affinity column and characterized. The SDS-PAGE analysis revealed native molecular weight of recombinant Brugia malayi 3-phosphoglycerate kinase (rBmPGK) to be ∼45 kDa. The enzyme was found sensitive to temperature and pH, it showed maximum activity at 25 °C and pH 8.5. The Km values for PGA and ATP were 1.77 and 0.967 mM, respectively. The PGK inhibitor, clorsulon and antifilarial drugs albendazole and ivermectin inhibited the enzyme. The specific inhibitor of PGK, clorsulon, competitively inhibited enzyme with Ki value 1.88 μM. Albendazole also inhibited PGK competitively with Ki value 35.39 μM. Further these inhibitory studies were confirmed by docking and molecular simulation of drugs with enzyme. Clorsulon interacted with substrate binding site with glutamine 37 as well as in hinge regions with aspartic acid 385 and valine 387 at ADP binding site. On the other hand albendazole interacted with asparagine 335 residues. These effects were in good association with binding interactions. Thus current study might help in designing and synthesis of effective inhibitors for this novel drug target and understanding their mode of interaction with the potent anthelmintic drugs.

  20. Progress in the Molecular Characterization of Hepatobiliary Transporters.

    PubMed

    Keppler, Dietrich

    2017-01-01

    Over the last 25 years, our understanding of the driving forces for hepatobiliary elimination and knowledge of the molecular basis of uptake and efflux transport in hepatocytes have undergone fundamental changes. This refers to bile acids and many other endogenous substances as well as to drugs that are eliminated on the hepatobiliary route. In this development, not only molecular cloning, functional characterization, and localization of transporters were decisive, but also the discovery of hereditary mutations in genes encoding sinusoidal uptake transporters and canalicular export pumps in humans and rodents. Uptake by passive diffusion and elimination into bile driven by the electrochemical gradient are no longer considered relevant for hepatobiliary elimination in the intact organism. Furthermore, insights into the relative roles of uptake transporters and unidirectional ATP-driven efflux pumps were obtained when we established double-transfected polarized cell lines stably expressing, as an example, the hepatocellular uptake transporter OATP1B3 and the apical (canalicular) efflux pump multidrug resistance protein 2 (MRP2; ABCC2). ATP-dependent efflux transporters localized to the basolateral (sinusoidal) hepatocyte membrane, particularly MRP3 (ABCC3) and MRP4 (ABCC4), pump substances from hepatocytes into sinusoidal blood. Bile acids are substrates for human MRP4 in the presence of physiological concentrations of reduced glutathione, which undergoes co-transport. These efflux pumps have been recognized in recent years to play an important compensatory role in cholestasis and to contribute to the balance between uptake and efflux of bile acids and other organic anions during the vectorial transport from blood into bile. This sinusoidal efflux not only enables subsequent renal elimination but also facilitates the re-uptake of substances into neighboring hepatocytes located more centrally and downstream in the sinusoid.

  1. 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.

  2. Global subcellular characterization of protein degradation using quantitative proteomics.

    PubMed

    Larance, Mark; Ahmad, Yasmeen; Kirkwood, Kathryn J; Ly, Tony; Lamond, Angus I

    2013-03-01

    Protein degradation provides an important regulatory mechanism used to control cell cycle progression and many other cellular pathways. To comprehensively analyze the spatial control of protein degradation in U2OS osteosarcoma cells, we have combined drug treatment and SILAC-based quantitative mass spectrometry with subcellular and protein fractionation. The resulting data set analyzed more than 74,000 peptides, corresponding to ~5000 proteins, from nuclear, cytosolic, membrane, and cytoskeletal compartments. These data identified rapidly degraded proteasome targets, such as PRR11 and highlighted a feedback mechanism resulting in translation inhibition, induced by blocking the proteasome. We show this is mediated by activation of the unfolded protein response. We observed compartment-specific differences in protein degradation, including proteins that would not have been characterized as rapidly degraded through analysis of whole cell lysates. Bioinformatic analysis of the entire data set is presented in the Encyclopedia of Proteome Dynamics, a web-based resource, with proteins annotated for stability and subcellular distribution.

  3. 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.

  4. Molecular characterization of novel circoviruses from finch and gull.

    PubMed

    Todd, D; Scott, A N J; Fringuelli, E; Shivraprasad, H L; Gavier-Widen, D; Smyth, J A

    2007-02-01

    The purpose of this study was to molecularly characterize circoviruses that infect finches and gulls. Circovirus-specific DNAs were isolated using polymerase chain reaction methods from bursa of Fabricius tissues from a Gouldian finch (Chloebia gouldiae) and a herring gull (Larus argentatus) that were known to be circovirus-infected. Nucleotide sequence determination and analysis of cloned genomic DNAs showed that these circoviruses represented novel members of the genus Circovirus of the family Circoviridae, and have been tentatively named Finch circovirus (FiCV) and Gull Circovirus (GuCV). Both new circoviruses shared genome organizational features with previously characterized circoviruses, such that both contained two major, inversely-arranged open reading frames encoding the putative replication-associated and capsid proteins, and both contained a potential stem-loop and nonanucleotide motif. Phylogenetic analyses based on genome nucleotide sequences and involving the seven additional genus members indicated that FiCV and GuCV were more closely related to canary circovirus, beak and feather disease virus and pigeon circovirus, and that FiCV and canary circovirus were the most closely related avian circoviruses. Pairwise comparisons showed that the capsid proteins of FiCV and GuCV shared highest amino acid identity values with those of canary circovirus (62.0%) and pigeon circovirus (40.6%), respectively. The 5' intergenic region of GuCV was longer (207 nucleotides) and contained more direct and inverse repeated sequences than those of other circoviruses, while the 3' intergenic region of FiCV was notable in being longer (307 nucleotides) than its counterparts in other circoviruses and in containing two long repeats of 77 nucleotides.

  5. 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.

  6. Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi.

    PubMed

    Öpik, Maarja; Zobel, Martin; Cantero, Juan J; Davison, John; Facelli, José M; Hiiesalu, Inga; Jairus, Teele; Kalwij, Jesse M; Koorem, Kadri; Leal, Miguel E; Liira, Jaan; Metsis, Madis; Neshataeva, Valentina; Paal, Jaanus; Phosri, Cherdchai; Põlme, Sergei; Reier, Ülle; Saks, Ülle; Schimann, Heidy; Thiéry, Odile; Vasar, Martti; Moora, Mari

    2013-07-01

    We aimed to enhance understanding of the molecular diversity of arbuscular mycorrhizal fungi (AMF) by building a new global dataset targeting previously unstudied geographical areas. In total, we sampled 96 plant species from 25 sites that encompassed all continents except Antarctica. AMF in plant roots were detected by sequencing the nuclear SSU rRNA gene fragment using either cloning followed by Sanger sequencing or 454-sequencing. A total of 204 AMF phylogroups (virtual taxa, VT) were recorded, increasing the described number of Glomeromycota VT from 308 to 341 globally. Novel VT were detected from 21 sites; three novel but nevertheless widespread VT (Glomus spp. MO-G52, MO-G53, MO-G57) were recorded from six continents. The largest increases in regional VT number were recorded in previously little-studied Oceania and in the boreal and polar climatic zones - this study providing the first molecular data from the latter. Ordination revealed differences in AM fungal communities between different continents and climatic zones, suggesting that both biogeographic history and environmental conditions underlie the global variation of those communities. Our results show that a considerable proportion of Glomeromycota diversity has been recorded in many regions, though further large increases in richness can be expected in remaining unstudied areas.

  7. 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.

  8. 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

    2015-11-06

    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.

  9. 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.

  10. 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.

  11. 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

  12. Molecular characterization of lactic acid populations associated with wine spoilage.

    PubMed

    Beneduce, L; Spano, G; Vernile, A; Tarantino, D; Massa, S

    2004-01-01

    We have investigated the prevalence of spoilage lactic acid bacteria (LAB) in table wines produced in the Apulia region. The occurrence of LAB was evaluated in wines produced with low sulphur dioxide doses and not supplemented with selected malolactic starters such as Oenococcus oeni. About 150 strains were isolated from wine must and a molecular characterization was performed using PCR-based techniques. Most of the strains analysed belonged to Lactobacillus plantarum species. However, some of the strains were identified as Pediococcus damnosus and Leuconostoc sp. The amplified fragments of Pediococcus damnosus were cloned and sequenced. The coding sequence was highly homologous to that of the ropy plasmid confirming that the isolated strain was a ropy(+) Pediococcus damnosus. In all the samples analysed, the final must pH value reached was relatively high (from 3.78 to 3.90). The high pH values had probably negatively influenced (counteracted) the activity of sulphur dioxide added, allowing proliferation of spoilage wine microorganisms.

  13. 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.

  14. Molecular Characterization and Identification of Biocontrol Isolates of Trichoderma spp.

    PubMed Central

    Hermosa, M. R.; Grondona, I.; Iturriaga, E. A.; Diaz-Minguez, J. M.; Castro, C.; Monte, E.; Garcia-Acha, I.

    2000-01-01

    The most common biological control agents (BCAs) of the genus Trichoderma have been reported to be strains of Trichoderma virens, T. harzianum, and T. viride. Since Trichoderma BCAs use different mechanisms of biocontrol, it is very important to explore the synergistic effects expressed by different genotypes for their practical use in agriculture. Characterization of 16 biocontrol strains, previously identified as “Trichoderma harzianum” Rifai and one biocontrol strain recognized as T. viride, was carried out using several molecular techniques. A certain degree of polymorphism was detected in hybridizations using a probe of mitochondrial DNA. Sequencing of internal transcribed spacers 1 and 2 (ITS1 and ITS2) revealed three different ITS lengths and four different sequence types. Phylogenetic analysis based on ITS1 sequences, including type strains of different species, clustered the 17 biocontrol strains into four groups: T. harzianum-T. inhamatum complex, T. longibrachiatum, T. asperellum, and T. atroviride-T. koningii complex. ITS2 sequences were also useful for locating the biocontrol strains in T. atroviride within the complex T. atroviride-T. koningii. None of the biocontrol strains studied corresponded to biotypes Th2 or Th4 of T. harzianum, which cause mushroom green mold. Correlation between different genotypes and potential biocontrol activity was studied under dual culturing of 17 BCAs in the presence of the phytopathogenic fungi Phoma betae, Rosellinia necatrix, Botrytis cinerea, and Fusarium oxysporum f. sp. dianthi in three different media. PMID:10788356

  15. 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.

  16. 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.

  17. 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.

  18. Molecular characterization and phylogenetic analysis of Fasciola gigantica from Nigeria.

    PubMed

    Ichikawa-Seki, Madoka; Tokashiki, Minami; Opara, Maxwell Nwachukwu; Iroh, Gabriel; Hayashi, Kei; Kumar, Uday Mohanta; Itagaki, Tadashi

    2017-02-01

    Fasciola gigantica is considered the major pathogen causing fasciolosis in Africa; however, molecular characterization of this fluke has not been adequately elucidated. It is important to scientifically elucidate the dispersal history of F. gigantica by analyzing its genetic diversity. Fasciola flukes from Nigeria were analyzed using nuclear and mitochondrial DNA markers. A total of 172 Fasciola flukes collected from cattle were identified as F. gigantica because they displayed the F. gigantica fragment pattern in multiplex PCR for the nuclear marker, phosphoenolpyruvate carboxykinase (pepck). In total, 70 haplotypes were detected from Nigerian F. gigantica on the basis of the concatenated sequence of mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase 1 (cox1). The index of neutrality (Fu's Fs) suggests rapid expansion of the Nigerian F. gigantica population. Although four haplogroups, Nigeria 1A, 1B, 2A, and 2B, were detected from Nigerian F. gigantica, a climate-specific genetic structure was not observed among F. gigantica populations from three agro-climatic regions (Sahel, Savannah, and Forest). This is probably because of the frequent transportation of livestock from one part of the country to the other. Nigeria 1A and 1B had close relationships with the Egyptian population of F. gigantica, whereas Nigeria 2A and 2B were comparatively related to the Zambian population. No haplotype was shared among the three countries, and it therefore is difficult to estimate the dispersal route of F. gigantica within the African continent.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Molecular engineering and characterization of self-assembled biorecognition surfaces

    NASA Astrophysics Data System (ADS)

    Pan, Sheng

    The development of molecular engineering techniques for the fabrication of biomaterial surfaces is of importance in the field of biomaterials. It offers opportunities for better understanding of biological processes on material surfaces and rational design of contemporary biomaterials. Our work in this area aims to develop novel engineering strategies to design biorecognition surfaces via self-assembly and surface derivatization. Fundamental issues regarding self-assembled monolayer (SAM) structure, formation kinetics, and chemical derivatization were investigated systematically using electron spectroscopy for chemical analysis (ESCA), time-of-flight secondary ion mass spectrometry (TOF-SIMS), infrared reflection absorption spectroscopy (IRAS), atomic force microscopy (AFM), and contact angle measurements. Novel engineering concepts based on multifunctionality and statistical pattern matching were introduced and applied to develop biomimetic surfaces. Our study illustrated that molecules underwent structural transition and orientation development during self-assembly formation, from a disordered, low-density, more liquid-like structure to a highly ordered, closed-packed crystalline-like structure. Surface properties, such as wettability and the reactivity of outermost functional groups can be related to film structure, packing density, as well as molecular orientation. Given the order and organization of SAMs, the accessibility and reactivity of the outermost functional groups, reaction kinetics, stoichiometry, and SAMs stability were studied systematically by surface derivatization of trifluoroacetic anhydride (TFAA). The TFAA derivatization reactions exhibited rapid kinetics on the hydroxyl-terminated SAMs. The data from complementary surface analytical techniques consistently indicated a nearly complete surface reaction. Biomimetic surfaces were made by random immobilization of amino acid of arginine (R), glycine (G), and aspartic acid (D) on well-defined SAMs

  4. Molecular Characterization of Squamous Cell Carcinomas From Recessive Dystrophic Epidermolysis Bullosa

    DTIC Science & Technology

    2006-09-01

    Biology Thomas Jefferson University, Philadelphia, Pennsylvania 19107, and **Unitat de Biologia Cellular Molecular , Institute Municipal d’Investigacio...AD Award Number: DAMD17-02-1-0215 TITLE: Molecular Characterization of Squamous Cell Carcinomas from Recessive Dystrophic Epidermolysis Bullosa...TYPE 3. DATES COVERED (From - To) 01-09-2006 Final 29 May 2002 - 31 Aug 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Molecular Characterization of

  5. Mechanical Characterization of Molecular Assemblies at Oil/Water Interfaces

    NASA Astrophysics Data System (ADS)

    Yuan, Wa

    The self-assembly of charged molecules in liquid phases and their ability to form functional layers at immiscible interfaces are areas of great interest. However, the implementation of these assemblies is often limited by a lack of understanding of the detailed assembly mechanisms. In order to enhance the performance of interfacial assemblies it is essential to be able to characterize the physical and mechanical properties of assembled layers, as well as develop model systems that will allow us to examine the factors that govern their interaction with the surrounding environment. The key purpose of this thesis is to develop an understanding of some of the important factors influencing interfacial assemblies at immiscible liquid interfaces. The first portion of the work involves mechanical characterization of interfacial layers formed by large amphiphilic molecules. The study of block and gradient copolymers, reveals the effect of copolymer sequence distribution on the ability of these molecules to form interfacial assemblies. Specifically, the unique network structure formed by gradient copolymers at oil/water interfaces enables us to create a robust membrane at the interface by ionic crosslinking. The second part of this thesis explores smaller molecule assemblies at liquid interfaces, including commonly used commercial surfactant (span 80) and nano particles (graphene oxide). Both studies demonstrate an interesting correlation between molecular structure and overall properties of the assembled layers. Factors such as interfacial density, particle sizes and pH can greatly influence the structure of the assembled layers, resulting in interesting phenomena such as spontaneous emulsification, wrinkling and layer collapse. The bulk of the oil/water interface study was performed using axisymmetric drop shape analysis (DSA), which successfully quantifies the mechanical tension in the interfacial layer. This analysis was further extended by a development of a double

  6. Molecular Characterization of Adeno-Associated Viruses Infecting Children

    PubMed Central

    Chen, Chun-Liang; Jensen, Ryan L.; Schnepp, Bruce C.; Connell, Mary J.; Shell, Richard; Sferra, Thomas J.; Bartlett, Jeffrey S.; Clark, K. Reed; Johnson, Philip R.

    2005-01-01

    Although adeno-associated virus (AAV) infection is common in humans, the biology of natural infection is poorly understood. Since it is likely that many primary AAV infections occur during childhood, we set out to characterize the frequency and complexity of circulating AAV isolates in fresh and archived frozen human pediatric tissues. Total cellular DNA was isolated from 175 tissue samples including freshly collected tonsils (n = 101) and archived frozen samples representing spleen (n = 21), lung (n = 16), muscle (n = 15), liver (n = 19), and heart (n = 3). Samples were screened for the presence of AAV and adenovirus sequences by PCR using degenerate primers. AAV DNA was detected in 7 of 101 (7%) tonsil samples and two of 74 other tissues (one spleen and one lung). Adenovirus sequences were identified in 19 of 101 tonsils (19%), but not in any other tissues. Complete capsid gene sequences were recovered from all nine AAV-positive tissues. Sequence analyses showed that eight of the capsid sequences were AAV2-like (∼98% amino acid identity), while the single spleen isolate was intermediate between serotypes 2 and 3. Comparison to the available AAV2 crystal structure revealed that the majority of the amino acid substitutions mapped to surface-exposed hypervariable domains. To further characterize the AAV capsid structure in these samples, we used a novel linear rolling-circle amplification method to amplify episomal AAV DNA and isolate infectious molecular clones from several human tissues. Serotype 2-like viruses were generated from these DNA clones and interestingly, failed to bind to a heparin sulfate column. Inspection of the capsid sequence from these two clones (and the other six AAV2-like isolates) revealed that they lacked arginine residues at positions 585 and 588 of the capsid protein, which are thought to be essential for interaction with the heparin sulfate proteoglycan coreceptor. These data provide a framework with which to explore wild-type AAV

  7. Molecular characterization of Corynebacterium pseudotuberculosis isolates using ERIC-PCR.

    PubMed

    Guimarães, Alessandro de Sá; Dorneles, Elaine Maria Seles; Andrade, Giovanna Ivo; Lage, Andrey Pereira; Miyoshi, Anderson; Azevedo, Vasco; Gouveia, Aurora Maria Guimarães; Heinemann, Marcos Bryan

    2011-12-15

    Caseous lymphadenitis is an infectious sheep and goats disease caused by Corynebacterium pseudotuberculosis and characterized by abscesses in superficial and visceral lymph nodes. C. pseudotuberculosis strains isolated from these hosts have been shown to be very difficult to type by the existing methods. The aim of this study is evaluating the potential of the Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) as a tool for molecular typing of C. pseudotuberculosis strains isolated in sheep. One hundred and twenty seven isolates of C. pseudotuberculosis were isolated from lesions suspected to have had caseous lymphadenitis collected from sheep at the slaughterhouse. Animals were from 24 flocks in 13 municipalities of the Minas Gerais State, Brazil. Species identification of the isolates was performed by routine biochemical tests and mPCR. Fingerprint was performed by RAPD using ERIC-1R, ERIC-2 and ERIC-1R+ERIC-2 primers. Seventeen different genotypes were generated by ERIC 1-PCR, 21 genotypes by ERIC 2-PCR and 21 genotypes by ERIC 1+2-PCR. Hunter-Gaston Discrimination Index (HGDI) found for ERIC 1, ERIC 2, ERIC 1+2 PCR were 0.69, 0.87, and 0.84, respectively. For most herds evaluated observed at most three different genotypes among isolates from animals of these property, in all ERIC-PCR assays. However a few flocks observed between four and nine genotypes per flock. The W Kendall value found for correlation among the three techniques of ERIC-PCR was 0.91 (P<5.0 x 10(-6)). The results show that ERIC-PCR has good discriminatory power and advantages over other DNA-based typing methods, making it a useful tool to discriminate C. pseudotuberculosis isolates.

  8. 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

  9. Molecular Characterization of Ciliate Diversity in Stream Biofilms▿ †

    PubMed Central

    Dopheide, Andrew; Lear, Gavin; Stott, Rebecca; Lewis, Gillian

    2008-01-01

    Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms. PMID:18223112

  10. Clinical, pathological, immunohistochemical and molecular characterization of feline chronic gingivostomatitis.

    PubMed

    Rolim, Veronica Machado; Pavarini, Saulo Petinatti; Campos, Fabrício Souza; Pignone, Viviam; Faraco, Cláudia; Muccillo, Marcelo de Souza; Roehe, Paulo Michel; da Costa, Fernanda Viera Amorim; Driemeier, David

    2017-04-01

    Objectives This study presents the clinical, pathological, immunohistochemical and molecular characterization of 26 cats with feline chronic gingivostomatitis (FCG). Methods Oral mucosal biopsies, blood and swabs were collected from cats presenting with oral lesions. The tissue sections were submitted for histopathology and immunohistochemical analysis for feline calicivirus (FCV), feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV). The swabs were subjected to PCR analysis for FCV, and blood for FeLV and FIV. Results The main clinical findings were dysphagia (88.2%), halitosis (76.5%), sialorrhea (47.1%), weight loss (41.2%), intense oral discomfort (35.3%), oral hemorrhage (17.6%), and lackluster and fragile coat (11.8%). Gross inspection revealed bilateral lesions across the palatoglossal fold to the lateral tongue base. The lesions were diffuse, proliferative, intensely red and friable, and bled easily upon examination in 80.8% of cases. In 23.1% of cases, the lesions were multifocal to coalescent, at times forming multiple vesicles on a reddened, edematous palatoglossal fold. Microscopic examination showed that 15.4% of lesions had moderate (grade 2) and 84.6% had severe (grade 3) inflammation. Immunohistochemistry revealed the presence of FeLV antigens in the epithelium and the inflammatory infiltrate of 30.8% of the cats with FCG. FCV antigens were not detected in the FCG lesions. Conclusions and relevance The FCG cases analyzed could not be correlated with FCV. It is possible that FeLV plays a role as a causal agent of lesions in cases where the presence of the virus has been confirmed by immunohistochemistry in epithelial samples.

  11. Molecular Characterization of Dendritic Cell-Derived Exosomes

    PubMed Central

    Théry, Clotilde; Regnault, Armelle; Garin, Jérôme; Wolfers, Joseph; Zitvogel, Laurence; Ricciardi-Castagnoli, Paola; Raposo, Graça; Amigorena, Sebastian

    1999-01-01

    Exosomes are membrane vesicles secreted by hematopoietic cells upon fusion of late multivesicular endosomes with the plasma membrane. Dendritic cell (DC)-derived exosomes induce potent antitumor immune responses in mice, resulting in the regression of established tumors (Zitvogel, L., A. Regnault, A. Lozier, J. Wolfers, C. Flament, D. Tenza, P. Ricciardi-Castagnoli, G. Raposo, and S. Amigorena. 1998. Nat. Med. 4:594–600). To unravel the molecular basis of exosome-induced immune stimulation, we now analyze the regulation of their production during DC maturation and characterize extensively their protein composition by peptide mass mapping. Exosomes contain several cytosolic proteins (including annexin II, heat shock cognate protein hsc73, and heteromeric G protein Gi2α), as well as different integral or peripherally associated membrane proteins (major histocompatiblity complex class II, Mac-1 integrin, CD9, milk fat globule-EGF-factor VIII [MFG-E8]). MFG-E8, the major exosomal component, binds integrins expressed by DCs and macrophages, suggesting that it may be involved in exosome targeting to these professional antigen-presenting cells. Another exosome component is hsc73, a cytosolic heat shock protein (hsp) also present in DC endocytic compartments. hsc73 was shown to induce antitumor immune responses in vivo, and therefore could be involved in the exosome's potent antitumor effects. Finally, exosome production is downregulated upon DC maturation, indicating that in vivo, exosomes are produced by immature DCs in peripheral tissues. Thus, DC-derived exosomes accumulate a defined subset of cellular proteins reflecting their endosomal biogenesis and accounting for their biological function. PMID:10545503

  12. Molecular characterization of α-amylase from Staphylococcus aureus.

    PubMed

    Lakshmi, Hanumanthu Prasanna; Prasad, Uppu Venkateswara; Yeswanth, Sthanikam; Swarupa, Vimjam; Prasad, Osuru Hari; Narasu, Mangamoori Lakshmi; Sarma, Potukuchi Venkata Gurunadha Krishna

    2013-01-01

    Staphylococcus aureus is one of the prominent Gram positive human pathogen secretes many surface and secretary proteins including various enzymes and pathogenic factors that favour the successful colonization and infection of host tissue. α-amylase is one of the enzymes secreted by S. aureus which catalyses the breakdown of complex sugars to monosaccharides, which are required for colonization and survival of this pathogen in any anatomical locales. In the present study we have cloned, sequenced, expressed and characterized α-amylase gene from S. aureus ATCC12600. The recombinant enzyme has a molecular weight of 58kDa and the kinetics showed Vmax 0.0208±0.033 (mg/ml)/mg/min and Km 10.633±0.737mg/ml. The multiple sequence analysis showed α- amylase of S. aureus exhibited large differences with Bacillus subtilis and Streptococcus bovis. As the crystal structure of S. aureus α- amylase was unavailable, we used homology modelling method to build the structure. The built structure was validated by Ramachandran plot which showed 90% of the residues in the allowed region while no residue was found in the disallowed region and the built structure was close to the crystal structure with Z-Score: -6.85. The structural superimposition studies with α- amylases of Bacillus subtilis and Streptococcus bovis showed distinct differences with RMSD values of 18.158Åand 7.091Å respectively which correlated with enzyme kinetics, indicating α-amylase is different among these bacteria.

  13. Molecular Beam Epitaxy Growth and Characterization of Thin Layers of Semiconductor Tin

    DTIC Science & Technology

    2016-09-01

    heating. The α-Sn layers were also characterized with high-resolution X-ray diffraction, Hall, and atomic force microscopy (AFM) measurements...ARL-TR-7838 ● SEP 2016 US Army Research Laboratory Molecular Beam Epitaxy Growth and Characterization of Thin Layers of...Laboratory Molecular Beam Epitaxy Growth and Characterization of Thin Layers of Semiconductor Tin by P Folkes, P Taylor, C Rong, B Nichols

  14. 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

  15. Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

    PubMed Central

    Ferreira, Pedro G.; Jares, Pedro; Rico, Daniel; Gómez-López, Gonzalo; Martínez-Trillos, Alejandra; Villamor, Neus; Ecker, Simone; González-Pérez, Abel; Knowles, David G.; Monlong, Jean; Johnson, Rory; Quesada, Victor; Djebali, Sarah; Papasaikas, Panagiotis; López-Guerra, Mónica; Colomer, Dolors; Royo, Cristina; Cazorla, Maite; Pinyol, Magda; Clot, Guillem; Aymerich, Marta; Rozman, Maria; Kulis, Marta; Tamborero, David; Gouin, Anaïs; Blanc, Julie; Gut, Marta; Gut, Ivo; Puente, Xose S.; Pisano, David G.; Martin-Subero, José Ignacio; López-Bigas, Nuria; López-Guillermo, Armando; Valencia, Alfonso; López-Otín, Carlos; Campo, Elías; Guigó, Roderic

    2014-01-01

    Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes—most of which are not differentially expressed—exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences. PMID:24265505

  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. Molecular characterization of rheumatoid arthritis with magnetic resonance imaging.

    PubMed

    Gu, Jeffrey T; Nguyen, Linda; Chaudhari, Abhijit J; MacKenzie, John D

    2011-04-01

    Several recent advances in the field of magnetic resonance imaging (MRI) may transform the detection and monitoring of rheumatoid arthritis (RA). These advances depict both anatomic and molecular alterations from RA. Previous techniques could detect specific end products of metabolism in vitro or were limited to providing anatomic information. This review focuses on the novel molecular imaging techniques of hyperpolarized carbon-13 MRI, MRI with iron-labeled probes, and fusion of MRI with positron emission tomography. These new imaging approaches go beyond the anatomic description of RA and lend new information into the status of this disease by giving molecular information.

  18. 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.

  19. 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

  20. A review of the global prevalence, molecular epidemiology and economics of cystic echinococcosis in production animals.

    PubMed

    Cardona, Guillermo A; Carmena, David

    2013-02-18

    Cystic echinococcosis (CE) is an important and widespread zoonotic infection caused by the larval stages of taeniid cestodes of the genus Echinococcus. The disease represents a serious animal health concern in many rural areas of the world, causing important economic losses derived from decreased productivity and viscera condemnation in livestock species. In this review we aim to provide a comprehensive overview on recent research progress in the epidemiology of CE in production animals from a global perspective. Particular attention has been paid to the discussion of the extent and significance of recent molecular epidemiologic data. The financial burden associated to CE on the livestock industry has also been addressed. Data presented are expected to improve our current understanding of the parasite's geographical distribution, transmission, host range, immunogenicity, pathogenesis, and genotype frequencies. This information should be also valuable for the design and implementation of more efficient control strategies against CE.

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

    PubMed

    Pääbo, S

    1989-03-01

    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.

  2. 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.

  3. The (FHCl)- molecular anion - Structural aspects, global surface, and vibrational eigenspectrum

    NASA Technical Reports Server (NTRS)

    Klepeis, Neil E.; East, Allan L. L.; Csaszar, Attila G.; Allen, Wesley D.; Lee, Timothy J.; Schwenke, David W.

    1993-01-01

    State of the art ab initio electronic structure methods have been used to investigate the (FHCl)- molecular anion. It is proposed that the geometric structure and binding energies of the complex are r(e)(H-F) = 0.963 +/- 0.003 A, R(e)(H-Cl) = 1.925 +/- 0.015 A, and D0(HF + Cl(-)) = 21.8 +/- 0.4 kcal/mol. A Morokuma decomposition of the ion-molecular bonding give the following electrostatic, polarization, exchange repulsion, dispersion, and charge-transfer plus higher-order mixing components of the vibrationless complexation energy: -27.3, -5.2, +18.3, -4.5, and -5.0 kcal/mol, respectively. A couples cluster single and doubles global surface is constructed from 208 and 228 energy points for linear and bent configurations, respectively, these being fit to rms errors of only 3.9 and 9.3/cm, respectively, below 8000/cm. Converged J = 0 and J = 1 variational eigenstates of the (FHCl)- surface to near the HF + Cl(-) dissociation threshold are determined. The fundamental vibrational frequencies are found to be nu1 = 247/cm, nu2 = 876/cm, and nu3 = 2884/cm. The complete vibrational eigenspectrum is analyzed.

  4. Molecular phylogeny of the small carpenter bees (Hymenoptera: Apidae: Ceratinini) indicates early and rapid global dispersal.

    PubMed

    Rehan, Sandra M; Chapman, Tom W; Craigie, Andrew I; Richards, Miriam H; Cooper, Steven J B; Schwarz, Michael P

    2010-06-01

    The small carpenter bees (tribe Ceratinini, family Apidae) are recorded from all continents except Antarctica. The Ceratinini have a near-global distribution which contrasts strongly with their sister tribe, the Allodapini which has a largely southern Old World distribution. The Ceratinini therefore provides an excellent group to understand the factors that help determine the biogeography and radiation of the bees. This is the first molecular study of ceratinine bees covering representatives from both northern and southern hemisphere Old and New World regions. We use two mitochondrial and one nuclear marker (totalling 2807 nucleotides) to examine the age, cladogenesis and historical biogeography of this tribe. Tree topology and molecular dating support an African origin at about 47 Mya with subsequent dispersal into Eurasia 44 Mya, and followed by an American invasion 32 Mya. Concentrated African and Malagasy sampling revealed there were two or three dispersals events into Madagascar ranging from 25 to 9 Mya. Lineage through time analyses suggest higher rates of cladogenesis close to the origin of the tribe, and this corresponds to both major dispersal events and divergences of lineages leading to extant subgenera. Ceratinini have potentially great importance for future studies to understand the relative roles of dispersal ability and time of origin in determining bee biogeography.

  5. 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...

  6. Molecular cloning and characterization of multidomain xylanase from manure library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The gene (manf-x10) encoding xylanase from an environmental genomic DNA library was cloned and expressed in Escherichia coli. The encoded enzyme was predicted to be 467 amino acids with a molecular mass of 50.3 kD. The recombinant ManF-X10 was purified by HisTrap affinity column and showed activit...

  7. Molecular characterization of an endornavirus from Cucumis spp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Endornaviruses infect hosts in the kingdoms Plantae, Fungi and Chromista. They are efficiently transmitted vertically and generally do not induce visible symptoms. In this investigation high molecular weight dsRNA, representing the genome of an endornavirus, was isolated from an unknown melon (Cucum...

  8. Molecular characterization of Staphylococcus aureus from outpatients in the Caribbean reveals the presence of pandemic clones

    PubMed Central

    Dumortier, C.; Hafer, C.; Taylor, B. S.; Sánchez E, J.; Rodriguez-Taveras, C.; Leon, P.; Rojas, R.; Olive, C.; Lowy, F. D.

    2011-01-01

    Staphylococcus aureus infections continue to pose a global public health problem. Frequently, this epidemic is driven by the successful spread of single S. aureus clones within a geographic region, but international travel has been recognized as a potential risk factor for S. aureus infections. To study the molecular epidemiology of S. aureus infections in the Caribbean, a major international tourist destination, we collected methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates from community-onset infections in the Dominican Republic (n=112) and Martinique (n=143). Isolates were characterized by a combination of pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing (MLST) typing. In Martinique, MRSA infections (n=56) were mainly caused by t304-ST8 strains (n=44), whereas MSSA isolates were derived from genetically diverse backgrounds. Among MRSA strains (n=22) from the Dominican Republic, ST5, ST30, and ST72 predominated, while ST30 t665-PVL+ (30/90) accounted for a substantial number of MSSA infections. Despite epidemiological differences in sample collections from both countries, a considerable number of MSSA infections (~10%) were caused by ST5 and ST398 isolates at each site. Further phylogenetic analysis suggests the presence of lineages shared by the two countries, followed by recent genetic diversification unique to each site. Our findings also imply the frequent import and exchange of international S. aureus strains in the Caribbean. PMID:21789605

  9. 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

  10. Molecular weight characterization of single globular proteins using optical nanotweezers.

    PubMed

    Wheaton, Skyler; Gordon, Reuven

    2015-07-21

    We trap a set of molecular weight standard globular proteins using a double nanohole optical trap. The root mean squared variation of the trapping laser transmission intensity gives a linear dependence with the molecular weight, showing the potential for analysis of globular proteins. The characteristic time of the autocorrelation of the trapping laser intensity variations scales with a -2/3 power dependence with the volume of the particle. A hydrodynamic laser tweezer model is used to explain these dependencies. Since this is a single particle technique that operates in solution and can be used to isolate an individual particle, we believe that it provides an interesting alternative to existing analysis methods and shows promise to expand the capabilities of protein related studies to the single particle level.

  11. Elemental and molecular characterization of aged polydimethylsiloxane foams.

    PubMed

    Patterson, Brian M; Havrilla, George J; Schoonover, Jon R

    2006-10-01

    The application and integration of micro X-ray fluorescence (MXRF) and Fourier transform infrared (FT-IR) imaging to polydimethylsiloxane (PDMS) foam aging issues have been applied to cross-sectional images. Previous work has shown the tin in the stannous 2-ethylhexanoate catalyst to be highly mobile and it typically migrates to the PDMS foam upper surface. The current paper discusses a method for the integration of full spectral MXRF and FT-IR imaging of aged foams. Solvent extractions have also been performed on both fresh and aged foams to further examine aged foam properties. Combining elemental and molecular imaging techniques and applying them to PDMS aging provides synergistic information that aids in understanding the sample composition and distribution of components. Application of chemometric analysis to the full spectral elemental and molecular maps demonstrates correlations within the foams of the residual tin, organo-tin functional group moieties, and the presence of nitroplasticizer from an exogenous source.

  12. 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

    2015-08-18

    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.

  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 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.

  15. 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.

  16. Characterization of QCM sensor surfaces coated with molecularly imprinted nanoparticles.

    PubMed

    Reimhult, Kristina; Yoshimatsu, Keiichi; Risveden, Klas; Chen, Si; Ye, Lei; Krozer, Anatol

    2008-07-15

    Molecularly imprinted polymers (MIPs) are gaining great interest as tailor-made recognition materials for the development of biomimetic sensors. Various approaches have been adopted to interface MIPs with different transducers, including the use of pre-made imprinted particles and the in situ preparation of thin polymer layers directly on transducer surfaces. In this work we functionalized quartz crystal microbalance (QCM) sensor crystals by coating the sensing surfaces with pre-made molecularly imprinted nanoparticles. The nanoparticles were immobilized on the QCM transducers by physical entrapment in a thin poly(ethylene terephthalate) (PET) layer that was spin-coated on the transducer surface. By controlling the deposition conditions, it was possible to gain a high nanoparticle loading in a stable PET layer, allowing the recognition sites in nanoparticles to be easily accessed by the test analytes. In this work, different sensor surfaces were studied by micro-profilometry and atomic force microscopy and the functionality was evaluated using quartz crystal microbalance with dissipation (QCM-D). The molecular recognition capability of the sensors were also confirmed using radioligand binding analysis by testing their response to the presence of the test compounds, (R)- and (S)-propranolol in aqueous buffer.

  17. Molecular Characterization of Brown Carbon in Biomass Burning Aerosol Particles.

    PubMed

    Lin, Peng; Aiona, Paige K; Li, Ying; Shiraiwa, Manabu; Laskin, Julia; Nizkorodov, Sergey A; Laskin, Alexander

    2016-11-01

    Emissions from biomass burning are a significant source of brown carbon (BrC) in the atmosphere. In this study, we investigate the molecular composition of freshly emitted biomass burning organic aerosol (BBOA) samples collected during test burns of sawgrass, peat, ponderosa pine, and black spruce. We demonstrate that both the BrC absorption and the chemical composition of light-absorbing compounds depend significantly on the type of biomass fuels. Common BrC chromophores in the selected BBOA samples include nitro-aromatics, polycyclic aromatic hydrocarbon derivatives, and polyphenols spanning a wide range of molecular weights, structures, and light absorption properties. A number of biofuel-specific BrC chromophores are observed, indicating that some of them may be used as source-specific markers of BrC. On average, ∼50% of the light absorption in the solvent-extractable fraction of BBOA can be attributed to a limited number of strong BrC chromophores. The absorption coefficients of BBOA are affected by solar photolysis. Specifically, under typical atmospheric conditions, the 300 nm absorbance decays with a half-life of ∼16 h. A "molecular corridor" analysis of the BBOA volatility distribution suggests that many BrC compounds in the fresh BBOA have low saturation mass concentration (<1 μg m(-3)) and will be retained in the particle phase under atmospherically relevant conditions.

  18. Molecular characterization and population structure of Blueberry mosaic associated virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blueberry mosaic disease was first described in the 1950s but the causal agent has not been characterized to date. Next generation sequencing was employed in the identification of the causal agent and an undescribed ophiovirus, tentatively named as Blueberry mosaic associated virus (BlMaV), was dete...

  19. Molecular Characterization of Canine Rabies Virus, Mali, 2006-2013.

    PubMed

    Traoré, Abdallah; Picard-Meyer, Evelyne; Mauti, Stephanie; Biarnais, Melanie; Balmer, Oliver; Samaké, Kassim; Kamissoko, Badian; Tembely, Saïdou; Sery, Amadou; Traoré, Abdel K; Coulibaly, Amy P; Robardet, Emmanuelle; Zinsstag, Jakob; Cliquet, Florence

    2016-05-01

    We genetically characterized 32 canine rabies viruses isolated in Mali during 2006-2013 and identified 3 subgroups that belonged to the Africa 2 lineage. We also detected subgroup F rabies virus. This information should be useful for development of mass vaccination campaigns for dogs and eventual large-scale control programs in this country.

  20. Molecular Characterization of Canine Rabies Virus, Mali, 2006–2013

    PubMed Central

    Traoré, Abdallah; Picard-Meyer, Evelyne; Mauti, Stephanie; Biarnais, Melanie; Balmer, Oliver; Samaké, Kassim; Kamissoko, Badian; Tembely, Saïdou; Sery, Amadou; Traoré, Abdel K.; Coulibaly, Amy P.; Robardet, Emmanuelle; Zinsstag, Jakob

    2016-01-01

    We genetically characterized 32 canine rabies viruses isolated in Mali during 2006–2013 and identified 3 subgroups that belonged to the Africa 2 lineage. We also detected subgroup F rabies virus. This information should be useful for development of mass vaccination campaigns for dogs and eventual large-scale control programs in this country. PMID:27089307

  1. 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.

  2. Molecular cloning and functional characterization of avian interleukin-19

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The present study describes the cloning and functional characterization of avian interleukin (IL)-19, a cytokine that, in mammals, alters the balance of Th1 and Th2 cells in favor of the Th2 phenotype. The full-length avian IL-19 gene, located on chromosome 26, was amplified from LPS-stimulated chi...

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Syntheses, Characterizations, and Applications of Molecular Metal Wires

    DTIC Science & Technology

    2011-08-05

    123). 6 A pyrazine-modulated oligo--pyridylamine ligand H3pzpz and its mononuclear copper (II) and cobalt (II) complexes have been synthesized and...structurally characterized. A pyrazine-modulated oligo--pyridylamino ligand H3pzpz and its mononuclear copper (II) and cobalt (II) complexes have...H3pzpz can be a quadridentate ligand and coordinates to metal atoms with all-anti mode in both copper and cobalt mononuclear complexes. The copper (II

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

    DOE PAGES

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

    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.

  9. 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

  10. 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.

  11. Molecular characterization of a catalase from Hydra vulgaris.

    PubMed

    Dash, Bhagirathi; Phillips, Timothy D

    2012-06-15

    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.

  12. Molecular characterization and RAPD analysis of Juniperus species from Iran.

    PubMed

    Kasaian, J; Behravan, J; Hassany, M; Emami, S A; Shahriari, F; Khayyat, M H

    2011-06-07

    The genus Juniperus L. (Cupressaceae), an aromatic evergreen plant, consists of up to 68 species around the world. We classified five species of Juniperus found in Iran using molecular markers to provide a means for molecular identification of Iranian species. Plants were collected (three samples of each species) from two different provinces of Iran (Golestan and East Azarbayejan). The DNA was extracted from the leaves using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using 18 ten-mer RAPD primers. Genetic distances were estimated based on 187 RAPD bands to construct a dendrogram by means of unweighted pair group method of arithmetic means. It was found that J. communis and J. oblonga were differentiated from the other species. Genetic distance values ranged from 0.19 (J. communis and J. oblonga) to 0.68 (J. communis and J. excelsa). Juniperus foetidissima was found to be most similar to J. sabina. Juniperus excelsa subspecies excelsa and J. excelsa subspecies polycarpos formed a distinct group.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  18. 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.

  19. 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

  20. The TRY Plant Trait Database - a Tool to Characterize Plant Responses to Global Changes

    NASA Astrophysics Data System (ADS)

    Kattge, J.

    2015-12-01

    Plant traits are fundamental for understanding and predicting vegetation responses to global changes, and they provide a promising basis towards a more quantitative and predictive approach to ecology. Plant traits have therefore been collected for a long time, but mostly been stored in small, separated and private databases, not accessible to the research community. The TRY initiative, a network of vegetation scientists (https://www.try-db.org), provides a global archive of plant traits, curated to be applicable for the characterization of species-specific responses in the context of terrestrial biosphere models. This contribution will (1) introduce the TRY initiative and the current state of the plant trait database, (2) provide examples of trait-based approaches to improve terrestrial biosphere models, (3) highlight future perspectives and challenges for trait based approaches in ecology and vegetation modeling.

  1. Webinar Presentation: Characterization of Emissions from Small, Variable Solid Fuel Combustion Sources for Determining Global Emissions and Climate Impact

    EPA Pesticide Factsheets

    This presentation, Characterization of Emissions from Small, Variable Solid Fuel Combustion Sources for Determining Global Emissions and Climate Impact, was given at the STAR Black Carbon 2016 Webinar Series.

  2. Characterization of ionic, dipolar and molecular mobility in polymer systems

    NASA Astrophysics Data System (ADS)

    Guo, Zhenrong

    Changes in the ionic and dipolar molecular mobility in a polymer system are the basis for the changes in the dielectric mechanical properties of polymer materials. Frequency Dependent Dielectric Measurements (FDEMS) and Ion Time-of-Flight (ITOF) are two important techniques to investigate ionic and dipolar molecular mobility in polymer systems. The results can be related to the macro- and molecular dielectric, electrical and dynamic properties of polymeric materials. The combination of these two methods provides a full view of electric, dielectric and dynamic behavior for the systems as they undergo chemical and/or physical changes during polymerization crystallization, vitrification, and/or phase separation. The research on microscopic mass mobility in polymer systems was done on three aspects: (1) ion mobility in an epoxy-amine reaction system; (2) dipolar mobility and relaxation during dimethacrylate resin cure and (3) dye molecule migration and diffusion in polymer films. In the ion mobility study, we separately monitor the changes in the ion mobility and the number of charge carriers during the epoxy-amine polymerization with FDEMS and ITOF measurements. The isolation of the number of carriers and their mobility allows significant improvement in monitoring changes in the state and structure of a material as it cures. For the dipolar mobility and relaxation study, FDEMS measurements were used to detect structural evolution and spatial heterogeneity formation during the polymerization process of dimethacrylate resins. The dielectric spectra, glass transition (Tg) profiles and dynamic mechanical measurements were used to investigate the existence of two cooperative regions of sufficient size to create two alpha-relaxation processes representing oligomer rich and polymer microgel regions during the polymerization. For the dye migration research, we tried to develop a visually color changing paper (VCP) due to dye molecule migration in polymer films. The mobility

  3. 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

  4. THE GLOBAL EVOLUTION OF GIANT MOLECULAR CLOUDS. II. THE ROLE OF ACCRETION

    SciTech Connect

    Goldbaum, Nathan J.; Krumholz, Mark R.; Matzner, Christopher D.; McKee, Christopher F.

    2011-09-01

    We present virial models for the global evolution of giant molecular clouds (GMCs). Focusing on the presence of an accretion flow and accounting for the amount of mass, momentum, and energy supplied by accretion and star formation feedback, we are able to follow the growth, evolution, and dispersal of individual GMCs. Our model clouds reproduce the scaling relations observed in both galactic and extragalactic clouds. We find that accretion and star formation contribute roughly equal amounts of turbulent kinetic energy over the lifetime of the cloud. Clouds attain virial equilibrium and grow in such a way as to maintain roughly constant surface densities, with typical surface densities of order 50-200 M{sub sun} pc{sup -2}, in good agreement with observations of GMCs in the Milky Way and nearby external galaxies. We find that as clouds grow, their velocity dispersion and radius must also increase, implying that the linewidth-size relation constitutes an age sequence. Lastly, we compare our models to observations of GMCs and associated young star clusters in the Large Magellanic Cloud and find good agreement between our model clouds and the observed relationship between H II regions, young star clusters, and GMCs.

  5. 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.

  6. 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

  7. Molecular Characterization of a Maize B Chromosome Centric Sequence

    PubMed Central

    Alfenito, M. R.; Birchler, J. A.

    1993-01-01

    Supernumerary chromosomes are widespread in the plant kingdom but little is known of their molecular nature or mechanism of origin. We report here the initial cloning of sequences from the maize B chromosome. Our analysis suggests that many sequences are highly repetitive and shared with the normal A chromosomes. However, all clones selected for B-specificity contain at least one copy of a particular repeat. Cytological mapping using B chromosome derivatives and in situ hybridization show that the B specific repeats are derived from the centric region of the chromosome. Sequence analysis of this repeat shows homology to motifs mapped to various plant and animal centromeres and to the maize neocentromere. A precise localization of these sequences among breakpoints within the B centromere and an homology to a facultative centromere, suggest a role for this sequence in centromere function. PMID:8244015

  8. Molecular and genetic characterization of an Alcaligenes eutrophus insertion element.

    PubMed Central

    Kung, S S; Chen, J; Chow, W Y

    1992-01-01

    An insertion element, ISAE1, was discovered during the molecular analysis of mutants defective in the autotrophic growth (Aut-) of Alcaligenes eutrophus H1-4, a mitomycin C-generated derivative of strain H1. ISAE1 is 1,313 bp long, has 12-bp nearly perfect inverted terminal repeats, and contains an open reading frame that has a coding capacity of 408 amino acids. Direct repeats of 8 bp were generated by insertion of ISAE1 into chromosomes or plasmids. Most insertion were found in the AT-rich target sites. The distribution of ISAE1 is limited to A. eutrophus H1 (ATCC 17698) and H16 (ATCC 17699). Variants with newly transposed copies of ISAE1 could be isolated at an elevated frequency by changing the growth conditions. Images PMID:1334068

  9. Molecular characterization of a glutathione transferase from Pinus tabulaeformis (Pinaceae).

    PubMed

    Zeng, Qing-Yin; Lu, Hai; Wang, Xiao-Ru

    2005-05-01

    Glutathione transferases (GSTs) play important roles in stress tolerance and detoxification metabolism in plants. To date, studies on GSTs in higher plants have focused largely on agricultural plants. In contrast, there is virtually no information on the molecular characteristics of GSTs in gymnosperms. The present study reports for the first time the cloning, expression and characteristics of a GST gene (PtGSTU1) from a pine, Pinus tabulaeformis, which is widely distributed from northern to central China covering cold temperate and drought regions. The PtGSTU1 gene encodes a protein of 228 amino acid residues with a calculated molecular mass of 26.37 kDa. Reverse transcription PCR revealed that PtGSTU1 was expressed in different tissues, both above and below ground, of P. tabulaeformis. The over-expressed recombinant PtGSTU1 showed high activity towards the substrates 1-chloro-2,4-dinitrobenzene (CDNB) and 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl). Kinetic analysis with respect to CDNB as substrate revealed a Km of 0.47 mM and Vmax of 169.1 micromol/min per mg of protein. The recombinant PtGSTU1 retained more than 60% of its maximum enzymatic activity from 15 degrees C to 45 degrees C with a broad optimum Tm range of 25 degrees C - 35 degrees C. The enzyme had a maximum activity at approximately pH 8.5 - 9.0. Site-directed mutagenesis revealed that Ser13 in the N-terminal domain is a critical catalytic residue, responsible for stabilisation of the thiolate anion of enzyme-bound glutathione. Based on comparative analyses of its amino acid sequence, phylogeny and predicted three-dimensional structure, the PtGSTU1 should be classified as a tau class GST.

  10. 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.

  11. 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.

  12. 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.

  13. Molecular characterization of Blau syndrome: Genetic linkage to chromosome 16

    SciTech Connect

    Tromp, G.; Duivaniemi, H.; Christiano, A.

    1994-09-01

    The Blau syndrome is an autosomal, dominantly-inherited disease characterized by multi-organ, tissue-specific inflammation. Its clinical phenotype includes granulomatous uveitis, arthritis and skin rash. The syndrome is unique in that it is the sole human model for a variety of multi-system inflammatory diseases that afflict a significant percentage of the population. Karyotypic analysis of the large, three generation kindred whose disease originally characterized the syndrome was unremarkable. Following exclusion of a number of extracellular matrix candidates genes, a genome-wide search was undertaken of the Blau susceptibility locus. Fifty-seven members of the family were genotyped for about 200 highly polymorphic dinucleotide repeat markers. Linkage analysis was performed using the LINKAGE package of programs under a model of dominant inheritance with reduced penetrance. Five liability classes were used to specify penetrances and phenocopy rates for those affected the arthritis, uveitis, skin rash and combinations thererof. In addition, five age-dependent penetrance classes were used for unaffected individuals. The marker D16S298 gave a maximum lod score of 3.6 at {theta} = 0.05 with two-point analysis. Lod scores for flanking markers were consistent. These data provide convincing evidence that the Blau susceptibility locus is situated within the 16p12-q21 interval. Fine mapping of the candidate interval with additional families exhibiting the Blau phenotype, as well as with more polymorphic markers, is underway.

  14. Molecular characterization of the uncultivatable hemotropic bacterium Mycoplasma haemofelis.

    PubMed

    Barker, Emily N; Darby, Alistair C; Helps, Chris R; Peters, Iain R; Heesom, Kate J; Arthur, Christopher J; Crossett, Ben; Hughes, Margaret A; Radford, Alan D; Tasker, Séverine

    2011-07-12

    Mycoplasma haemofelis is a pathogenic feline hemoplasma. Despite its importance, little is known about its metabolic pathways or mechanism of pathogenicity due to it being uncultivatable. The recently sequenced M. haemofelis str. Langford 1 genome was analysed and compared to those of other available hemoplasma genomes.Analysis showed that in hemoplasmas genes involved in carbohydrate metabolism are limited to enzymes of the glycolytic pathway, with glucose appearing to be the sole energy source. The majority of the pentose phosphate pathway enzymes that catalyze the de novo synthesis of ribonucleotides were absent, as were cell division protein FtsZ and chaperonins GroEL/ES. Uncharacterized protein paralogs containing putative surface expression motifs, comprised 62% of M. haemofelis and 19% of Mycoplasma suis genome coverage respectively, the majority of which were present in a small number of unstructured islands. Limited mass spectrometry and immunoblot data matched a number of characterized proteins and uncharacterized paralogs, confirming their expression and immunogenicity in vivo.These data have allowed further characterization of these important pathogens, including their limited metabolic capabilities, which may contribute to their uncultivatable status. A number of immunogenic proteins, and a potential mechanism for host immune system evasion, have been identified.

  15. Molecular characterization of the uncultivatable hemotropic bacterium Mycoplasma haemofelis

    PubMed Central

    2011-01-01

    Mycoplasma haemofelis is a pathogenic feline hemoplasma. Despite its importance, little is known about its metabolic pathways or mechanism of pathogenicity due to it being uncultivatable. The recently sequenced M. haemofelis str. Langford 1 genome was analysed and compared to those of other available hemoplasma genomes. Analysis showed that in hemoplasmas genes involved in carbohydrate metabolism are limited to enzymes of the glycolytic pathway, with glucose appearing to be the sole energy source. The majority of the pentose phosphate pathway enzymes that catalyze the de novo synthesis of ribonucleotides were absent, as were cell division protein FtsZ and chaperonins GroEL/ES. Uncharacterized protein paralogs containing putative surface expression motifs, comprised 62% of M. haemofelis and 19% of Mycoplasma suis genome coverage respectively, the majority of which were present in a small number of unstructured islands. Limited mass spectrometry and immunoblot data matched a number of characterized proteins and uncharacterized paralogs, confirming their expression and immunogenicity in vivo. These data have allowed further characterization of these important pathogens, including their limited metabolic capabilities, which may contribute to their uncultivatable status. A number of immunogenic proteins, and a potential mechanism for host immune system evasion, have been identified. PMID:21749699

  16. 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.

  17. Using room temperature current noise to characterize single molecular spectra.

    PubMed

    Vasudevan, Smitha; Ghosh, Avik W

    2014-03-25

    We propose a way to use room temperature random telegraph noise to characterize single molecules adsorbed on a backgated silicon field-effect transistor. The overlap of molecule and silicon electronic wave functions generates a set of trap levels that impose their unique scattering signatures on the voltage-dependent current noise spectrum. Our results are based on numerical modeling of the current noise, obtained by coupling a density functional treatment of the trap placement within the silicon band gap, a quantum kinetic treatment of the output current, and a Monte Carlo evaluation of the trap occupancy under resonance. As an illustrative example, we show how we can extract molecule-specific "fingerprints" of four benzene-based molecules directly from a frequency-voltage colormap of the noise statistics. We argue that such a colormap carries detailed information about the trap dynamics at the Fermi energy, including the presence of correlated interactions, observed experimentally in backgated carbon nanotubes.

  18. Characterization of molecularly imprinted polymer nanoparticles by photon correlation spectroscopy.

    PubMed

    Malm, Björn; Yoshimatsu, Keiichi; Ye, Lei; Krozer, Anatol

    2014-12-01

    We follow template-binding induced aggregation of nanoparticles enantioselectively imprinted against (S)-propranolol, and the non-imprinted ones, using photon correlation spectroscopy (dynamic light scattering). The method requires no separation steps. We have characterized binding of (R,S)-propranolol to the imprinted polymers and determined the degree of non-specificity by comparing the specific binding with the results obtained using non-imprinted nanoparticles. Using (S)-propranolol as a template for binding to (S)-imprinted nanoparticle, and (R)-propranolol as a non-specific control, we have determined range of concentrations where chiral recognition can be observed. By studying aggregation induced by three analytes related to propranolol, atenolol, betaxolol, and 1-amino-3-(naphthalen-1-yloxy)propan-2-ol, we were able to determine which parts of the template are involved in the specific binding, discuss several details of specific adsorption, and the structure of the imprinted site.

  19. 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

  20. Molecular characterization of novel progranulin (GRN) mutations in frontotemporal dementia.

    PubMed

    Mukherjee, Odity; Wang, Jun; Gitcho, Michael; Chakraverty, Sumi; Taylor-Reinwald, Lisa; Shears, Shantia; Kauwe, John S K; Norton, Joanne; Levitch, Denise; Bigio, Eileen H; Hatanpaa, Kimmo J; White, Charles L; Morris, John C; Cairns, Nigel J; Goate, Alison

    2008-04-01

    Frontotemporal dementia (FTD) is a clinical term encompassing dementia characterized by the presence of two major phenotypes: 1) behavioral and personality disorder, and 2) language disorder, which includes primary progressive aphasia and semantic dementia. Recently, the gene for familial frontotemporal lobar degeneration (FTLD) with ubiquitin-positive, tau-negative inclusions (FTLD-U) linked to chromosome 17 was cloned. In the present study, 62 unrelated patients from the Washington University Alzheimer's Disease Research Center and the Midwest Consortium for FTD with clinically diagnosed FTD and/or neuropathologically characterized cases of FTLD-U with or without motor neuron disease (MND) were screened for mutations in the progranulin gene (GRN; also PGRN). We discovered two pathogenic mutations in four families: 1) a single-base substitution within the 3' splice acceptor site of intron 6/exon 7 (g.5913A>G [IVS6-2A>G]) causing skipping of exon 7 and premature termination of the coding sequence (PTC); and 2) a missense mutation in exon 1 (g.4068C>A) introducing a charged amino acid in the hydrophobic core of the signal peptide at residue 9 (p.A9D). Functional analysis in mutation carriers for the splice acceptor site mutation revealed a 50% decrease in GRN mRNA and protein levels, supporting haploinsufficiency. In contrast, there was no significant difference in the total GRN mRNA between cases and controls carrying the p.A9D mutation. Further, subcellular fractionation and confocal microscopy indicate that although the mutant protein is expressed, it is not secreted, and appears to be trapped within an intracellular compartment, possibly resulting in a functional haploinsufficiency.

  1. [Molecular characterizations of two dehydroascorbate reductases from Selaginella moellendorffii].

    PubMed

    Cheng, Zishuo; Lan, Ting; Li, Di; Yang, Hailing; Zeng, Qingyin

    2011-01-01

    Plant dehydroascorbate reductase (DHAR) is a physiologically important reducing enzyme in the ascorbate-glutathione recycling reaction. In this study, two DHARs genes (SmDHAR1 and SmDHAR2) were isolated from Selaginella moellendorffii. The SmDHAR1 and SmDHAR2 genes encode two proteins of 218 and 241 amino acid residues, with a calculated molecular mass of 23.97 kDa and 27.33 kDa, respectively. The genomic sequence analysis showed SmDHAR1 and SmDHAR2 contained five and six introns, respectively. Reverse transcription PCR revealed that the SmDHAR1 and SmDHAR2 were constitutive expression genes in S. moellendorffii. The recombinant SmDHAR1 and SmDHAR2 proteins were overexpressed in E. coli, and were purified by Ni-affinity chromatography. The recombinant SmDHAR1 showed 116-fold higher enzymatic activity towards the substrate dehydroascorbate than recombinant SmDHAR2. The recombinant SmDHAR1 showed higher thermal stability than recombinant SmDHAR2. These results indicated obvious functional divergence between the duplicate genes SmDHAR1 and SmDHAR2.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Proteomic Characterization Reveals a Molecular Portrait of Nasopharyngeal Carcinoma Differentiation

    PubMed Central

    Xiao, Zhefeng; Li, Maoyu; Li, Guoqing; Fu, Ying; Peng, Fang; Chen, Yongheng; Chen, Zhuchu

    2017-01-01

    Nasopharyngeal carcinoma (NPC) is categorized into three different differentiated subtypes by World Health Organization (WHO). Based on an earlier comparative proteomic database of the three histological subtypes, the study was to deepen our understanding of molecular mechanisms associated with NPC differentiation through bio-information mining. Among the three subtypes were 194 differentially expressed proteins (DEPs) of 725 identified proteins. Two DEPs, heat shock protein family B (small) member 1 (HSPB1) and keratin 5 (KRT5), were validated in a series of NPC tissue samples by using immunohistochemistry. Quantified protein families including keratins, S100 proteins (S100s) and heat shock proteins exhibited characteristic expression alterations. Comparisons of predicted bio-function activation states among different subtypes, including formation of cellular protrusion, metastasis, cell death, and viral infections, were conducted. Canonical pathway analysis inferred that Rho GTPases related signaling pathways regulated the motility and invasion of dedifferentiated NPC. In conclusion, the study explored the proteomic characteristics of NPC differentiation, which could deepen our knowledge of NPC tumorigenesis and allow the development of novel targets of therapeutic and prognostic value in NPC. PMID:28367237

  7. 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.

  8. Molecular Cloning, Characterization, and Chromosome Mapping of Reptilian Estrogen Receptors

    PubMed Central

    Katsu, Yoshinao; Matsubara, Kazumi; Kohno, Satomi; Matsuda, Yoichi; Toriba, Michihisa; Oka, Kaori; Guillette, Louis J.; Ohta, Yasuhiko; Iguchi, Taisen

    2010-01-01

    In many vertebrates, steroid hormones are essential for ovarian differentiation during a critical developmental stage as well as promoting the growth and differentiation of the adult female reproductive system. Although studies have been extensively conducted in mammals and a few fish, amphibians, and bird species, the molecular mechanisms of sex steroid hormone (estrogens) action have been poorly examined in reptiles. Here, we evaluate hormone receptor and ligand interactions in two species of snake, the Okinawa habu (Protobothrops flavoviridis, Viperidae) and the Japanese four-striped rat snake (Elaphe quadrivirgata, Colubridae) after the isolation of cDNAs encoding estrogen receptor α (ESR1) and estrogen receptor β (ESR2). Using a transient transfection assay with mammalian cells, the transcriptional activity of reptilian (Okinawa habu, Japanese four-striped rat snake, American alligator, and Florida red-belly freshwater turtle) ESR1 and ESR2 was examined. All ESR proteins displayed estrogen-dependent activation of transcription via an estrogen-response element-containing promoter; however, the responsiveness to various estrogens was different. Further, we determined the chromosomal locations of the snake steroid hormone receptor genes. ESR1 and ESR2 genes were localized to the short and long arms of chromosome 1, respectively, whereas androgen receptor was localized to a pair of microchromosomes in the two snake species examined. These data provide basic tools that allow future studies examining receptor-ligand interactions and steroid endocrinology in snakes and also expands our knowledge of sex steroid hormone receptor evolution. PMID:20926589

  9. 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.

  10. Hemoprotozoa of domestic animals in France: prevalence and molecular characterization.

    PubMed

    Criado-Fornelio, A; Buling, A; Pingret, J L; Etievant, M; Boucraut-Baralon, C; Alongi, A; Agnone, A; Torina, A

    2009-01-22

    Very limited information is available on epizootiology of haematozoan infections in French domestic animals. In an attempt to address this issue, prevalence of piroplasmida was studied in carnivores and ruminants, whereas prevalence of Hepatozoon spp. was only investigated in carnivores. In total, 383 animals were included in the survey (namely 116 cats, 108 dogs, 91 sheep and 68 cows). Parasite diagnosis was carried out using molecular methods such as PCR and sequencing of the 18S rRNA gene. In addition, ruminant samples were analyzed with the reverse line blotting technique (RLB). Results of RLB and PCR plus sequencing were in total agreement. In carnivores, haematozoan prevalence was close to 1%. Two cats were infected by H. canis (1.7% prevalence) and one of them was co-infected by Cytauxzoon sp. (0.8%). This represents the first finding of both pathogens in French cats. One dog was infected by H. canis (0.9%) and another by Babesia canis vogeli (0.9%). In ruminants, haematozoan prevalence (piroplasmida) was significantly higher than in carnivores (4.8% in sheep and 8.8% in cow). Theileria ovis was found in 1 sheep, Theileria sp. in 2 sheep, Theileria buffeli in 5 cows and B. major in 1 cow. Evidence presented in this contribution indicates that haematic protozoa are not widely distributed in domestic mammal populations of France.

  11. 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.

  12. Molecular analysis and phylogenetic characterization of HIV in Iran.

    PubMed

    Sarrami-Forooshani, Ramin; Das, Suman Ranjan; Sabahi, Farzaneh; Adeli, Ahmad; Esmaeili, Rezvan; Wahren, Britta; Mohraz, Minoo; Haji-Abdolbaghi, Mahboubeh; Rasoolinejad, Mehrnaz; Jameel, Shahid; Mahboudi, Fereidoun

    2006-07-01

    The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years. While the earliest cases were found in hemophiliacs, intravenous drug users are now fueling the outbreak. In this study, both the 122 clones of HIV-1 gag p17 and the 131 clones of env V1-V5 region were obtained from 61 HIV-1 seropositives belonging to these two groups in Iran. HIV-1 subtyping and phylogenetic analysis was done by heteroduplex mobility assays (HMA) and multiple clone sequencing. The result indicated all hemophiliacs are infected with HIV-1 subtype B and all intravenous drug users are infected with HIV-1 subtype A. Since intravenous drug abuse is the major transmission route in Iran, HIV-1 subtype A is likely to be the dominant viral subtype circulating in the country. The analysis of genetic distances showed subtype B viruses in Iran to be twice as heterogeneous as the subtype A viruses. In conclusion, this first molecular study of HIV-1 genotypes in Iran suggests two parallel outbreaks in distinct high-risk populations and may offer clues to the origin and spread of infection in Iran.

  13. 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

  14. 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.

  15. 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.

  16. Global reaction route mapping of isomerization pathways of exotic C6H molecular species

    NASA Astrophysics Data System (ADS)

    Vikas, Kaur, Gurpreet

    2013-12-01

    C6H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C6H is explored to search isomers of C6H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C6H. 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 C6H) 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-C6H can readily isomerize to a six-member ring isomer.

  17. Molecular Characterization of Prunus angustifolia Genotypes from Turkey.

    PubMed

    Akbulut, Mustafa; Polat, Mehmet; Ercisli, Sezai; Sorkheh, Karim

    2016-08-25

    Prunus angustifolia var. angustifolia is a deciduous shrub with 1.5-3.0 m plant height and mostly found in rural areas between 1400 and 1600 m in northeastern Turkey including Bayburt, Gumushane, and Kars provinces. The plant has multistems and well known to adapt severe winter and dry-hot summer conditions. In this study, we aimed to explore the genetic diversity within this specie and also to investigate its phylogenetic relationship with economically important the other cherry species; Prunus avium, Prunus cerasus, Prunus laurocerasus, and Prunus mahaleb. A total of 50 simple sequence repeats (SSRs) markers used to elucidate the genetic variation among 32 P. angustifolia var. angustifolia genotypes selected from three locations (Bayburt, Gumushane, and Kars) in northeastern Turkey. The cross-species transportability of used 50 SSRs was 80 % indicating a high degree of homology between P. angustifolia and the other Prunus species. The genetic distance between P. angustifolia var. angustifolia genotypes belonging to a particular geographic site was lower than that between genotypes of different geographic origins. Cluster analysis in general differentiated P. angustifolia var. angustifolia genotypes according to their geographic sites and separated them from the other Prunus species. P. angustifolia found more closer to P. mahaleb and P. cerasus, in the subgenus Cerasus, The analysis of molecular variance revealed that genetic variation among individuals within populations was much higher than among Prunus groups and among P. angustifolia var. angustifolia populations of different geographic sites. The results indicate a substantial genetic diversity in P. angustifolia var. angustifolia and the need of exploring a wider area to increase the chance of finding a particular genotype.

  18. Molecular characterization of 25 Chinese pedigrees with 21-hydroxylase deficiency.

    PubMed

    Yu, Yongguo; Wang, Jian; Huang, Xiaodong; Wang, Ying; Yang, Peirong; Li, Juan; Tsuei, Sian Hsiang-Te; Shen, Yongnian; Fu, Qihua

    2011-03-01

    Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders mainly caused by a defect in the steroid 21-hydroxylase gene (CYP21A2). In this study, we investigated the molecular defects of 25 Chinese pedigrees with 21-hydroxylase deficiency (21-OHD). Diagnosis of the probands in the families was based on their typical clinical presentations, such as inborn ambiguous genitalia, or early onset of salt wasting and biochemical metabolite abnormalities. All 10 exons and exon-intron boundaries of the CYP21A2 gene were amplified from the genomic DNA of the probands and then analyzed by direct sequencing. The phenotypes of the 26 patients from 25 pedigrees were classified as the classical form of 21-OHD. One novel mutation (c.1223 G>T) and 13 recurrent mutations of CYP21A2 were identified in the 25 pedigrees by genetic analysis. The novel c.1223 G>T mutation results in the substitution of arginine by leucine at amino acid position 408 (p.Arg408Leu). The most frequent mutation alleles were IVS2-13A/C>G (14/52) and I172N (11/52), followed by chimeric mutations (10/52). Forty six of 52 mutated alleles resulted from pseudogene conversion and 6 of 52 from random mutations. The spectrum of CYP21A2 mutation in our study was slightly different from those previously reported in Chinese and in other ethnic groups of the world. Although microconversion events were the main cause of mutations in the CYP21 gene, random mutations with a common origin can also be the reason for 21-OHD.

  19. 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.

  20. 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.

  1. Isolation & molecular characterization of human parainfluenza virus in Chennai, India

    PubMed Central

    Indumathi, C.P.; Gunanasekaran, P.; Kaveri, K.; Arunagiri, Kavita; Mohana, S.; Sheriff, A. Khaleefathullah; SureshBabu, B.V.; Padmapriya, P.; Senthilraja, R.; Fathima, Gracy

    2015-01-01

    Background & objectives: Human parainfluenza virus (HPIV) accounts for a significant proportion of lower respiratory tract infections in children as well as adults. This study was done to detect the presence of different subtypes of HPIV from patients having influenza like illness (ILI). Methods: Throat and nasal swabs from 232 patients with ILI who were negative for influenza viruses were tested by multiplex reverse transcription polymerase chain reaction(mRT-PCR) for the detection of human parainfluenza virus. All samples were inoculated in rhesus monkey kidney (LLC-MK2) cell line. Results: Of the 232 samples, 26(11.2%) were positive by mRT-PCR and nine (34.6%) showed cytopathic effect with syncytium formation for HPIV and all were HPIV-3 serotype, other serotypes like 1,2,4 were negative. The HPIV-3 strains (HN gene) were sequenced and analysed. Two novel mutations were identified at amino acid residues 295 and 297. Interpretation & conclusions: The mRT-PCR assay offers a rapid, sensitive and accurate diagnostic method for detection of HPIV which enables early detection and control. In our study there was a predominance of HPIV among 1-5 yr age group and the school going age group was less affected. Further studies need to be done to characterize HPIV isolated from different parts of the country. PMID:26658594

  2. 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.

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

    PubMed

    2012-07-18

    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.

  4. Clinical characterization and molecular mechanisms of statin myopathy.

    PubMed

    Toth, Peter P; Harper, Charles R; Jacobson, Terry A

    2008-08-01

    Myopathy has been reported in a small percentage of statin-treated patients for the past 30 years, but the etiologic mechanisms for inducing muscle injury have not yet been fully characterized. Statin-induced myopathy is now understood to be a heterogeneous condition that may be due to: mechanisms of the drug itself; interactions with other drugs; or genetic, metabolic and immunological vulnerabilities in individual patients. In some cases, statins may unmask latent conditions (e.g., asymptomatic baseline myopathy) that predispose patients to muscle toxicity. The definitions, epidemiology, clinical features, risk factors and proposed mechanisms of statin-induced myopathy are reviewed. Muscle metabolism can be adversely impacted by statin therapy, including changes in fatty acid oxidation, possibly reduced coenzyme Q(10) biosynthesis, and increased myocyte protein degradation via the activity of atrogin-1 and the ubiquitin-proteasome pathway. Statin therapy may also activate a variety of autoimmune phenomena that potentiate myocellular injury. Improving our understanding of statin-induced myopathy is a high clinical priority given the large number of patients eligible for statin therapy and the fact that the development of myalgia and myopathy are leading reasons cited by patients for statin discontinuation.

  5. Clinical and molecular characterization of patients with Jacobsen syndrome

    SciTech Connect

    Penny, L.A.; Aquila, M.; Iones, O.W.

    1994-09-01

    Jacobsen (11q-) syndrome is caused by segmental aneusomy for the distal end of the long arm of chromosome 11. Typical features include mental retardation, trigonocephaly, facial dysmorphism, cardiac defects and thrombocytopenia, among others. We studied 14 Jacobsen syndrome patients with de novo terminal deletions of 11q. The deletions were characterized in a loss of heterozygosity analysis using polymorphic dinucleotide repeats. There was no preference in the parental origin of the deleted chromosome. Seven patients with the largest deletions, extending from 11q23.3-qter, appear to share the same breakpoint, between D11S924 and D11S1341. Terminal deletions extending proximal to this common breakpoint may be lethal. The remaining seven patients had various smaller deletions of 11q23.3, 11q24 or 11q25. Three patients with small terminal deletions had several major features of Jacobsen syndrome, including facial dysmorphism, cardiac defects and thrombocytopenia, suggesting that the genes responsible for these features lie near the end of the chromosome. These three patients did not have trigonocephaly, suggesting that, if hemizygosity for a single gene is responsible, it may lie proximal to D11S934.

  6. Morphological and molecular characterization of bovine coenurosis in Sardinia, Italy.

    PubMed

    Varcasia, A; Pipia, A P; Arru, D; Pes, A M; Tamponi, C; Dore, F; Garippa, G; Scala, A

    2013-05-01

    Coenurosis is a central nervous system disease of wild and domestic ruminants caused by Coenurus cerebralis, a bladder worm stage of Taenia multiceps). Even in Sardinia island, this metacestode seems to be widespread in sheep (Scala et al. Vet Parasitol 143(3-4):294-298, 2007) where coenurosis is an important health problem (Varcasia et al. Parasitol Res 99(5):622-626, 2006) the last and unique report of coenurosis in cattle was in 1990 (Cubeddu et al. 1990). In the present paper, a case of bovine coenurosis in Sardinia was described 22 years after the first report with a morphological a biomolecular characterization. A 2-year-old Limousine bull was euthanized in the Bolotana (NU) municipality (Central Sardinia). The remote anamnesis achieved from the farmer reporting that the bull showed neurological symptoms from 1 year of age previously classified as nutritional problems by the farm's veterinary. The breeder also says that the bull have by self-produced the skull fracture by hitting a gaff in the farm. The skull was opened and the brain removed and carefully examined showing two coenurus cysts containing clear fluid with numerous scoleces both in the right hemisphere. Morphological features of the cysts and mt-DNA sequencing confirm that the parasites were T. multiceps Coenuri.

  7. Molecular characterization of a novel antimicrobial peptide from Mytilus coruscus.

    PubMed

    Liao, Zhi; Wang, Xin-chao; Liu, Hui-hui; Fan, Mei-hua; Sun, Jing-jing; Shen, Wang

    2013-02-01

    Antimicrobial peptides (AMPs) are components of the innate immune responses that form the first line of host defense against pathogens. Marine mussels can produce a surprising abundance of cysteine-rich AMPs pertaining to the defensin, myticin, mytilin and mytimycin families, particularly in the circulating hemocytes. In the current study, we purified and characterized a novel cysteine-rich peptide with remarkable antibacterial activity from Mytilus coruscus and designated with myticusin-1, a 104-amino acid long polypeptide including 10 cysteine residues forming an unusual cysteine pattern. Antimicrobial assays demonstrated that myticusin-1 exhibited stronger anti-microbial properties against Gram-positive bacteria more than Gram-negative bacteria and fungus. Furthermore, myticusin-1 caused significant morphological alterations in both Sarcina luteus and Escherichia coli as shown by transmission electron microscopy (TEM). The cDNA of myticusin-1 was cloned and sequenced from the hemocytes cDNA library of M. coruscus. The mRNA transcripts of myticusin-1 are mainly detected in hemocyte, which indicates that myticusin-1 are specifically synthesized and stored in circulating hemocytes. The expression level of myticusin-1 in hemocytes was up-regulated and reached the highest level at 36 h after S. luteus challenge, which was 20-fold increase compared to that of the control group. These results indicated that myticusin-1 was involved in the host immune response against bacterial infection and might contribute to the clearance of invading bacteria.

  8. 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

  9. 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.

  10. 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

  11. Molecular characterization of enolase gene from Taenia multiceps.

    PubMed

    Li, W H; Qu, Z G; Zhang, N Z; Yue, L; Jia, W Z; Luo, J X; Yin, H; Fu, B Q

    2015-10-01

    Taenia multiceps is a cestode parasite with its larval stage, known as Coenurus cerebralis, mainly encysts in the central nervous system of sheep and other livestocks. Enolase is a key glycolytic enzyme and represents multifunction in most organisms. In the present study, a 1617bp full-length cDNA encoding enolase was cloned from T. multiceps and designated as TmENO. A putative encoded protein of 433 amino acid residues that exhibited high similarity to helminth parasites. The recombinant TmENO protein (rTmENO) showed the catalytic and plasminogen-binding characteristics after the TmENO was subcloned and expressed in the pET30a(+) vector. The TmENO gene was transcribed during the adult and larval stages and was also identified in both cyst fluid and as a component of the adult worms and the metacestode by western blot analysis. Taken together, our results will facilitate further structural characterization for TmENO and new potential control strategies for T. multiceps.

  12. Molecular characterization and analysis of TLR-1 in rabbit tissues

    PubMed Central

    Algammal, Abdelazeem M.; Abouelmaatti, Reham R.; Gerdouh, Ahmed; Abdeldaim, Mohamed

    2016-01-01

    The rabbit has great commercial importance as a source of meat and fur, as well as its uses as a laboratory animal for the production of antibodies, used to detect the presence or absence of disease and for research in infectious diseases and immunology. One of the most critical problems in immunology is to understand how the immune system detects the presence of infectious agents and disposes the invader without destroying the self-tissues. Genetic characterization of Toll-like receptors has established that innate immunity is a skillful system that detects invasion of microbial pathogens. Our work aimed to identify, clone and express the Oryctolagus cuniculus (rabbit) TLR-1 mRNA and its encoding protein. We cloned the complete mRNA sequence of Oryctolagus cuniculus TLR-1 and deposit it in the GenBank under accession number (KC349941), which has 2388 base pair and it encodes encode an open reading frame (ORF) translated into 796 amino acids mRNA and consist of 20 types of amino acids. The analysis of amino acid sequence revealed that the rabbit TLR-1 has a typical protein components belonging to the TLR family. Rabbit TLR-1 was expressed in a wide variety of rabbit tissues, which indicate an important role in immune system in different organs. PMID:27833439

  13. Isolation, Molecular Characterization, and Mapping of Four Rose MLO Orthologs

    PubMed Central

    Kaufmann, Helgard; Qiu, Xianqin; Wehmeyer, Juliane; Debener, Thomas

    2012-01-01

    Powdery mildew is a major disease of economic importance in cut and pot roses. As an alternative to conventional resistance breeding strategies utilizing single-dominant genes or QTLs, mildew resistance locus o (MLO)-based resistance might offer some advantages. In dicots such as Arabidopsis, pea, and tomato, loss-of-function mutations in MLO genes confer high levels of broad-spectrum resistance. Here, we report the isolation and characterization of four MLO homologs from a large rose EST collection isolated from leaves. These genes are phylogenetically closely related to other dicot MLO genes that are involved in plant powdery mildew interactions. Therefore, they are candidates for MLO genes involved in rose powdery mildew interactions. Two of the four isolated genes contain all of the sequence signatures considered to be diagnostic for MLO genes. We mapped all four genes to three linkage groups and conducted the first analysis of alternative alleles. This information is discussed in regards to a reverse genetics approach aimed at the selection of rose plants that are homozygous for loss-of-function in one or more MLO genes. PMID:23130018

  14. Phyical and molecular characterization of a genetic switch

    NASA Astrophysics Data System (ADS)

    Finzi, Laura; Zurla, Chiara; Manzo, Carlo; Wang, Haowei; Dunlap, David

    2009-11-01

    The lambda bacteriophage epigenetic switch determines the growth lifestyle of the virus after infection of its host (E. coli). It is now clear that the switch consists of a ˜2.3 kbp-long DNA loop mediated by the lambda repressor protein. Using tethered particle microscopy (TPM), magnetic tweezers and AFM, our laboratory has novel, direct evidence of loop formation and breakdown by the repressor, the first characterization of the thermodynamics and kinetics of the looping reaction and its dependence on repressor non-specific binding and DNA supercoiling. These in vitro data provide insight into the different possible nucleoprotein complexes and into the lambda repressor-mediated looping mechanism which leads to predictions for that in vivo. The significance of this work consists not only of the new insight into the physical parameters at the basis of a paradigmatic epigenetic switch that governs lysogeny vs. lysis, but also the detailed mechanics of regulatory DNA loops mediated by proteins bound to multipartite operators and capable of different levels of oligomerization.

  15. Molecular characterization of Cryptosporidium spp. in children from Mexico.

    PubMed

    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.

  16. Standoff characterization of high-molecular components of oil disperse systems

    NASA Astrophysics Data System (ADS)

    Ganeeva, Y. M.; Yusupova, T. N.; Romanov, G. V.; Bashkirtseva, N. Y.; Rafailov, Michael K.

    2012-06-01

    Here we report work done toward standoff characterization of high-molecular components responsible for forming nano-structures in oil disperse system. Complex physical and chemical studies have been conducted specifically on bitumen extracted from rich and poor grade oil sand from Canada. Standoff characterization of oil disperse system highmolecular components is discussed here based on prospective of ultra-fast broadband tunable MWIR laser absorption spectroscopy.

  17. 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

  18. 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

  19. 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.

  20. Molecular cloning and characterization of novel ficolins from Xenopus laevis.

    PubMed

    Kakinuma, Yuji; Endo, Yuichi; Takahashi, Minoru; Nakata, Munehiro; Matsushita, Misao; Takenoshita, Seiichi; Fujita, Teizo

    2003-04-01

    Ficolins are proteins characterized by the presence of collagen- and fibrinogen-like domains. Two of three human ficolins, L-ficolin and H-ficolin, are serum lectins and are thought to play crucial roles in host defense through opsonization and complement activation. To elucidate the evolution of ficolins and the primordial complement lectin pathway, we cloned four ficolin cDNAs from Xenopus laevis, termed Xenopus ficolin (XeFCN) 1, 2, 3 and 4. The deduced amino acid sequences of the four ficolins revealed the conserved collagen- and fibrinogen-like domains. The full sequences of the four ficolins showed a 42-56% identity to human ficolins, and 60-83% between one another. Northern blots showed that XeFCN1 was expressed mainly in liver, spleen and heart, and XeFCN2 and XeFCN4 mainly in peripheral blood leukocytes, lung and spleen. We isolated ficolin proteins from Xenopus serum by affinity chromatography on N-acetylglucosamine-agarose, followed by ion-exchange chromatography. The final eluate showed polymeric bands composed of two components of 37 and 40 kDa. The N-terminal amino acid sequences and treatment with endoglycosidase F showed that the two bands are the same XeFCN1 protein with different masses of N-linked sugar. The polymeric form of the two types of XeFCN1 specifically recognized GlcNAc and GalNAc residues. These results suggest that like human L-ficolin, XeFCN1 functions in the circulation through its lectin activity.

  1. 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

  2. Genetic and molecular characterization of multiflorous spikelet in oat.

    PubMed

    Zimmer, C M; Ubert, I P; Pellizzaro, K; Federizzi, L C; Nava, I C

    2017-03-30

    Multiflorous spikelets are found in several grass species of agricultural and economic interest. In oat, this morphological characteristic is associated with the production of naked grains. Although many genetic studies have been performed over the past century, the inheritance of the multiflorous spikelet trait is not fully understood in oat. The objectives of this study were to evaluate environmental effects on the multiflorous spikelet trait, to estimate the number of genes controlling the trait, and to clone and characterize sequences of the AP2 gene in oat. Two genetic populations of recombinant inbreed lines were screened for the multiflorous spikelet trait from different years and sowing dates under field experiments. Normal, multiflorous, and mosaic spikelets were analyzed in the whole panicle for both years and sowing dates. Specific primer pairs for the AP2 gene was utilized to amplify and clone oat sequences. The results demonstrate that under higher temperature and day-length conditions, the variable expressivity of the multiflorous spikelet trait was less pronounced in both populations. Genetic analyses indicated the action of one major gene and two or three modifying genes controlling the expression of the multiflorous spikelet trait in oat, depending on the genetic background. Sequences with similarity to the AP2 gene were isolated from the oat lines UFRGS 017004-2 and URS Taura, and genetic polymorphisms were identified, which are valuable to confirm the action of AP2 on the multiflorous spikelet trait. Our results provide information to assist in the development of future studies of the multiflorous spikelet trait in oat.

  3. 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

  4. Molecular characterization of Haemophilus ducreyi isolates from different geographical locations.

    PubMed

    Mbwana, J; Bölin, I; Lyamuya, E; Mhalu, F; Lagergård, T

    2006-01-01

    The technique of random amplified polymorphic DNA (RAPD) was adapted and optimized to study Haemophilus ducreyi isolates. A panel of 43 strains isolated from chancroid patients from different countries in Africa, Europe, North America, and Asia were characterized. The strains were also studied with respect to lipooligosaccharide (LOS) migration and immunoblotting patterns and the presence of cytolethal distending toxin genes. The RAPD method with the OPJ20 primer generated nine banding patterns (1 to 9). The majority of the isolates were clustered into two major profiles, 14 and 13 strains into profiles 1 and 2, respectively, and just a few strains revealed patterns 3 and 4. The isolates from Thailand were exceptional in that they showed greater diversity and were represented by six different RAPD patterns, i.e., patterns 3 and 5 to 9. The LOS migration and immunoblotting analyses revealed two different patterns, which indicated long and short forms of LOS; the former was found in 20/23 tested strains. Two strains that expressed the short form of LOS were grouped into RAPD pattern 4. The absence of cdtABC genes was observed in only 4/23 strains, and three of these isolates were assigned to RAPD pattern 4. Our results showed limited genotypic and phenotypic variations among H. ducreyi strains, as supported by the conserved RAPD and LOS profiles shared by the majority of the studied strains. However, the RAPD method identified differences between strains, including those from different geographic areas, which indicate the potential of RAPD as an epidemiological tool for the typing of H. ducreyi isolates in countries where chancroid is endemic.

  5. Molecular characterization of bacteriophages for microbial source tracking in Korea.

    PubMed

    Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo

    2009-11-01

    We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

  6. Molecular and Phenotypic Characterization of Pseudomonas spp. Isolated from Milk

    PubMed Central

    Wiedmann, Martin; Weilmeier, Denise; Dineen, Sean S.; Ralyea, Robert; Boor, Kathryn J.

    2000-01-01

    Putative Pseudomonas spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. Isolates were biochemically profiled using the Biolog system and API 20 NE and by determining the production of proteases, lipases, and lecithinases for each isolate. Isolates grouped into five coherent clusters, predominated by the species P. putida (cluster A), P. fluorescens (cluster B), P. fragi (as identified by Biolog) or P. fluorescens (as identified by API 20 NE) (cluster C), P. fragi (as identified by Biolog) or P. putida (as identified by API 20 NE) (cluster D), and P. fluorescens (cluster E). Isolates within each cluster also displayed similar enzyme activities. Isolates in clusters A, C, and D were generally negative for all three enzyme activities; isolates in cluster B were predominantly positive for all three enzyme activities; and isolates in cluster E were negative for lecithinase but predominantly positive for protease and lipase activities. Thus, only isolates from clusters B and E produced enzyme activities associated with dairy product flavor defects. Thirty-eight ribogroups were differentiated among the 70 isolates. Ribotyping was highly discriminatory for dairy Pseudomonas isolates, with a Simpson's index of discrimination of 0.955. Isolates of the same ribotype were never classified into different clusters, and ribotypes within a given cluster generally showed similar ribotype patterns; thus, specific ribotype fragments may be useful markers for tracking the sources of pseudomonads in dairy production systems. Our results suggest that ribogroups are generally homogeneous with respect to nomenspecies and biovars, confirming the identification potential of ribotyping for Pseudomonas spp. PMID:10788386

  7. 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.

  8. Flour Quality and Related Molecular Characterization of High Molecular Weight Glutenin Subunit Genes from Wild Emmer Wheat Accession TD-256.

    PubMed

    Zhang, Da-Le; He, Ting-Ting; Liang, Hui-Hui; Huang, Lu-Yu; Su, Ya-Zhong; Li, Yu-Ge; Li, Suo-Ping

    2016-06-22

    To clarify the effect of high molecular weight glutenin subunit (HMW-GS) from wild emmer wheat on flour quality, which has the same mobility as that from common wheat, the composition and molecular characterization of HMW-GS from wild emmer wheat accession TD-256, as well as its flour quality, were intensively analyzed. It is found that the mobilities of Glu-A1 and Glu-B1 subunits from TD-256 are consistent with those of bread wheat cv. 'XiaoYan 6'. Nevertheless, dough rheological properties of TD-256 reveal its poor flour quality. In the aspect of molecular structure from HMW-GS, only two conserved cysteine residues can be observed in the deduced protein sequence of 1Bx14* from TD-256, while most Glu-1Bx contain four conserved cysteine residues. In addition, as can be predicted from secondary structure, the quantity both of α-helixes and their amino acid residues of the subunits from TD-256 is fewer than those of common wheat. Though low molecular weight glutenin subunit (LMW-GS) and gliadin can also greatly influence flour quality, the protein structure of the HMW-GS revealed in this work can partly explain the poor flour quality of wild emmer accession TD-256.

  9. Molecular Characterization of Pneumococcal Isolates from Pets and Laboratory Animals

    PubMed Central

    van der Linden, Mark; Al-Lahham, Adnan; Nicklas, Werner; Reinert, Ralf René

    2009-01-01

    Background Between 1986 and 2008 Streptococcus pneumoniae was isolated from 41 pets/zoo animals (guinea pigs (n = 17), cats (n = 12), horses (n = 4), dogs (n = 3), dolphins (n = 2), rat (n = 2), gorilla (n = 1)) treated in medical veterinary laboratories and zoos, and 44 laboratory animals (mastomys (multimammate mice; n = 32), mice (n = 6), rats (n = 4), guinea pigs (n = 2)) during routine health monitoring in an animal facility. S. pneumoniae was isolated from nose, lung and respiratory tract, eye, ear and other sites. Methodology/Principal Findings Carriage of the same isolate of S. pneumoniae over a period of up to 22 weeks was shown for four mastomys. Forty-one animals showed disease symptoms. Pneumococcal isolates were characterized by optochin sensitivity, bile solubility, DNA hybridization, pneumolysin PCR, serotyping and multilocus sequence typing. Eighteen of the 32 mastomys isolates (56%) were optochin resistant, all other isolates were optochin susceptible. All mastomys isolates were serotype 14, all guinea pig isolates serotype 19F, all horse isolates serotype 3. Rats had serotypes 14 or 19A, mice 33A or 33F. Dolphins had serotype 23F, the gorilla serotype 14. Cats and dogs had many different serotypes. Four isolates were resistant to macrolides, three isolates also to clindamycin and tetracyclin. Mastomys isolates were sequence type (ST) 15 (serotype 14), an ST/serotype combination commonly found in human isolates. Cats, dogs, pet rats, gorilla and dolphins showed various human ST/serotype combinations. Lab rats and lab mice showed single locus variants (SLV) of human STs, in human ST/serotype combinations. All guinea pig isolates showed the same completely new combination of known alleles. The horse isolates showed an unknown allele combination and three new alleles. Conclusions/Significance The isolates found in mastomys, mice, rats, cats, dogs, gorilla and dolphins are most likely identical to human

  10. Characterization and analysis of the molecular weight of lignin for biorefining studies

    SciTech Connect

    Tolbert, Allison; Akinosho, Hannah; Khunsupat, Ratayakorn; Naskar, Amit K.; Ragauskas, Arthur J.

    2014-06-04

    The molecular weight of lignin is a fundamental property that infl uences the recalcitrance of biomass and the valorization of lignin. The determination of the molecular weight of lignin in native biomass is dependent on the bioresources used and the isolation and purifi cation procedures employed. The three most commonly employed isolation methods are milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL). Common characterization techniques for determining the molecular weight of lignin will be addressed, with an emphasis on gel permeation chromatography (GPC). This review also examines the mechanisms behind several biological, physical, and chemical pre-treatments and their impact on the molecular weight of lignin. The number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (D) all vary in magnitude depending on the biomass source, pre-treatment conditions, and isolation method. Additionally, there is a growing body of literature that supports changes in the molecular weight of lignin in response to genetic modifi cations in the lignin biosynthetic pathways. This review summarizes different procedures for obtaining the molecular weight of lignin that have been used in recent years and highlight future opportunities for applications of lignin.

  11. Molecular Characterization of Invasive Neisseria meningitidis Strains Isolated in Chile during 2010–2011

    PubMed Central

    Barra, Gisselle N.; Araya, Pamela A.; Fernandez, Jorge O.; Gabastou, Jean-Marc; Hormazábal, Juan Carlos; Seoane, Mabel; Pidal, Paola C.; Valenzuela, Maria T.; Ibarz-Pavón, Ana Belén

    2013-01-01

    Background With the upcoming licensure of Outer Membrane Protein-based vaccines against meningococcal disease, data on disease incidence and molecular characteristic of circulating N. meningitidis strains in Latin American countries is needed. Chile is, to date, one of the few countries in the region that has performed this type of work in a comprehensive collection of disease-associated strains from two consecutive years, 2010–2011. Methods A total of 119 N. meningitidis strains isolated from patients with invasive disease in Chile in 2010–2011 were characterized by the National Reference Laboratory. Serogroup determination, MLST and porA typing were performed. Results Serogroup B was predominant in both study years, but W135 experienced a noticeable increase in 2011 compared to 2010. ST-11 complex, ST-41/44 complex ST-32 complex were the most prevalent among the isolates, and were strongly associated with serogroups W135 (ST-11 Complex) and B (ST-41/44 and ST-32 complexes). Likewise, the major porA types detected were strongly associated with these three clonal complexes: P1.5,2 was found exclusively among W135:ST-11 isolates, whereas P1.7, 2–3 was only detected in C:ST-11. ST-41/44 isolates mainly had P1.10-8, and ST-32 complex were associated with a P1.18-8 porA. Conclusions Our data show disease-associated N. meningitidis circulating in Chile are similar to those found in other parts of the world. The increase on W135:ST-11 isolates observed in 2011 foretold the unusual epidemiological situation experienced in the country in 2012, and MLST data show that this strain is indistinguishable from the one linked to the global Hajj 2000-related outbreak that occurred in 2001. Finally, this work demonstrates the importance of maintaining a strong national surveillance program integrating clinical, epidemiological and laboratory data and incorporating gold standard diagnostic and characterization techniques that allow the data to be compared all over the world

  12. Molecular characterization and population structure of a new ampelovirus associated with blackberry yellow vein disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blackberry yellow vein disease is the most important viral disease of blackberry in the United States. Experiments were conducted to characterize a new virus identified in symptomatic plants. Molecular analysis revealed a genome organization resembling Grapevine leafroll-associated virus 3, the type...

  13. Characterization of molecular identity and pathogenicity of rice blast fungus in Hunan province of China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Characterization of molecular identity and pathogenicity of the rice blast fungus benefits the deployment of effective blast resistance (R) genes. In order to identify blast resistance genes in rice producing areas where most of the hybrid rice is grown in Hunan province, 182 M. oryzae strains were ...

  14. First molecular detection and characterization of Akabane virus in small ruminants in Turkey.

    PubMed

    Oğuzoğlu, T Ç; Toplu, N; Koç, B T; Doğan, F; Epikmen, E T; İpek, E; Akkoç, A N

    2015-10-01

    Abortion outbreaks associated with congenital malformations in two distinct small-ruminant flocks were reported in Turkey in 2013-2014. This paper describes the first molecular characterization of Turkish Akabane virus strains in small-ruminant flocks using partial sequence analysis of the S segment and pathological findings.

  15. 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...

  16. 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...

  17. Biological and molecular characterization of a US isolate of Hosta virus X

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hosta virus X (HVX) is rapidly becoming a serious pathogen of commercially important hosta plants worldwide. We report here a biological and molecular characterization of a US isolate of HVX, HVX-37. HVX-37 infectivity was tested in 21 hosta cultivars over three growth seasons, and three types of re...

  18. 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.

  19. Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Causing Fatal Purulent Pericarditis

    PubMed Central

    Kumar, Vasudevan Anil; Nair, Nisha; Thachathodiyl, Rajesh; Nandakumar, Aswathy; Dinesh, Kavitha R; Thatcher, Eileen; Karim, Shamsul; Biswas, Raja

    2013-01-01

    Though pericardial disease is common in patients with renal disease, purulent pericarditis is very rare. We report a fatal case of purulent pericarditis and sepsis due to methicillin-resistant Staphylococcus aureus in a 78-year-old male with systemic hypertension and renal disease along with the molecular characterization of its resistant mechanism. PMID:24701111

  20. Characterization of the mixed self-assembled monolayer at the molecular scale.

    PubMed

    Ta, Van-Thao; Nimse, Satish Balasaheb; Song, Keum-Soo; Kim, Junghoon; Sayyed, Danishmalik Rafiq; Nguyen, Van-Thuan; Kim, Taisun

    2011-10-28

    The mixed SAM obtained by the self-assembly of the monothiolated calix[4]crown-5 receptor 1 and the subsequent addition of the thiolated alkylferrocene guest 3 was characterized at the molecular scale by the favorable receptor-guest interactions by using cyclic voltammetry (CV).

  1. Molecular ordering and molecular dynamics in isotactic-polypropylene characterized by solid state NMR.

    PubMed

    Miyoshi, Toshikazu; Mamun, Al; Hu, Wei

    2010-01-14

    The order-disorder phenomenon of local packing structures, space heterogeneity, and molecular dynamics and average lamellar thickness, , of the alpha form of isotactic polypropylene (iPP) crystallized at various supercooling temperatures, DeltaT, are investigated by solid-state (SS) NMR and SAXS, respectively. increases with lowering DeltaT, and extrapolations of (-1) versus averaged melting point, , gives an equilibrium melting temperature, T(m)(0) = 457 +/- 4 K. High-power TPPM decoupling with a field strength of 110 kHz extremely improves (13)C high-resolution SS-NMR spectral resolution of the ordered crystalline signals at various DeltaT. A high-resolution (13)C SS-NMR spectrum combined with a conventional spin-lattice relaxation time in the rotating frame (T(1rhoH)) filter easily accesses an order-disorder phenomenon for upward and downward orientations of stems and their packing in the crystalline region. It is found that ordered packing fraction, f(order), increases with lowering DeltaT and reaches a maximum value of 62% at DeltaT = 34 K. The ordering phenomenon of stem packing indicates that chain-folding direction changes from random in the disordered packing to order in the ordered packing along the a sin theta axis under a hypothesis of adjacent re-entry structures. It is also found that f(order) significantly increases prior to enhancement of lamellar thickness. Additionally, annealing experiments indicate that is significantly enhanced after a simultaneous process of partial melting and recrystallization/reorganization into the ordered packing at annealing temperature >/=423 K. Furthermore, the center-bands only detection of exchange (CODEX) NMR method demonstrates that time-kinetic parameters of helical jump motions are highly influenced by DeltaT. These dynamic constraints are interpreted in terms of increment of and packing ordering. Through these new results related to molecular structures and dynamics, roles of polymer

  2. Molecular detection and characterization of goat isolate of Taenia hydatigena in Turkey.

    PubMed

    Utuk, Armagan Erdem; Piskin, Fatma Cigdem

    2012-01-01

    The aim of this study was to provide molecular detection and characterization of the goat isolate of Taenia hydatigena from Ankara province of Turkey. For this purpose, PCR amplification of small subunit ribosomal RNA (rrnS) and partial sequencing of mitochondrial cytochrome c oxidase subunit 1 (mt-CO1) genes were performed in a one-month-old dead goat. According to rrnS-PCR results, parasites were identified as Taenia spp., and partial sequence of mt-CO1 gene was corresponding to T. hydatigena. At the end of the study, we concluded that molecular tools can be used to define species of parasites in cases where the key morphologic features cannot be detected. Nucleotide sequence data of Turkish goat isolate of T. hydatigena was submitted to GenBank for other researchers interested in this subject. By this study, molecular detection and characterization of T. hydatigena was done for the first time in Turkey.

  3. Molecular Detection and Characterization of Goat Isolate of Taenia hydatigena in Turkey

    PubMed Central

    Utuk, Armagan Erdem; Piskin, Fatma Cigdem

    2012-01-01

    The aim of this study was to provide molecular detection and characterization of the goat isolate of Taenia hydatigena from Ankara province of Turkey. For this purpose, PCR amplification of small subunit ribosomal RNA (rrnS) and partial sequencing of mitochondrial cytochrome c oxidase subunit 1 (mt-CO1) genes were performed in a one-month-old dead goat. According to rrnS-PCR results, parasites were identified as Taenia spp., and partial sequence of mt-CO1 gene was corresponding to T. hydatigena. At the end of the study, we concluded that molecular tools can be used to define species of parasites in cases where the key morphologic features cannot be detected. Nucleotide sequence data of Turkish goat isolate of T. hydatigena was submitted to GenBank for other researchers interested in this subject. By this study, molecular detection and characterization of T. hydatigena was done for the first time in Turkey. PMID:22500144

  4. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections

    PubMed Central

    Tang, Yi-Wei; Ou, Chin-Yih

    2012-01-01

    Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics. PMID:26038427

  5. Molecular characterization of antibodies bearing Id-460. II. Molecular basis for Id-460 expression

    PubMed Central

    1985-01-01

    Id-460+ immunoglobulins can be induced in vivo by immunization with dinitrophenyl (DNP) or P. pneumotropica and form two nonoverlapping groups of antibodies with respect to antigen binding specificity. In this study, using Id-460+ antibodies of differing antigen binding specificities, we compared on the molecular genetic level the five gene segment combinations (VH, DH, JH, VL, and JL) that encode the variable regions of these idiotype-positive immunoglobulins. The Id-460 determinant appears to be a conformational or combinatorial determinant encoded by VH460 and VK1 crosshybridizing genes. DH, JH, and JK gene segments appear to have no measurable effect upon expression of Id-460. Finally, antigen binding specificity does not appear to simply localize to any particular gene segment but may in part be the result of somatic mutation and/or VDJH junctional sequences, whose length correlates roughly with antigen binding specificity. PMID:3932578

  6. 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.

  7. Molecular characterization of multivalent bioconjugates by size-exclusion chromatography with multiangle laser light scattering.

    PubMed

    Pollock, Jacob F; Ashton, Randolph S; Rode, Nikhil A; Schaffer, David V; Healy, Kevin E

    2012-09-19

    The degree of substitution and valency of bioconjugate reaction products are often poorly judged or require multiple time- and product-consuming chemical characterization methods. These aspects become critical when analyzing and optimizing the potency of costly polyvalent bioactive conjugates. In this study, size-exclusion chromatography with multiangle laser light scattering was paired with refractive index detection and ultraviolet spectroscopy (SEC-MALS-RI-UV) to characterize the reaction efficiency, degree of substitution, and valency of the products of conjugation of either peptides or proteins to a biopolymer scaffold, i.e., hyaluronic acid (HyA). Molecular characterization was more complete compared to estimates from a protein quantification assay, and exploitation of this method led to more accurate deduction of the molecular structures of polymer bioconjugates. Information obtained using this technique can improve macromolecular engineering design principles and help to better understand multivalent macromolecular interactions in biological systems.

  8. Enrichment and characterization of marine anammox bacteria associated with global nitrogen gas production.

    PubMed

    van de Vossenberg, Jack; Rattray, Jayne E; Geerts, Wim; Kartal, Boran; van Niftrik, Laura; van Donselaar, Elly G; Sinninghe Damsté, Jaap S; Strous, Marc; Jetten, Mike S M

    2008-11-01

    Microbiological investigation of anaerobic ammonium oxidizing (anammox) bacteria has until now been restricted to wastewater species. The present study describes the enrichment and characterization of two marine Scalindua species, the anammox genus that dominates almost all natural habitats investigated so far. The species were enriched from a marine sediment in the Gullmar Fjord (Sweden) using a medium based on Red Sea salt. Anammox cells comprised about 90% of the enrichment culture after 10 months. The enriched Scalindua bacteria displayed all typical features known for anammox bacteria, including turnover of hydrazine, the presence of ladderane lipids, and a compartmentalized cellular ultrastructure. The Scalindua species also showed a nitrate-dependent use of formate, acetate and propionate, and performed a formate-dependent reduction of nitrate, Fe(III) and Mn(IV). This versatile metabolism may be the basis for the global distribution and substantial contribution of the marine Scalindua anammox bacteria to the nitrogen loss from oxygen-limited marine ecosystems.

  9. Characterization of molecular recognition of STAT3 SH2 domain inhibitors through molecular simulation.

    PubMed

    Park, In-Hee; Li, Chenglong

    2011-01-01

    Signal transducer and activator of transcription 3 (STAT3) is an anti-cancer target protein due to its over-activation in tumor cells. The Tyr705-phosphorylated (pTyr) STAT3 binds to the pTyr-recognition site of its Src Homology 2 (SH2) domain of another STAT3 monomer to form a homo-dimer, which then causes cellular anti-apoptosis, proliferation, and tumor invasion. Recently, many STAT3 SH2 dimerization inhibitors have been discovered via both computational and experimental methods. To systematically assess their binding affinities and specificities, for eight representative inhibitors, we utilized molecular docking, molecular dynamics simulation, and ensuing energetic analysis to compare their binding characteristics. The inhibitors' binding free energies were calculated via MMPB(GB)SA, and the STAT3 SH2 binding "hot spots" were evaluated through binding energy decomposition and hydrogen bond (H-bond) distribution analysis. Several conclusions can be drawn: (1) the overall enthalpy-entropy compensation paradigm is preserved for the STAT3 SH2/ligand binding thermodynamics; (2) at one end of the binding spectrum, two compounds bind to SH2 due to their minimum entropic penalties that result from their relative rigidities and increased dynamics of SH2 upon their binding; at the other end of the binding spectrum, one compound shows a typical weak binder behavior due to its loose binding in the SH2's strongest enthalpy-contributing binding subsite; (3) hydrogen bonding seems a strong indicator to evaluate the SH2/ligand binding potency, which echoes a finding that CH/π non-classical H-bond is responsible for some pTyr peptides binding to their corresponding SH2 domains; (4) STAT3 SH2 domain possesses three binding "hot spots": pTyr705-binding pocket with polar residues and contributing the largest binding enthalpy (two-thirds); Leu706 subsite which is the most dynamic and hardest to target; a hydrophobic side pocket which is unique to STAT3 and very targetable, which

  10. Characterizing uncertainties in recent trends of global terrestrial net primary production through ensemble modeling

    NASA Astrophysics Data System (ADS)

    Wang, W.; Hashimoto, H.; Ganguly, S.; Votava, P.; Nemani, R. R.; Myneni, R. B.

    2010-12-01

    Large uncertainties exist in our understanding of the trends and variability in global net primary production (NPP) and its controls. This study attempts to address this question through a multi-model ensemble experiment. In particular, we drive ecosystem models including CASA, LPJ, Biome-BGC, TOPS-BGC, and BEAMS with a long-term climate dataset (i.e., CRU-NCEP) to estimate global NPP from 1901 to 2009 at a spatial resolution of 0.5 x 0.5 degree. We calculate the trends of simulated NPP during different time periods and test their sensitivities to climate variables of solar radiation, air temperature, precipitation, vapor pressure deficit (VPD), and atmospheric CO2 levels. The results indicate a large diversity among the simulated NPP trends over the past 50 years, ranging from nearly no trend to an increasing trend of ~0.1 PgC/yr. Spatial patterns of the NPP generally show positive trends in boreal forests, induced mainly by increasing temperatures in these regions; they also show negative trends in the tropics, although the spatial patterns are more diverse. These diverse trends result from different climatic sensitivities of NPP among the tested models. Depending the ecological processes (e.g., photosynthesis or respiration) a model emphasizes, it can be more or less responsive to changes in solar radiation, temperatures, water, or atmospheric CO2 levels. Overall, these results highlight the limit of current ecosystem models in simulating NPP, which cannot be easily observed. They suggest that the traditional single-model approach is not ideal for characterizing trends and variability in global carbon cycling.

  11. 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.

  12. 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.

  13. 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.

  14. Genetic and molecular characterization of genomic regions surrounding specific loci of the mouse

    SciTech Connect

    Russell, L.B.; Rinchik, E.M.

    1987-01-01

    Mutations detected by the mouse specific-locus test (SLT) include multilocus deletions as well as intragenic lesions. Genetic analyses have characterized sets of presumed overlapping deletions and have mapped previously unrecognized genes to the regions surrounding each of several specific loci. Molecular entry to one of these regions, d se, was achieved by utilizing a viral integration at, or near, a marker locus. Presumed deletions were shown to be, in fact deleted for DNA sequences, and the physical map was oriented relative to the earlier functional map. Presently, a random-clone approach is being used for initiating molecular characterization of regions, which, in aggregate, span a minimum of 9 cM. Mapping to subregions already identified by functional units will facilitate the generation of comprehensive molecular maps and the identification of numerous structure-function correlations for the regions. Results of the genetic and molecular analyses of multilocus deletions have enhanced the value of the SLT by adding qualitative to quantitative capabilities. Studies of the heterozygous effects of deletions (which are the predominant lesions induced by many mutagens) provide information important to assessment of genetic risk. Long deletions are, further, providing tools for targeted mutagenesis studies that will generate information on the number of loci within segments of defined length that are capable of mutating to detectable alleles, as well as providing new mutations important for strategies of refining molecular and functional maps. 28 refs., 2 tabs.

  15. 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.

  16. 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.

  17. 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.

  18. Characterization of nanoparticle-based contrast agents for molecular magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Shan, Liang; Chopra, Arvind; Leung, Kam; Eckelman, William C.; Menkens, Anne E.

    2012-09-01

    The development of molecular imaging agents is currently undergoing a dramatic expansion. As of October 2011, 4,800 newly developed agents have been synthesized and characterized in vitro and in animal models of human disease. Despite this rapid progress, the transfer of these agents to clinical practice is rather slow. To address this issue, the National Institutes of Health launched the Molecular Imaging and Contrast Agents Database (MICAD) in 2005 to provide freely accessible online information regarding molecular imaging probes and contrast agents for the imaging community. While compiling information regarding imaging agents published in peer-reviewed journals, the MICAD editors have observed that some important information regarding the characterization of a contrast agent is not consistently reported. This makes it difficult for investigators to evaluate and meta-analyze data generated from different studies of imaging agents, especially for the agents based on nanoparticles. This article is intended to serve as a guideline for new investigators for the characterization of preclinical studies performed with nanoparticle-based MRI contrast agents. The common characterization parameters are summarized into seven categories: contrast agent designation, physicochemical properties, magnetic properties, in vitro studies, animal studies, MRI studies, and toxicity. Although no single set of parameters is suitable to define the properties of the various types of contrast agents, it is essential to ensure that these agents meet certain quality control parameters at the preclinical stage, so that they can be used without delay for clinical studies.

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

    NASA Astrophysics Data System (ADS)

    Bubeck, Robert; Keinath, Steven

    2014-03-01

    Molecular simulation and characterization 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 (environs of 300°C) using variable temperature synchrotron-based WAXS. 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 are useful for future experimental guidance because the level of order in the glassy phase near ambient temperature was found to be low (approx. 5%) regardless of melt processing history. The biphasic nature of the melt may also be a contributor to more difficult melt processing. Based on both the modeling and WAXS measurements, it is believed that increasing m-phenylene content might improve toughness and processibility relative to the interrogated samples. Beam time at the Cornell High Energy Synchrotron Source is gratefully acknowledged.

  20. 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.

  1. 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.

  2. 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

  3. Characterization of polar molecular species adsorbed on LiNbO3 surfaces

    NASA Astrophysics Data System (ADS)

    Bharath, Satyaveda; Pearl, Thomas

    2008-10-01

    In order to explore the mechanisms of adsorption on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3: LN), `Z-cut'; along the (0001) plane, has been prepared and characterized and subsequently exposed to a polar molecule. 4-n-octyl-4'-cyanobiphenyl (8CB) liquid crystal was chosen as our model system. Low-energy electron diffraction, atomic force microscopy, surface contact angle measurement, and X-ray photoelectron spectroscopy were used to characterize the surface of LN as well as the nature of the films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Preferential attachment for positive domains was observed indicating an interaction between the polar end group of the molecule and the surface charge of the surface. Understanding anchoring mechanisms for polarizable molecules on uniformly poled surfaces allows for a fuller appreciation of how ferroelectric surfaces can be used for controlling molecular organization.

  4. 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.

  5. Molecular characterization of a proteolysis-resistant lipase from Bacillus pumilus SG2.

    PubMed

    Sangeetha, R; Arulpandi, I; Geetha, A

    2014-01-01

    Proteolysis-resistant lipases can be well exploited by industrial processes which employ both lipase and protease as biocatalysts. A proteolysis resistant lipase from Bacillus pumilus SG2 was isolated, purified and characterized earlier. The lipase was resistant to native and commercial proteases. In the present work, we have characterized the lip gene which encodes the proteolysis-resistant lipase from Bacillus pumilus SG2. The parameters and structural details of lipase were analysed. The lip gene consisted of 650 bp. The experimental molecular weight of SG2 lipase was nearly double that of its theoretical molecular weight, thus suggesting the existence of the functional lipase as a covalent dimer. The proteolytic cleavage sites of the lipase would have been made inaccessible by dimerisation, thus rendering the lipase resistant to protease.

  6. Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough.

    PubMed

    Zhou, Aifen; Chen, Yunyu I; Zane, Grant M; He, Zhili; Hemme, Christopher L; Joachimiak, Marcin P; Baumohl, Jason K; He, Qiang; Fields, Matthew W; Arkin, Adam P; Wall, Judy D; Hazen, Terry C; Zhou, Jizhong

    2012-02-01

    Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.

  7. Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

    PubMed Central

    Zhou, Aifen; Chen, Yunyu I.; Zane, Grant M.; He, Zhili; Hemme, Christopher L.; Joachimiak, Marcin P.; Baumohl, Jason K.; He, Qiang; Fields, Matthew W.; Arkin, Adam P.; Wall, Judy D.; Hazen, Terry C.

    2012-01-01

    Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ΔDVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ΔDVU2547 mutant (JW9011) under nitrite stress conditions and a ΔDVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses. PMID:22156435

  8. First isolation and molecular characterization of Ehrlichia canis in Costa Rica, Central America.

    PubMed

    Romero, L E; Meneses, A I; Salazar, L; Jiménez, M; Romero, J J; Aguiar, D M; Labruna, M B; Dolz, G

    2011-08-01

    The present study investigated Ehrlichia species in blood samples from dogs suspected of clinical ehrlichiosis, using molecular and isolation techniques in cell culture. From a total of 310 canine blood samples analyzed by 16S rRNA nested PCR, 148 (47.7%) were positive for Ehrlichia canis. DNA from Ehrlichia chaffeensis or Ehrlichia ewingii was not detected in any sample using species-specific primers in separated reactions. Leukocytes from five PCR-positive dogs were inoculated into DH82 cells; successful isolation of E. canis was obtained in four samples. Partial sequence of the dsb gene of eight canine blood samples (including the five samples for in vitro isolation) was obtained by PCR and their analyses through BLAST showed 100% of identity with the corresponding sequence of E. canis in GenBank. This study represents the first molecular diagnosis, isolation, and molecular characterization of E. canis in dogs from Costa Rica.

  9. Computational characterization of the molecular structure and properties of Dye 7 for organic photovoltaics.

    PubMed

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguin, Norma; Calderón-Guillén, Joel; Glossman-Mitnik, Daniel

    2012-03-01

    Organic dyes have great potential for its use in solar cells. In this recent work, the molecular structure and properties of Dye 7 were obtained using density functional theory (DFT) and different levels of calculation. Upon comparing the molecular structure and the ultraviolet visible spectrum with experimental data reported in the literature, it was found that the M05-2X/6-31G(d) level of calculation gave the best approximation. Once the appropriate methodology had been obtained, the molecule was characterized by obtaining the infrared spectrum, dipole moment, total energy, isotropic polarizability, molecular orbital energies, free energy of solvation in different solvents, and the chemical reactivity sites using the condensed Fukui functions.

  10. Cutaneous Pythiosis in calves: An epidemiologic, pathologic, serologic and molecular characterization.

    PubMed

    Konradt, Guilherme; Bassuino, Daniele Mariath; Bianchi, Matheus Viezzer; Castro, Lismara; Caprioli, Rafaela Albuquerque; Pavarini, Saulo Petinatti; Santurio, Janio M; Azevedo, Maria Isabel; Jesus, Francielli P; Driemeier, David

    2016-12-01

    This study reports the epidemiological, pathological and mycological findings of cutaneous pythiosis in cattle in southern Brazil. 23 calves, that were kept next to a river with extensive marshy regions, presented ulcerated cutaneous lesions in thoracic and pelvic limbs, sometimes extending to the ventral thoracic region. Histopathological examination revealed multifocal pyogranulomas in the superficial and deep dermis. The Grocott-Methenamine silver, immunohistochemistry anti-Pythium insidiosum, ELISA serology and molecular characterization demonstrated the agent P. insidiosum in these cases.

  11. Molecular Characterization of Clostridium tetani Strains by Pulsed-Field Gel Electrophoresis and Colony PCR

    PubMed Central

    Plourde-Owobi, Lucile; Seguin, Delphine; Baudin, Marie-Anne; Moste, Catherine; Rokbi, Bachra

    2005-01-01

    Pulsed-field gel electrophoresis and PCR were applied for the first time to the molecular characterization of Clostridium tetani. Among five strains tested, one (CN1339) turned out to contain a mixture of two genetically different clones and two (D11 and G761) to contain bacteria differing by the presence or absence of the 74-kb plasmid harboring the tetX gene. PMID:16151158

  12. Molecular characterization of Clostridium tetani strains by pulsed-field gel electrophoresis and colony PCR.

    PubMed

    Plourde-Owobi, Lucile; Seguin, Delphine; Baudin, Marie-Anne; Moste, Catherine; Rokbi, Bachra

    2005-09-01

    Pulsed-field gel electrophoresis and PCR were applied for the first time to the molecular characterization of Clostridium tetani. Among five strains tested, one (CN1339) turned out to contain a mixture of two genetically different clones and two (D11 and G761) to contain bacteria differing by the presence or absence of the 74-kb plasmid harboring the tetX gene.

  13. Modeling and characterization of multipath in global navigation satellite system ranging signals

    NASA Astrophysics Data System (ADS)

    Weiss, Jan Peter

    The Global Positioning System (GPS) provides position, velocity, and time information to users in anywhere near the earth in real-time and regardless of weather conditions. Since the system became operational, improvements in many areas have reduced systematic errors affecting GPS measurements such that multipath, defined as any signal taking a path other than the direct, has become a significant, if not dominant, error source for many applications. This dissertation utilizes several approaches to characterize and model multipath errors in GPS measurements. Multipath errors in GPS ranging signals are characterized for several receiver systems and environments. Experimental P(Y) code multipath data are analyzed for ground stations with multipath levels ranging from minimal to severe, a C-12 turboprop, an F-18 jet, and an aircraft carrier. Comparisons between receivers utilizing single patch antennas and multi-element arrays are also made. In general, the results show significant reductions in multipath with antenna array processing, although large errors can occur even with this kind of equipment. Analysis of airborne platform multipath shows that the errors tend to be small in magnitude because the size of the aircraft limits the geometric delay of multipath signals, and high in frequency because aircraft dynamics cause rapid variations in geometric delay. A comprehensive multipath model is developed and validated. The model integrates 3D structure models, satellite ephemerides, electromagnetic ray-tracing algorithms, and detailed antenna and receiver models to predict multipath errors. Validation is performed by comparing experimental and simulated multipath via overall error statistics, per satellite time histories, and frequency content analysis. The validation environments include two urban buildings, an F-18, an aircraft carrier, and a rural area where terrain multipath dominates. The validated models are used to identify multipath sources, characterize signal

  14. 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.

  15. 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

  16. 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

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 Tq 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.

  19. Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment

    PubMed Central

    Rojas, Veronica; Hirshfield, Kim M.; Ganesan, Shridar; Rodriguez-Rodriguez, Lorna

    2016-01-01

    Epithelial ovarian cancer is a highly heterogeneous disease characterized by multiple histological subtypes. Molecular diversity has been shown to occur within specific histological subtypes of epithelial ovarian cancer, between different tumors of an individual patient, as well as within individual tumors. Recent advances in the molecular characterization of epithelial ovarian cancer tumors have provided the basis for a simplified classification scheme in which these cancers are classified as either type I or type II tumors, and these two categories have implications regarding disease pathogenesis and prognosis. Molecular analyses, primarily based on next-generation sequencing, otherwise known as high-throughput sequencing, are allowing for further refinement of ovarian cancer classification, facilitating the elucidation of the site(s) of precursor lesions of high-grade serous ovarian cancer, and providing insight into the processes of clonal selection and evolution that may be associated with development of chemoresistance. Potential therapeutic targets have been identified from recent molecular profiling studies of these tumors, and the effectiveness and safety of a number of specific targeted therapies have been evaluated or are currently being studied for the treatment of women with this disease. PMID:27983698

  20. 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.

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

    PubMed

    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.

  2. Isolation, characterization, molecular cloning and molecular modelling of two lectins of different specificities from bluebell (Scilla campanulata) bulbs.

    PubMed Central

    Wright, L M; Van Damme, E J; Barre, A; Allen, A K; Van Leuven, F; Reynolds, C D; Rouge, P; Peumans, W J

    1999-01-01

    Two lectins have been isolated from bluebell (Scilla campanulata) bulbs. From their isolation by affinity chromatography, they are characterized as a mannose-binding lectin (SCAman) and a fetuin-binding lectin (SCAfet). SCAman preferentially binds oligosaccharides with alpha(1,3)- and alpha(1,6)-linked mannopyranosides. It is a tetramer of four identical protomers of approx. 13 kDa containing 119 amino acid residues; it is not glycosylated. The fetuin-binding lectin (SCAfet), which is not inhibited by any simple sugars, is also unglycosylated. It is a tetramer of four identical subunits of approx. 28 kDa containing 244 residues. Each 28 kDa subunit is composed of two 14 kDa domains. Both lectins have been cloned from a cDNA library and sequenced. X-ray crystallographic analysis and molecular modelling studies have demonstrated close relationships in sequence and structure between these lectins and other monocot mannose-binding lectins. A refined model of the molecular evolution of the monocot mannose-binding lectins is proposed. PMID:10229686

  3. Molecular characterization of multidrug-resistant Shigella spp. of food origin.

    PubMed

    Ahmed, Ashraf M; Shimamoto, Tadashi

    2015-02-02

    Shigella spp. are the causative agents of food-borne shigellosis, an acute enteric infection. The emergence of multidrug-resistant clinical isolates of Shigella presents an increasing challenge for clinicians in the treatment of shigellosis. Several studies worldwide have characterized the molecular basis of antibiotic resistance in clinical Shigella isolates of human origin, however, to date, no such characterization has been reported for Shigella spp. of food origin. In this study, we characterized the genetic basis of multidrug resistance in Shigella spp. isolated from 1600 food samples (800 meat products and 800 dairy products) collected from different street venders, butchers, retail markets, and slaughterhouses in Egypt. Twenty-four out of 27 Shigella isolates (88.9%) showed multidrug resistance phenotypes to at least three classes of antimicrobials. The multidrug-resistant Shigella spp. were as follows: Shigella flexneri (66.7%), Shigella sonnei (18.5%), and Shigella dysenteriae (3.7%). The highest resistance was to streptomycin (100.0%), then to kanamycin (95.8%), nalidixic acid (95.8%), tetracycline (95.8%), spectinomycin (93.6%), ampicillin (87.5%), and sulfamethoxazole/trimethoprim (87.5%). PCR and DNA sequencing were used to screen and characterize integrons and antibiotic resistance genes. Our results indicated that 11.1% and 74.1% of isolates were positive for class 1 and class 2 integrons, respectively. Beta-lactamase-encoding genes were identified in 77.8% of isolates, and plasmid-mediated quinolone resistance genes were identified in 44.4% of isolates. These data provide useful information to better understand the molecular basis of antimicrobial resistance in Shigella spp. To the best of our knowledge, this is the first report of the molecular characterization of antibiotic resistance in Shigella spp. isolated from food.

  4. 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.

  5. 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

  6. Characterization of molecularly imprinted polymers using a new polar solvent titration method.

    PubMed

    Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

    2014-07-01

    A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs.

  7. Characterizing learning deficits and hippocampal neuron loss following transient global cerebral ischemia in rats.

    PubMed

    Hartman, Richard E; Lee, Jin M; Zipfel, Greg J; Wozniak, David F

    2005-05-10

    The 2-vessel-occlusion + hypotension (2VO + H) model of transient global cerebral ischemia results in neurodegeneration within the CA1 field of the hippocampus, but previous research has failed to demonstrate robust or reliable learning/memory deficits in rats subjected to this treatment. In the present study, sensitive behavioral protocols were developed in an effort to characterize the cognitive impairments following 2VO + H more precisely. Adult rats were exposed to 10 min of bilateral carotid occlusion with simultaneous hypotension. Following recovery, 2VO + H and control rats were subjected to a series of behavioral tests (locomotor activity, sensorimotor battery, water maze [cued, place, learning set], object recognition, and radial arm maze) over an extended recovery period followed by an assessment of neuronal loss in the dorsal hippocampus. The 2VO + H treatment was associated with long-lasting spatial learning deficits in the absence of other behavioral impairments and with neurodegeneration in dorsal hippocampal CA1. Water maze protocols that placed higher memory demands upon the rats (relatively "hard" vs. "easy") were more sensitive for detecting ischemia-induced deficits. We have shown that the use of appropriate behavioral tests (e.g., a relatively difficult place learning task) allowed for the observation of robust spatial learning deficits in a model previously shown to induce relatively subtle behavioral effects. Thus, the 2VO + H model induces both hippocampal neuronal loss and long-term learning deficits in rats, providing a potentially useful model for evaluating therapeutic efficacy.

  8. Complex Network Analysis for Characterizing Global Value Chains in Equipment Manufacturing.

    PubMed

    Xiao, Hao; Sun, Tianyang; Meng, Bo; Cheng, Lihong

    2017-01-01

    The rise of global value chains (GVCs) characterized by the so-called "outsourcing", "fragmentation production", and "trade in tasks" has been considered one of the most important phenomena for the 21st century trade. GVCs also can play a decisive role in trade policy making. However, due to the increasing complexity and sophistication of international production networks, especially in the equipment manufacturing industry, conventional trade statistics and the corresponding trade indicators may give us a distorted picture of trade. This paper applies various network analysis tools to the new GVC accounting system proposed by Koopman et al. (2014) and Wang et al. (2013) in which gross exports can be decomposed into value-added terms through various routes along GVCs. This helps to divide the equipment manufacturing-related GVCs into some sub-networks with clear visualization. The empirical results of this paper significantly improve our understanding of the topology of equipment manufacturing-related GVCs as well as the interdependency of countries in these GVCs that is generally invisible from the traditional trade statistics.

  9. Complex Network Analysis for Characterizing Global Value Chains in Equipment Manufacturing

    PubMed Central

    Meng, Bo; Cheng, Lihong

    2017-01-01

    The rise of global value chains (GVCs) characterized by the so-called “outsourcing”, “fragmentation production”, and “trade in tasks” has been considered one of the most important phenomena for the 21st century trade. GVCs also can play a decisive role in trade policy making. However, due to the increasing complexity and sophistication of international production networks, especially in the equipment manufacturing industry, conventional trade statistics and the corresponding trade indicators may give us a distorted picture of trade. This paper applies various network analysis tools to the new GVC accounting system proposed by Koopman et al. (2014) and Wang et al. (2013) in which gross exports can be decomposed into value-added terms through various routes along GVCs. This helps to divide the equipment manufacturing-related GVCs into some sub-networks with clear visualization. The empirical results of this paper significantly improve our understanding of the topology of equipment manufacturing-related GVCs as well as the interdependency of countries in these GVCs that is generally invisible from the traditional trade statistics. PMID:28081201

  10. 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...

  11. 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.

  12. 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

    2015-07-10

    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.

  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. Characterization of landfill leachates by molecular size distribution, biodegradability, and inert chemical oxygen demand.

    PubMed

    Amaral, Míriam C S; Ferreira, Cynthia F A; Lange, Liséte Celina; Aquino, Sérgio F

    2009-05-01

    This work presents results from a detailed characterization of landfill leachates of different ages from a landfill in a major Brazilian city. This characterization consists of determining the molecular size distribution and the inert chemical oxygen demand (COD) and the biodegradability of both aerobic and anaerobic processes. Results show that leachate with a high COD concentration leachate has low biodegradability. A significant fraction of the COD is not characterized as protein, carbohydrate, or lipids, which reinforces the hypothesis that the remaining fraction was present in all leachate fractions (less than 1 kDa; between 1 and 10 kDa; between 10 and 100 kDa; and greater than 100 kDa) and is refractory. These results suggest that leachates with such characteristics require treatment systems that use physical-chemical processes as a pre- or post-treatment step to biological processes.

  15. 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.

  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. The Vaginal Microbiota: What Have We Learned after a Decade of Molecular Characterization?

    PubMed Central

    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

  18. 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.

  19. 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

  20. Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites

    PubMed Central

    Severino, Patricia; Alvares, Adriana M; Michaluart, Pedro; Okamoto, Oswaldo K; Nunes, Fabio D; Moreira-Filho, Carlos A; Tajara, Eloiza H

    2008-01-01

    Background Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis. Results Samples of primary OSCCs and their corresponding surgical margins were obtained from male patients during surgery and their gene expression profiles were screened using whole-genome microarray technology. Hierarchical clustering and Principal Components Analysis were used for data visualization and One-way Analysis of Variance was used to identify differentially expressed genes. Samples clustered mostly according to disease subsite, suggesting molecular heterogeneity within tumor stages. In order to corroborate our results, two publicly available datasets of microarray experiments were assessed. We found significant molecular differences between OSCC anatomic subsites concerning groups of genes presently or potentially important for drug development, including mRNA processing, cytoskeleton organization and biogenesis, metabolic process, cell cycle and apoptosis. Conclusion Our results corroborate literature data on molecular heterogeneity of OSCCs. Differences between disease subsites and among samples belonging to the same TNM class highlight the importance of gene expression-based classification and challenge the development of targeted therapies. PMID:19014556

  1. 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

  2. Single cell PCR from archival stained bone marrow slides: a method for molecular diagnosis and characterization.

    PubMed

    Zanssen, Stefanie

    2004-01-01

    Molecular analysis of isolated single cells is a powerful tool for clarifying issues of cell origin and clonality. Previous reports have described PCR amplifications from total DNA and RNA extracted from archival bone marrow and peripheral blood smears and have also shown the feasibility of amplifications from single cells, microdissected from stained histological sections. In this study, a method is described for performing PCR from morphologically defined single cells isolated from archival May-Gruenwald-Giemsa-stained bone-marrow and blood smears. Using three DNA extraction procedures, the organic lysis showed reproducible high efficiencies of amplifications. With this method, we were able to amplify long range amplicons up to 14.5 kb from mitochondrial DNA as well as PCR products of conventional length. The usability of such products for molecular diagnosis is demonstrated by restriction fragment length polymorphism (RFLP)characterization of a mitochondrial disorder. In conclusion, this method has the power to perform molecular diagnosis and characterization of diseases on the single cell level, and should provide valuable information to aid disease treatment and prognosis of hematological disorders.

  3. Mass-spectrometry-based molecular characterization of extracellular vesicles: lipidomics and proteomics.

    PubMed

    Kreimer, Simion; Belov, Arseniy M; Ghiran, Ionita; Murthy, Shashi K; Frank, David A; Ivanov, Alexander R

    2015-06-05

    This review discusses extracellular vesicles (EVs), which are submicron-scale, anuclear, phospholipid bilayer membrane enclosed vesicles that contain lipids, metabolites, proteins, and RNA (micro and messenger). They are shed from many, if not all, cell types and are present in biological fluids and conditioned cell culture media. The term EV, as coined by the International Society of Extracellular Vesicles (ISEV), encompasses exosomes (30-100 nm in diameter), microparticles (100-1000 nm), apoptotic blebs, and other EV subsets. EVs have been implicated in cell-cell communication, coagulation, inflammation, immune response modulation, and disease progression. Multiple studies report that EV secretion from disease-affected cells contributes to disease progression, e.g., tumor niche formation and cancer metastasis. EVs are attractive sources of biomarkers due to their biological relevance and relatively noninvasive accessibility from a range of physiological fluids. This review is focused on the molecular profiling of the protein and lipid constituents of EVs, with emphasis on mass-spectrometry-based "omic" analytical techniques. The challenges in the purification and molecular characterization of EVs, including contamination of isolates and limitations in sample quantities, are discussed along with possible solutions. Finally, the review discusses the limited but growing investigation of post-translational modifications of EV proteins and potential strategies for future in-depth molecular characterization of EVs.

  4. 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

  5. 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.

  6. Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

    PubMed

    Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

    2016-09-16

    The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

  7. Molecular and Genetic Characterization of Depression: Overlap with other Psychiatric Disorders and Aging.

    PubMed

    Ding, Ying; Chang, Lun-Ching; Wang, Xingbin; Guilloux, Jean-Philippe; Parrish, Jenna; Oh, Hyunjung; French, Beverly J; Lewis, David A; Tseng, George C; Sibille, Etienne

    2015-05-01

    Genome-wide expression and genotyping technologies have uncovered the genetic bases of complex diseases at unprecedented rates; However despite its heavy burden and high prevalence, the molecular characterization of major depressive disorder (MDD) has lagged behind. Transcriptome studies report multiple brain disturbances but are limited by small sample sizes. Genome-wide association studies (GWAS) report weak results but suggest overlapping genetic risk with other neuropsychiatric disorders. We performed systematic molecular characterization of altered brain function in MDD, using meta-analysis of differential expression in eight gene array studies in three corticolimbic brain regions in 101 subjects. The identified "metaA-MDD" genes suggest altered neurotrophic support, brain plasticity and neuronal signaling in MDD. Notably, metaA-MDD genes display low connectivity and hubness in coexpression networks, and uniform genomic distribution, consistent with diffuse polygenic mechanisms. We next integrated these findings with results from over 1800 published GWAS and show that genetic variations nearby metaA-MDD genes predict greater risk for neuropsychiatric disorders and notably for age-related phenotypes, but not for other medical illnesses, including those frequently co-morbid with depression, or body characteristics. Collectively, the intersection of unbiased investigations of gene function (transcriptome) and structure (GWAS) provides novel leads to investigate molecular mechanisms of MDD and suggest common biological pathways between depression, other neuropsychiatric diseases, and brain aging.

  8. Natriuretic peptides in cetaceans: identification, molecular characterization and changes in plasma concentration after landing.

    PubMed

    Naka, Tadaomi; Katsumata, Etsuko; Sasaki, Kazuki; Minamino, Naoto; Yoshioka, Motoi; Takei, Yoshio

    2007-06-01

    Dolphins are aquatic animals free from gravity, and this may have imposed significant changes in their cardiovascular status and its hormonal regulation compared with terrestrial animals. This study molecularly characterized two major cardiovascular hormones, atrial and B-type natriuretic peptides (ANP and BNP) and measured their changes in dolphin plasma concentrations in relation to the cardiovascular status of the animal. We initially identified ANP and BNP in three species of dolphins (Lagenorhynchus obliquidens, Phocoenoides dalli and Tursiops truncatus). ANP precursors are highly conserved in most mammals, but dolphin BNP precursors were more variable. In molecular phylogenetic analyses, dolphin ANP and BNP precursors grouped with those of artiodactyls, particularly to the camel peptides. The chromatographic characterization of tissue and plasma molecular forms using specific radioimmunoassays showed that the predominant ANP and BNP in the atrium are prohormone and mature peptide, respectively, whereas mature ANP and BNP are circulating in the dolphin blood. A mass spectrometric analysis showed that atrial BNP consists of 26 amino acids, rather than the 32-amino-acid form detected in other mammals. Finally, changes in plasma ANP and BNP concentrations were examined in captive bottlenose dolphins (Tursiops truncatus) after their pool was drained. Plasma ANP and BNP concentrations did not change after landing, unlike terrestrial mammals. Plasma angiotensin II and cortisol concentrations did not change either, showing minor stress after landing. Since landed dolphins show a different cardiovascular status on land than terrestrial mammals, plasma ANP and BNP concentrations seem to reflect the cardiovascular status characteristic of dolphins.

  9. Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

    PubMed Central

    Chavshin, Ali Reza; Oshaghi, Mohammad Ali; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Raeisi, Ahmad; Nikpoor, Fatemeh

    2014-01-01

    Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

  10. Diagnosis and Molecular Characterization of Mycobacterium avium subsp. paratuberculosis from Dairy Cows in Colombia

    PubMed Central

    Fernández-Silva, J. A.; Abdulmawjood, A.; Bülte, M.

    2011-01-01

    The objective of this study was the serological, bacteriological and molecular diagnosis, as well as the molecular characterization of Mycobacterium avium subsp. paratuberculosis (Map) in adult cows of five Colombian dairy herds. Serum samples were tested by an indirect absorbed enzyme–linked immunosorbent assay (ELISA-C). All fecal samples were tested by pooled culture. After that, fecal samples of Map positive pools were tested individually by culture and polymerase chain reaction (PCR). In one herd, slurry and tissue samples from one animal were also taken and tested by PCR and culture. Map isolates were analyzed by the Multilocus Short Sequence Repeat (MLSSR) and the Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) methods. ELISA produced positive results in 1.8% (6/329) of the animals and 40% (2/5) of the herds. Four fecal, two tissue, and two slurry samples from a herd were Map positive by culture and PCR. MLSSR and MIRU-VNTR revealed two different strain profiles among eight Map isolates recovered. This study reports the first molecular characterization of Map in one dairy herd in Colombia, the limitations for individual diagnosis of subclinical Map infections in cattle, and the usefulness of pooled fecal samples and environmental sampling for Map diagnosis. PMID:21785685

  11. Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis).

    PubMed

    Lu, Xiaopeng; Cao, Xiongjun; Li, Feifei; Li, Jing; Xiong, Jiang; Long, Guiyou; Cao, Shangyin; Xie, Shenxi

    2016-12-01

    Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange.

  12. Global Profiling and Molecular Characterization of Alternative Splicing Events Misregulated in Lung Cancer ▿ †

    PubMed Central

    Misquitta-Ali, Christine M.; Cheng, Edith; O'Hanlon, Dave; Liu, Ni; McGlade, C. Jane; Tsao, Ming Sound; Blencowe, Benjamin J.

    2011-01-01

    Alternative splicing (AS) is a widespread mechanism underlying the generation of proteomic and regulatory complexity. However, which of the myriad of human AS events play important roles in disease is largely unknown. To identify frequently occurring AS events in lung cancer, we used AS microarray profiling and reverse transcription-PCR (RT-PCR) assays to survey patient-matched normal and adenocarcinoma tumor tissues from the lungs of 29 individuals diagnosed with non-small cell lung cancer (NSCLC). Of 5,183 profiled alternative exons, four displayed tumor-associated changes in the majority of the patients. These events affected transcripts from the VEGFA, MACF1, APP, and NUMB genes. Similar AS changes were detected in NUMB and APP transcripts in primary breast and colon tumors. Tumor-associated increases in NUMB exon 9 inclusion correlated with reduced levels of NUMB protein expression and activation of the Notch signaling pathway, an event that has been linked to tumorigenesis. Moreover, short hairpin RNA (shRNA) knockdown of NUMB followed by isoform-specific rescue revealed that expression of the exon 9-skipped (nontumor) isoform represses Notch target gene activation whereas expression of the exon 9-included (tumor) isoform lacks this activity and is capable of promoting cell proliferation. The results thus reveal widespread AS changes in NSCLC that impact cell signaling in a manner that likely contributes to tumorigenesis. PMID:21041478

  13. 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.

  14. Molecular characterization of a wild poliovirus type 3 epidemic in The Netherlands (1992 and 1993).

    PubMed Central

    Mulders, M N; van Loon, A M; van der Avoort, H G; Reimerink, J H; Ras, A; Bestebroer, T M; Drebot, M A; Kew, O M; Koopmans, M P

    1995-01-01

    An outbreak of poliomyelitis due to wild poliovirus type 3 (PV3) occurred in an unvaccinated community in The Netherlands between September 1992 and February 1993. The outbreak involved 71 patients. The aim of this study was to characterize the virus at the molecular level and to analyze the molecular evolution of the epidemic virus. Molecular analysis was carried out by sequencing the VP1/2A junction region (150 nucleotides) of 50 PV3 strains isolated in association with this outbreak and the entire VP1 gene of 14 strains. In addition, the sequence of the VP1/2A junction region of strains from geographical regions endemic for PV3 (Egypt, India, and Central Asia) was analyzed and compared with the nucleotide sequence of the epidemic strain from The Netherlands. The earliest isolate was obtained from river water sampled 3 weeks before diagnosis of the first poliomyelitis patient and was found by VP1/2A sequence analysis to be genetically identical to the strain isolated from the first patient. Sequence divergence among the strains from the epidemic in The Netherlands was less than 2%. The closest genetic similarity (97.3%) was found with an Indian isolate (New Delhi, December 1991), indicating the likely source of the virus. A more than 99% sequence similarity was found in the VP1/2A region. Finally, the sequence information was used to design primers for the specific and highly sensitive molecular detection of PV3 strains during the epidemic. PMID:8586711

  15. 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.

  16. 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.

  17. From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry

    NASA Astrophysics Data System (ADS)

    Simpson, A.

    2009-04-01

    NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

  18. 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.

  19. 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.

  20. 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.

  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. 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.

  3. Molecular characterization of the plant biopolyester cutin by AFM and spectroscopic techniques.

    PubMed

    Benítez, José J; Matas, Antonio J; Heredia, Antonio

    2004-08-01

    Atomic force microscopy, FT-IR spectroscopy, and solid-state nuclear magnetic resonance have been used to improve our current knowledge on the molecular characteristics of the biopolyester cutin, the main component of the plant cuticle. After comparison of samples of cutin isolated from young and mature tomato fruit cuticles has been possible to establish different degrees of cross-linking in the biopolymer and that the polymer is mainly formed after esterification of secondary hydroxyl groups of the monomers that form this type of cutin. Atomic force microscopy gave useful structural information on the molecular topography of the outer surface of the isolated samples. The texture of these samples is a consequence of the cross-linking degree or chemical status of the polymer. Thus, the more dense and cross-linked cutin from ripe or mature tomato fruit is characterized by a flatter and more globular texture in addition to the development of elongated and orientated superstructures.

  4. Morphological redescription and molecular characterization of three species of Travassosinematidae (Nematoda: Oxyurida: Thelastomatoidea) from Gryllotalpa africana Beauv (Orthoptera: Gryllotalpidae).

    PubMed

    Singh, Neetu; Chaudhary, Anshu; Singh, Hridaya Shanker

    2013-01-01

    Binema mirzaia (Basir, 1942a) Basir, 1956, Cameronia nisari (Parveen and Jairajpuri, 1985) Adamson and Van Waerebeke, 1992a and Mirzaiella meerutensis Singh and Malti, 2003 are redescribed morphologically along with molecular identification from the intestine of mole cricket Gryllotalpa africana. Molecular characterization was carried out using the D2-D3 expansion domains of the 18S ribosomal DNA region. This study first time presents molecular data for the above three nematode species.

  5. Clinical, biochemical and molecular characterization of cystinuria in a cohort of 12 patients.

    PubMed

    Barbosa, M; Lopes, A; Mota, C; Martins, E; Oliveira, J; Alves, S; De Bonis, P; Mota, M do Céu; Dias, C; Rodrigues-Santos, P; Fortuna, A M; Quelhas, D; Lacerda, L; Bisceglia, L; Cardoso, M L

    2012-01-01

    Cystinuria is a rare autosomal inherited disorder characterized by impaired transport of cystine and dibasic aminoacids in the proximal renal tubule. Classically, cystinuria is classified as type I (silent heterozygotes) and non-type I (heterozygotes with urinary hyperexcretion of cystine). Molecularly, cystinuria is classified as type A (mutations on SLC3A1 gene) and type B (mutations on SLC7A9 gene). The goal of this study is to provide a comprehensive clinical, biochemical and molecular characterization of a cohort of 12 Portuguese patients affected with cystinuria in order to provide insight into genotype-phenotype correlations. We describe seven type I and five non-type I patients. Regarding the molecular classification, seven patients were type A and five were type B. In SLC3A1 gene, two large genomic rearrangements and 13 sequence variants, including four new variants c.611-2A>C; c.1136+44G>A; c.1597T (p.Y533N); c.*70A>G, were found. One large genomic rearrangement was found in SLC7A9 gene as well as 24 sequence variants including 3 novel variants: c.216C>T (p.C72C), c.1119G>A (p.S373S) and c.*82C>T. In our cohort the most frequent pathogenic mutations were: large rearrangements (33.3% of mutant alleles) and a missense mutation c.1400T>C (p.M467T) (11.1%). This report expands the spectrum of SLC3A1 and SLC7A9 mutations and provides guidance in the clinical implementation of molecular assays in routine genetic counseling of Portuguese patients affected with cystinuria.

  6. Molecular characterization of human calicivirus associated with acute diarrheal disease in mexican children

    PubMed Central

    2012-01-01

    Background Human caliciviruses (HuCV) are emerging enteric pathogens that are a common cause of diarrhea in humans worldwide. Due to the paucity of information on the molecular characterization of HuCV circulating in Mexico, the aim of this work was to investigate the diversity and molecular epidemiology of the HuCV infection associated with acute diarrheal disease in Mexican children aged up to 5 years. Results Of the 131/414 (32%) HuCV positive-specimens analyzed, 128 were identified as Norovirus (NoV) and three as Sapovirus (SaV). Of the NoV positive specimens, 118/128 (92%) were NoV GII and 10/128(8%) were untypeable by RT-PCR in both polymerase and capsid genes, whereas one SaV isolate was further confirmed by sequencing as GI.2. Phylogenetic analysis based on polymerase partial gene sequences from 89/131 (68%) HuCV isolates showed that 86/89 (97%) belong to NoV GII.4 with three main variant clusters of this genotype, 2/89 (2%) to NoV GII.2, and 1/89 (1%) to SaV GI.2. Furthermore, partial sequencing of the capsid gene VP1 of 63/131 (48%) strains indicated that 61/63 (97%) correlated with NoV GII.4, whereas only 2/63 (3%) clustered to NoV GII.2. HuCV infections were detected throughout the year, and the highest number of cases positive for NoV was found in children between 7 and 18 months of age (60%). Conclusions This study highlights the usefulness of analyzing both polymerase and capsid genes for molecular characterization of HuCV and demonstrates the relatedness and predominance of NoV GII.4 with acute diarrheal disease in young Mexican children, thus contributing to better understanding of the molecular epidemiology of this disease. PMID:22361160

  7. Morphological variability in leaves and molecular characterization of novel table grape candidate cultivars (Vitis vinifera L.).

    PubMed

    Alba, Vittorio; Bergamini, Carlo; Cardone, Maria Francesca; Gasparro, Marica; Perniola, Rocco; Genghi, Rosalinda; Antonacci, Donato

    2014-06-01

    The present work report the characterization of twenty-one table grapes candidate cultivars plus five registered ones included as reference, by means of 47 ampelographic traits, 23 ampelometric measurements and six microsatellite loci. The final goal of the research was to analyse the possibility of reducing the number of morphological and molecular tools required for a precise and effective description of a grape genotype or cultivar. This would be of great help for future biodiversity description on a larger sample of more than 300 table grapes accessions today grown at the 'Consiglio per la Ricerca e la sperimentazione in Agricoltura (C.R.A.)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo (Bari-Italy)'. OIV ampelographic traits showed a clear distinction among all twenty-six genotypes analysed, suggesting the relevant morphological variability investigated. Principal component analysis based on ampelometric traits revealed main veins ON(3), ON(4) and O(3)N(4); ratios between main veins; angles between main veins and of petiolar sinus, to be the most effective records in differentiating cultivars, for a total variation of 69.9 % described by the first three components. Molecular analysis based on six microsatellite loci was performed on all genotypes, providing a detailed molecular profile and a dendrogram of genetic similarity, in which all genotypes were clearly distinguishable. Finally, with the goal of using the minimum possible number of markers to differentiate genotypes, microsatellites VVMD5 and VVMD27 were selected to be sufficient to distinguish among all the candidate cultivars included in the analysis, representing a possible 'step by step' approach when a molecular characterization has to be undertaken on a large number of genotypes, by first testing few markers and increasing their number only if necessary.

  8. Comparison of Molecular and Phenotypic Methods for the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae.

    PubMed

    Somily, Ali M; Garaween, Ghada A; Abukhalid, Norah; Absar, Muhammad M; Senok, Abiola C

    2016-03-01

    In recent years, there has been a rapid dissemination of carbapenem resistant Enterobacteriaceae (CRE). This study aimed to compare phenotypic and molecular methods for detection and characterization of CRE isolates at a large tertiary care hospital in Saudi Arabia. This study was carried out between January 2011 and November 2013 at the King Khalid University Hospital (KKUH) in Saudi Arabia. Determination of presence of extended-spectrum beta-lactamases (ESBL) and carbapenem resistance was in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Phenotypic classification was done by the MASTDISCS(TM) ID inhibitor combination disk method. Genotypic characterization of ESBL and carbapenemase genes was performed by the Check-MDR CT102. Diversilab rep-PCR was used for the determination of clonal relationship. Of the 883 ESBL-positive Enterobacteriaceae detected during the study period, 14 (1.6%) isolates were carbapenem resistant. Both the molecular genotypic characterization and phenotypic testing were in agreement in the detection of all 8 metalo-beta-lactamases (MBL) producing isolates. Of these 8 MBL-producers, 5 were positive for blaNDM gene and 3 were positive for blaVIM gene. Molecular method identified additional blaOXA gene isolates while MASTDISCS(TM) ID detected one AmpC producer isolate. Both methods agreed in identifying 2 carbapenem resistant isolates which were negative for carbapenemase genes. Diversilab rep-PCR analysis of the 9 Klebsiella pneumoniae isolates revealed polyclonal distribution into eight clusters. MASTDISCS(TM) ID is a reliable simple cheap phenotypic method for detection of majority of carbapenemase genes with the exception of the blaOXA gene. We recommend to use such method in the clinical laboratory.

  9. 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

  10. Brain and Plasma Molecular Characterization of the Pathogenic TBI-AD Interrelationship in Mouse Models

    DTIC Science & Technology

    2015-10-01

    AWARD NUMBER: W81XWH-13-1-0253 TITLE: Brain and Plasma Molecular Characterization of the Pathogenic TBI-AD Interrelationship in Mouse Models ... brain and plasma responses in mouse models of TBI, AD and other neurodegenerative conditions (Abdullah et al., 2014; Abdullah et al., 2013; Crawford...identify age/time-dependent expression of brain proteins and lipids in mouse models of AD (PSAPP and hTau) and of mTBI (single and repetitive mTBI in hTau

  11. Definitive molecular level characterization of defects in UiO-66 crystals.

    PubMed

    Trickett, Christopher A; Gagnon, Kevin J; Lee, Seungkyu; Gándara, Felipe; Bürgi, Hans-Beat; Yaghi, Omar M

    2015-09-14

    The identification and characterization of defects, on the molecular level, in metal-organic frameworks (MOFs) remain a challenge. With the extensive use of single-crystal X-ray diffraction (SXRD), the missing linker defects in the zirconium-based MOF UiO-66, Zr6 O4 (OH)4 (C8 H4 O4 )6 , have been identified as water molecules coordinated directly to the zirconium centers. Charge balancing is achieved by hydroxide anions, which are hydrogen bonded within the pores of the framework. Furthermore, the precise nature of the defects and their concentration can be manipulated by altering the starting materials, synthesis conditions, and post-synthetic modifications.

  12. 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.

  13. 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

  14. First molecular identification and characterization of classical swine fever virus isolates from Nepal.

    PubMed

    Postel, Alexander; Jha, Vijay C; Schmeiser, Stefanie; Becher, Paul

    2013-01-01

    Classical swine fever (CSF) is a major constraint to pig production worldwide, and in many developing countries, the epidemiological status is unknown. Here, for the first time, molecular identification and characterization of CSFV isolates from two recent outbreaks in Nepal are presented. Analysis of full-length E2-encoding sequences revealed that these isolates belonged to CSFV subgenotype 2.2 and had highest genetic similarity to isolates from India. Hence, for CSFV, Nepal and India should be regarded as one epidemiological unit. Both Nepalese isolates exhibited significant sequence differences, excluding a direct epidemiological connection and suggesting that CSFV is endemic in that country.

  15. 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

  16. Molecular and stable carbon isotopic characterization of PAH contaminants at McMurdo Station, Antarctica.

    PubMed

    Kim, Moonkoo; Kennicutt, Mahlon C; Qian, Yaorong

    2006-12-01

    The molecular and stable carbon isotopic compositions of contaminant polycyclic aromatic hydrocarbons (PAHs) at McMurdo Station, Antarctica were analyzed in samples collected from land and sub-tidal area. PAHs in the study areas were characterized by high amounts of naphthalene and alkylated naphthalenes from petroleum products introduced by human activities in the area. Principal component analysis (PCA) of PAH composition data identified multiple sources of PAH contamination in the study area. Compositional assignments of origins were confirmed using compound specific stable carbon isotopic analysis.

  17. 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.

  18. Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

    PubMed

    Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J

    2017-03-01

    Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom(®) genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'.

  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. 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

  1. Characterization of Plant Cell Wall Damage-Associated Molecular Patterns Regulating Immune Responses.

    PubMed

    Bacete, Laura; Mélida, Hugo; Pattathil, Sivakumar; Hahn, Michael G; Molina, Antonio; Miedes, Eva

    2017-01-01

    The plant cell wall is one of the first defensive barriers that pathogens need to overcome to successfully colonize plant tissues. Plant cell wall is considered a dynamic structure that regulates both constitutive and inducible defense mechanisms. The wall is a potential source of a diverse set of Damage-Associated Molecular Patterns (DAMPs), which are signalling molecules that trigger immune responses. However, just a few active wall ligands, such as oligogalacturonic acids (OGs), have been characterized so far. To identify additional wall-derived DAMPs, we obtained different plant wall fractions and tested their capacity to trigger immune responses using a calcium read-out system. To characterize the active DAMPs structures present in these fractions, we applied Glycome Profiling, a technology that uses a large and diverse set of specific monoclonal antibodies against wall carbohydrate ligands. The methods describe here can be used in combination with other biochemical approaches to identify and purify new plant cell wall DAMPs.

  2. 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.

  3. Morphological, physiological and molecular genetic characterization ofArabidopsis himalaica, with reference toA. thaliana.

    PubMed

    Tsukaya, H; Yokoyama, J; Ikeda, H; Kuroiwa, H; Kuroiwa, T; Iwatsuki, K

    1997-03-01

    Arabidopsis himalaica (Edgeworth) O.E. Schulz, a poorly characterized species typical of HimalayanArabidopsis, was analyzed in terms of its morphology, physiology, chromosome number and molecular genetics, in comparison withA. thaliana which is the standard species in the genusArabidopsis. From view point of developmental genetics, several features which are specific toA. himalaica seem not to be derived by single-gene mutations inA. thaliana. Phylogenetic analyses based onrbcL sequences suggested that genusArabidopsis is not monophyletic. The detailed characterization ofA. himalaica should provide clues to understand the trait of evolution of particular features of Himalayan species ofArabidopsis and their genetic basis.

  4. 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...

  5. Microbiological and molecular characterization of Corynebacterium diphtheriae isolated in Algeria between 1992 and 2015.

    PubMed

    Benamrouche, N; Hasnaoui, S; Badell, E; Guettou, B; Lazri, M; Guiso, N; Rahal, K

    2016-12-01

    The objectives of this study were to undertake the microbiological and molecular characterization of Corynebacterium diphtheriae isolates collected in Algeria during epidemic and post-epidemic periods between 1992 and 2015. Microbiological characterization includes the determination of biotype and toxigenicity status using phenotypic and genotypic methods. Antimicrobial susceptibility was determined by the E-test method. Molecular characterization was performed by multi-locus sequence typing. In total, there were 157 cases of C. diphtheriae isolates, 127 in patients with respiratory diphtheria and 30 with ozena. Isolates with a mitis biotype were predominant (122 out of 157; 77.7%) followed by belfanti (28 out of 157; 17.8%) and gravis biotype (seven out of 157; 4.5%). Toxigenic isolates were predominant in the period 1992-2006 (74 out of 134) whereas in the period 2007-2015, only non-toxigenic isolates circulated (23 out of 23). All 157 isolates were susceptible to erythromycin, gentamicin, vancomycin and cotrimoxazole. Reduced susceptibility to penicillin G, cefotaxime, tetracycline and chloramphenicol was detected in 90 (57.3%), 88 (56.1%), 112 (71.3%) and 90 (57.3%) isolates, respectively. Multi-locus sequence typing analysis indicates that sequence type 116 (ST-116) was the most frequent, with 65 out of 100 isolates analysed, in particular during the epidemic period 1992-1999 (57 out of 65 isolates). In the post-epidemic period, 2000-2015, 13 different sequence types were isolated. All belfanti isolates (ten out of 100 isolates) belonged to closely related sequence types grouped in a phylogenetically distinct eBurst group and were collected exclusively in ozena cases. In conclusion, the epidemic period was associated with ST-116 while the post-epidemic period was characterized by more diversity. Belfanti isolates are grouped in a phylogenetically distinct clonal complex.

  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.

  7. The pharmaceuticalisation of security: Molecular biomedicine, antiviral stockpiles, and global health security.

    PubMed

    Elbe, Stefan

    2014-12-01

    Pharmaceuticals are now critical to the security of populations. Antivirals, antibiotics, next-generation vaccines, and antitoxins are just some of the new 'medical countermeasures' that governments are stockpiling in order to defend their populations against the threat of pandemics and bioterrorism. How has security policy come to be so deeply imbricated with pharmaceutical logics and solutions? This article captures, maps, and analyses the 'pharmaceuticalisation' of security. Through an in-depth analysis of the prominent antiviral medication Tamiflu, it shows that this pharmaceutical turn in security policy is intimately bound up with the rise of a molecular vision of life promulgated by the biomedical sciences. Caught in the crosshairs of powerful commercial, political, and regulatory pressures, governments are embracing a molecular biomedicine promising to secure populations pharmaceutically in the twenty-first century. If that is true, then the established disciplinary view of health as a predominantly secondary matter of 'low' international politics is mistaken. On the contrary, the social forces of health and biomedicine are powerful enough to influence the core practices of international politics - even those of security. For a discipline long accustomed to studying macrolevel processes and systemic structures, it is in the end also our knowledge of the minute morass of molecules that shapes international relations.

  8. Molecular Characterization of Collagen Hydroxylysine O-Glycosylation by Mass Spectrometry: Current Status

    PubMed Central

    Perdivara, Irina; Yamauchi, Mitsuo; Tomer, Kenneth B.

    2014-01-01

    The most abundant proteins in vertebrates – the collagen family proteins – play structural and biological roles in the body. The predominant member, type I collagen, provides tissues and organs with structure and connectivity. This protein has several unique post-translational modifications that take place intra- and extra-cellularly. With growing evidence of the relevance of such post-translational modifications in health and disease, the biological significance of O-linked collagen glycosylation has recently drawn increased attention. However, several aspects of this unique modification – the requirement for prior lysyl hydroxylation as a substrate, involvement of at least two distinct glycosyl transferases, its involvement in intermolecular crosslinking – have made its molecular mapping and quantitative characterization challenging. Such characterization is obviously crucial for understanding its biological significance. Recent progress in mass spectrometry has provided an unprecedented opportunity for this type of analysis. This review summarizes recent advances in the area of O-glycosylation of fibrillar collagens and their characterization using state-of-the-art liquid chromatography–mass spectrometry-based methodologies, and perspectives on future research. The analytical characterization of collagen crosslinking and advanced glycation end-products are not addressed here. PMID:25414518

  9. Low molecular weight protamine (LMWP) as nontoxic heparin/low molecular weight heparin antidote (I): preparation and characterization.

    PubMed

    Chang, L C; Lee, H F; Yang, Z; Yang, V C

    2001-01-01

    Low molecular weight protamine (LMWP) appears to be a promising solution for heparin neutralization without the protamine-associated catastrophic toxic effects. The feasibility of this hypothesis was proven previously by using a peptide mixture produced from proteolytic digestion of protamine. To further examine the utility of this compound as an ultimate nontoxic protamine substitute, detailed studies on the purification and characterization of LMWP including the precise amino acid sequence, structure-function relationship, and possible mechanism were conducted. A number of LWMP fragments, composed of highly cationic peptides with molecular weights ranging from 700 to 1900 d, were prepared by digestion of native protamine with the protease thermolysin. These fragments were fractionated using a heparin affinity chromatography, and their relative binding strengths toward heparin were elucidated. Five distinct fractions were eluted at NaCl concentration ranging from 0.4 to 1.0 M and were denoted as TDSP1 to TDSP5, in increasing order of eluting ionic strength. Among these 5 fractions, TDSP4 and TDSP5 contained 3 LMWP peptide fragments, and they were found to retain the complete heparin-neutralizing function of protamine. By using a peptide mass spectrometry (MS) fingerprint mapping technique, the amino acid sequences of the microheterogeneous LMWP fragments in all these 5 elution fractions were readily identified. A typical structural scaffold made by arginine clusters in the middle and nonarginine residues at the N-terminal of the peptide sequence was observed for all these LMWP fragments. By aligning the sequences with the potency in heparin neutralization of these LMWP fragments, it was found that retention of potency similar to that of protamine required the presence of at least 2 arginine clusters in the LMWP fragments; such as the sequence of VSRRRRRRGGRRRR seen in the most potent LMWP fraction-TDSP5. The above finding was further validated by using a synthetic

  10. Molecular characterization of multidrug resistant hospital isolates using the antimicrobial resistance determinant microarray.

    PubMed

    Leski, Tomasz A; Vora, Gary J; Barrows, Brian R; Pimentel, Guillermo; House, Brent L; Nicklasson, Matilda; Wasfy, Momtaz; Abdel-Maksoud, Mohamed; Taitt, Chris Rowe

    2013-01-01

    Molecular methods that enable the detection of antimicrobial resistance determinants are critical surveillance tools that are necessary to aid in curbing the spread of antibiotic resistance. In this study, we describe the use of the Antimicrobial Resistance Determinant Microarray (ARDM) that targets 239 unique genes that confer resistance to 12 classes of antimicrobial compounds, quaternary amines and streptothricin for the determination of multidrug resistance (MDR) gene profiles. Fourteen reference MDR strains, which either were genome, sequenced or possessed well characterized drug resistance profiles were used to optimize detection algorithms and threshold criteria to ensure the microarray's effectiveness for unbiased characterization of antimicrobial resistance determinants in MDR strains. The subsequent testing of Acinetobacter baumannii, Escherichia coli and Klebsiella pneumoniae hospital isolates revealed the presence of several antibiotic resistance genes [e.g. belonging to TEM, SHV, OXA and CTX-M classes (and OXA and CTX-M subfamilies) of β-lactamases] and their assemblages which were confirmed by PCR and DNA sequence analysis. When combined with results from the reference strains, ~25% of the ARDM content was confirmed as effective for representing allelic content from both Gram-positive and -negative species. Taken together, the ARDM identified MDR assemblages containing six to 18 unique resistance genes in each strain tested, demonstrating its utility as a powerful tool for molecular epidemiological investigations of antimicrobial resistance in clinically relevant bacterial pathogens.

  11. 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.

  12. Assembly and Characterization ofWell-DefinedHigh-Molecular-Weight Poly(p-phenylene) Polymer Brushes

    SciTech Connect

    Chen, Jihua; Dadmun, Mark D; Mays, Jimmy; Messman, Jamie M; Hong, Kunlun; Britt, Phillip F; Sumpter, Bobby G; Alonzo Calderon, Jose E; Kilbey, II, S Michael; Ankner, John Francis; Bredas, Jean-Luc E; Malagoli, Massimo; Deng, Suxiang; Swader, Onome A; Yu, Xiang

    2011-01-01

    The assembly and characterization of well-de ned, end-tethered poly- (p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of poly- merizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry, atomic force microscopy, grazing angle attenuated total re ectance Fourier transform infrared spectroscopy, and UV-Vis spectros- copy. The properties of the PPP brushes are compared with those of lms made using oligo- paraphenylenes and with ab initio density functional theory simulations of optical proper- ties. Our results suggest conversion to fully aromatized, end-tetheredPPPpolymerbrusheshaving eective conjugation lengths of 5 phenyl units.

  13. Assembly and Characterization of Well Defined High Molecular Weight Poly(p-phenylene) Polymer Brushes

    SciTech Connect

    Alonzo Calderon, Jose E; Kilbey, II, S Michael; Ankner, John Francis; Britt, Phillip F; Chen, Jihua; Dadmun, Mark D; Deng, Suxiang; Hong, Kunlun; Mays, Jimmy; Messman, Jamie M; Sumpter, Bobby; Swader, Onome A; Yu, Xiang; Bredas, Jean-Luc E; Malagoli, Massimo

    2011-01-01

    The assembly and characterization of well-defined, end-tethered poly(p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of polymerizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry, atomic force microscopy, grazing angle attenuated total reflectance Fourier transform infrared spectroscopy, and UV-Vis spectroscopy. The properties of the PPP brushes are compared with those of films made using oligo-paraphenylenes and with ab initio density functional theory simulations of optical properties. Our results suggest conversion to fully aromatized, end-tethered PPP polymer brushes having effective conjugation lengths of 5 phenyl units.

  14. Characterization and Molecular Profiling of PSEN1 Familial Alzheimer's Disease iPSC-Derived Neural Progenitors

    PubMed Central

    Sproul, Andrew A.; Jacob, Samson; Pre, Deborah; Kim, Soong Ho; Nestor, Michael W.; Navarro-Sobrino, Miriam; Santa-Maria, Ismael; Zimmer, Matthew; Aubry, Soline; Steele, John W.; Kahler, David J.; Dranovsky, Alex; Arancio, Ottavio; Crary, John F.; Gandy, Sam; Noggle, Scott A.

    2014-01-01

    Presenilin 1 (PSEN1) encodes the catalytic subunit of γ-secretase, and PSEN1 mutations are the most common cause of early onset familial Alzheimer's disease (FAD). In order to elucidate pathways downstream of PSEN1, we characterized neural progenitor cells (NPCs) derived from FAD mutant PSEN1 subjects. Thus, we generated induced pluripotent stem cells (iPSCs) from affected and unaffected individuals from two families carrying PSEN1 mutations. PSEN1 mutant fibroblasts, and NPCs produced greater ratios of Aβ42 to Aβ40 relative to their control counterparts, with the elevated ratio even more apparent in PSEN1 NPCs than in fibroblasts. Molecular profiling identified 14 genes differentially-regulated in PSEN1 NPCs relative to control NPCs. Five of these targets showed differential expression in late onset AD/Intermediate AD pathology brains. Therefore, in our PSEN1 iPSC model, we have reconstituted an essential feature in the molecular pathogenesis of FAD, increased generation of Aβ42/40, and have characterized novel expression changes. PMID:24416243

  15. Molecular characterization of environmental Cryptococcus neoformans VNII isolates in Jos, Plateau State, Nigeria.

    PubMed

    Nnadi, N E; Enweani, I B; Cogliati, M; Ayanbimpe, G M; Okolo, M O; Kim, E; Sabitu, M Z; Criseo, G; Romeo, O; Scordino, F

    2016-12-01

    Cryptococcus neoformans and Cryptococcus gattii are encapsulated yeasts able to cause fatal neurological infections in both human and other mammals. Cryptococcosis is the most common fungal infection of the central nervous system and has a huge burden in sub-Saharan Africa and South East Asia. Bird excreta are considered an environmental reservoir for C. neoformans in urban areas, therefore a study aimed at isolating and characterizing this yeast is important in disease management. In this study, one hundred samples of pigeon droppings were collected in Jos, Plateau State, Nigeria. C. neoformans was isolated from three samples and initially identified using standard phenotypic and biochemical tests. Molecular analysis revealed that all three isolates belonged to C. neoformans genotype VNII, mating type α and were assigned to the sequence type ST43 by multilocus sequence typing analysis. This study reports, for the first time, the molecular characterization of C. neoformans in Nigeria, where little is still known about the environmental distribution of the genotypes, serotypes and mating types of this important human pathogen.

  16. Molecular cloning and characterization of CD4 in an aquatic mammal, the white whale Delphinapterus leucas.

    PubMed

    Romano, T A; Ridgway, S H; Felten, D L; Quaranta, V

    1999-05-01

    Given the importance of the cell surface recognition protein, CD4, in immune function, the cloning and characterization of CD4 at the molecular level from an odontocete cetacean, the white whale (Delphinapterus leucas), was carried out. Whale CD4 cDNA contains 2662 base pairs and translates into a protein containing 455 amino acids. Whale CD4 shares 64% and 51% identity with the human and mouse CD4 protein, respectively, and is organized in a similar manner. Unlike human and mouse, however, the cytoplasmic domain, which is highly conserved, contains amino acid substitutions unique to whale. Moreover, only one of the seven potential N-linked glycosylation sites present in whale is shared with human and mouse. Evolutionarily, the whale CD4 sequence is most similar to pig and structurally similar to dog and cat, in that all lack the cysteine pair in the V2 domain. These differences suggest that CD4 may have a different secondary structure in these species, which may affect binding of class II and subsequent T-cell activation, as well as binding of viral pathogens. Interestingly, as a group, species with these CD4 characteristics all have high constitutive expression of class II molecules on T lymphocytes, suggesting potential uniqueness in the interaction of CD4, class II molecules, and the immune response. Molecular characterization of CD4 in an aquatic mammal provides information on the CD4 molecule itself and may provide insight into adaptive evolutionary changes of the immune system.

  17. 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.

  18. Molecular and phenotypic characterization of ring chromosome 22 in two unrelated patients.

    PubMed

    Hannachi, H; Mougou, S; Benabdallah, I; Soayh, N; Kahloul, N; Gaddour, N; Le Lorc'h, M; Sanlaville, D; El Ghezal, H; Saad, A

    2013-01-01

    We report on the cytogenetic and molecular characterization of a constitutional de novo ring chromosome 22 (r(22)) in 2 unrelated patients with emphasis on different hypotheses proposed to explain the phenotypic variability characterizing this genomic disorder. In both patients, molecular investigations using FISH and array-CGH techniques revealed a 22q terminal deletion involving the 22q13.33 critical region. The size of the deletion was estimated to at least 1.35 Mb in the first proband and to only 300 kb in the second. They both exhibited the major features of r(22) syndrome, but the first patient was more profoundly affected. He had a more severe phenotype, further complicated by behavioral anomalies, autistic-like features with abnormal EEG pattern and brain MRI profile. Haploinsufficiency of the SHANK3 gene, lying in the minimal critical region, is nowadays considered as responsible for most neurobehavioral anomalies. Nevertheless, phenotypic severity and occurrence of additional features in the first patient suggest a potential involvement of one or more specific gene(s) located proximally to SHANK3 (as PLXNB2, PANX2, ALG12 or MLC1), acting either independently of it or by regulating or promoting its expression and thus disrupting its function when deleted.

  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.

  20. Molecular expression and enzymatic characterization of thioredoxin from the carcinogenic human liver fluke Opisthorchis viverrini.

    PubMed

    Suttiprapa, Sutas; Matchimakul, Pitchaya; Loukas, Alex; Laha, Thewarach; Wongkham, Sopit; Kaewkes, Sasithorn; Brindley, Paul J; Sripa, Banchob

    2012-03-01

    The human liver fluke, Opisthorchis viverrini, induces inflammation of the hepatobiliary system. Despite being constantly exposed to inimical oxygen radicals released from inflammatory cells, the parasite survives for years. Defense against oxidative damage can be mediated through glutathione and/or thioredoxin utilizing systems. Here, we report the molecular expression and biochemical characterization of a thioredoxin (Trx) from O. viverrini. O. viverrini Trx cDNA encoded a polypeptide of 105 amino acid residues, of molecular mass 11.63 kDa. The predicted protein has similarity to previously characterized thioredoxins with 26-51% identity. Recombinant O. viverrini Trx (Ov-Trx-1) was expressed as soluble protein in E. coli. The recombinant protein showed insulin reduction activity and supported the enzymatic function of O. viverrini thioredoxin peroxidase. Expression of Ov-Trx-1 at mRNA and protein levels was observed in all obtainable developmental stages of the liver fluke. Ov-Trx-1 was also detected in excretory-secretory products released by adult O. viverrini. Immunohistochemistry, Ov-Trx-1 was expressed in nearly all parasite tissue excepted ovary and mature sperms. Interestingly, Ov-Trx-1 was observed in the infected biliary epithelium but not in normal bile ducts. These results suggest that Ov-Trx-1 is essential for the parasite throughout the life cycle. In the host-parasite interaction aspect, Ov-Trx-1 may support thioredoxin peroxidase in protecting the parasite against damage induced by reactive oxygen species from inflammation.

  1. Molecular Characterization of Multidrug Resistant Hospital Isolates Using the Antimicrobial Resistance Determinant Microarray

    PubMed Central

    Leski, Tomasz A.; Vora, Gary J.; Barrows, Brian R.; Pimentel, Guillermo; House, Brent L.; Nicklasson, Matilda; Wasfy, Momtaz; Abdel-Maksoud, Mohamed; Taitt, Chris Rowe

    2013-01-01

    Molecular methods that enable the detection of antimicrobial resistance determinants are critical surveillance tools that are necessary to aid in curbing the spread of antibiotic resistance. In this study, we describe the use of the Antimicrobial Resistance Determinant Microarray (ARDM) that targets 239 unique genes that confer resistance to 12 classes of antimicrobial compounds, quaternary amines and streptothricin for the determination of multidrug resistance (MDR) gene profiles. Fourteen reference MDR strains, which either were genome, sequenced or possessed well characterized drug resistance profiles were used to optimize detection algorithms and threshold criteria to ensure the microarray's effectiveness for unbiased characterization of antimicrobial resistance determinants in MDR strains. The subsequent testing of Acinetobacter baumannii, Escherichia coli and Klebsiella pneumoniae hospital isolates revealed the presence of several antibiotic resistance genes [e.g. belonging to TEM, SHV, OXA and CTX-M classes (and OXA and CTX-M subfamilies) of β-lactamases] and their assemblages which were confirmed by PCR and DNA sequence analysis. When combined with results from the reference strains, ∼25% of the ARDM content was confirmed as effective for representing allelic content from both Gram-positive and –negative species. Taken together, the ARDM identified MDR assemblages containing six to 18 unique resistance genes in each strain tested, demonstrating its utility as a powerful tool for molecular epidemiological investigations of antimicrobial resistance in clinically relevant bacterial pathogens. PMID:23936031

  2. Molecular Characterization and Antioxidant Potential of Three Wild Culinary-Medicinal Mushrooms from Tripura, Northeast India.

    PubMed

    Das, Aparajita Roy; Borthakur, Madhusmita; Saha, Ajay Krishna; Joshi, Santa Ram; Das, Panna

    2017-01-01

    The aim of this study was to characterize 3 wild culinary-medicinal mushrooms using molecular tools and to analyze their antioxidant activity. Antioxidant properties were studied by evaluating free radical scavenging, reducing power, and chelating effect. The mushrooms were identified as Lentinus squarrosulus, L. tuber-regium, and Macrocybe gigantean by amplifying internal transcribed spacer regions of ribosomal DNA. The results demonstrated that the methanolic extract of M. gigantean has the highest free radical scavenging effect and chelating effect, whereas the methanolic extract of L. squarrosulus has the highest reducing power. The highest total phenol content and the most ascorbic acid were found in the M. gigantean extracts. Among the 3 mushroom extracts, M. gigantean displayed the most potent antioxidant activity. Molecular characterization using the nuclear ribosomal internal transcribed spacer region as a universal DNA marker was an effective tool in the identification and phylogenetic analysis of the studied mushrooms. The study also indicated that these wild macrofungi are rich sources of natural antioxidants.

  3. Quantitative molecular sensing in biological tissues: an approach to non-invasive optical characterization

    NASA Astrophysics Data System (ADS)

    Chandra, Malavika; Vishwanath, Karthik; Fichter, Greg D.; Liao, Elly; Hollister, Scott J.; Mycek, Mary-Ann

    2006-06-01

    A method to non-invasively and quantitatively characterize thick biological tissues by combining both experimental and computational approaches in tissue optical spectroscopy was developed and validated on fifteen porcine articular cartilage (AC) tissue samples. To the best of our knowledge, this study is the first to couple non-invasive reflectance and fluorescence spectroscopic measurements on freshly harvested tissues with Monte Carlo computational modeling of time-resolved propagation of both excitation light and multi-fluorophore emission. For reflectance, quantitative agreement between simulation and experiment was achieved to better than 11%. Fluorescence data and simulations were used to extract the ratio of the absorption coefficients of constituent fluorophores for each measured AC tissue sample. This ratio could be used to monitor relative changes in concentration of the constituent fluorophores over time. The samples studied possessed the complexity and variability not found in artificial tissue-simulating phantoms and serve as a model for future optical molecular sensing studies on tissue engineered constructs intended for use in human therapeutics. An optical technique that could non-invasively and quantitatively assess soft tissue composition or physiologic status would represent a significant advance in tissue engineering. Moreover, the general approach described here for optical characterization should be broadly applicable to quantitative, non-invasive molecular sensing applications in complex, three-dimensional biological tissues.

  4. Molecular cloning and biochemical characterization of a Drosophila phosphatidylinositol-specific phosphoinositide 3-kinase.

    PubMed

    Linassier, C; MacDougall, L K; Domin, J; Waterfield, M D

    1997-02-01

    Molecular, biochemical and genetic characterization of phosphoinositide 3-kinases (PI3Ks) have identified distinct classes of enzymes involved in processes mediated by activation of cell-surface receptors and in constitutive intracellular protein trafficking events. The latter process appears to involve a PtdIns-specific PI3K first described in yeast as a mutant, vps34, defective in the sorting of newly synthesized proteins from the Golgi to the vacuole. We have identified a representative member of each class of PI3Ks in Drosophila using a PCR-based approach. In the present paper we describe the molecular cloning of a PI3K from Drosophila, P13K_59F, that shows sequence similarity to Vps34. PI3K_59F encodes a protein of 108 kDa co-linear with Vps34 homologues, and with three regions of sequence similarity to other PI3Ks. Biochemical characterization of the enzyme, by expression of the complete coding sequence as a glutathione S-transferase fusion protein in Sf9 cells, demonstrates that PI3K_59F is a PtdIns-specific PI3K that can utilize either Mg2+ or Mn2+. This activity is sensitive to inhibition both by non-ionic detergent (Nonidet P40) and by wortmannin (IC50 10 nM). PI3K_59F, therefore, conserves both the structural and biochemical properties of the Vps34 class of enzymes.

  5. Structural and functional characterization of Pseudomonas aeruginosa global regulator AmpR.

    PubMed

    Caille, Olivier; Zincke, Diansy; Merighi, Massimo; Balasubramanian, Deepak; Kumari, Hansi; Kong, Kok-Fai; Silva-Herzog, Eugenia; Narasimhan, Giri; Schneper, Lisa; Lory, Stephen; Mathee, Kalai

    2014-11-01

    Pseudomonas aeruginosa is a dreaded pathogen in many clinical settings. Its inherent and acquired antibiotic resistance thwarts therapy. In particular, derepression of the AmpC β-lactamase is a common mechanism of β-lactam resistance among clinical isolates. The inducible expression of ampC is controlled by the global LysR-type transcriptional regulator (LTTR) AmpR. In the present study, we investigated the genetic and structural elements that are important for ampC induction. Specifically, the ampC (PampC) and ampR (PampR) promoters and the AmpR protein were characterized. The transcription start sites (TSSs) of the divergent transcripts were mapped using 5' rapid amplification of cDNA ends-PCR (RACE-PCR), and strong σ(54) and σ(70) consensus sequences were identified at PampR and PampC, respectively. Sigma factor RpoN was found to negatively regulate ampR expression, possibly through promoter blocking. Deletion mapping revealed that the minimal PampC extends 98 bp upstream of the TSS. Gel shifts using membrane fractions showed that AmpR binds to PampC in vitro whereas in vivo binding was demonstrated using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR). Additionally, site-directed mutagenesis of the AmpR helix-turn-helix (HTH) motif identified residues critical for binding and function (Ser38 and Lys42) and critical for function but not binding (His39). Amino acids Gly102 and Asp135, previously implicated in the repression state of AmpR in the enterobacteria, were also shown to play a structural role in P. aeruginosa AmpR. Alkaline phosphatase fusion and shaving experiments suggest that AmpR is likely to be membrane associated. Lastly, an in vivo cross-linking study shows that AmpR dimerizes. In conclusion, a potential membrane-associated AmpR dimer regulates ampC expression by direct binding.

  6. Structural and Functional Characterization of Pseudomonas aeruginosa Global Regulator AmpR

    PubMed Central

    Caille, Olivier; Zincke, Diansy; Merighi, Massimo; Balasubramanian, Deepak; Kumari, Hansi; Kong, Kok-Fai; Silva-Herzog, Eugenia; Narasimhan, Giri; Schneper, Lisa; Lory, Stephen

    2014-01-01

    Pseudomonas aeruginosa is a dreaded pathogen in many clinical settings. Its inherent and acquired antibiotic resistance thwarts therapy. In particular, derepression of the AmpC β-lactamase is a common mechanism of β-lactam resistance among clinical isolates. The inducible expression of ampC is controlled by the global LysR-type transcriptional regulator (LTTR) AmpR. In the present study, we investigated the genetic and structural elements that are important for ampC induction. Specifically, the ampC (PampC) and ampR (PampR) promoters and the AmpR protein were characterized. The transcription start sites (TSSs) of the divergent transcripts were mapped using 5′ rapid amplification of cDNA ends-PCR (RACE-PCR), and strong σ54 and σ70 consensus sequences were identified at PampR and PampC, respectively. Sigma factor RpoN was found to negatively regulate ampR expression, possibly through promoter blocking. Deletion mapping revealed that the minimal PampC extends 98 bp upstream of the TSS. Gel shifts using membrane fractions showed that AmpR binds to PampC in vitro whereas in vivo binding was demonstrated using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR). Additionally, site-directed mutagenesis of the AmpR helix-turn-helix (HTH) motif identified residues critical for binding and function (Ser38 and Lys42) and critical for function but not binding (His39). Amino acids Gly102 and Asp135, previously implicated in the repression state of AmpR in the enterobacteria, were also shown to play a structural role in P. aeruginosa AmpR. Alkaline phosphatase fusion and shaving experiments suggest that AmpR is likely to be membrane associated. Lastly, an in vivo cross-linking study shows that AmpR dimerizes. In conclusion, a potential membrane-associated AmpR dimer regulates ampC expression by direct binding. PMID:25182487

  7. Molecular, biochemical, and morphometric characterization of Fasciola species potentially causing zoonotic disease in Egypt.

    PubMed

    El-Rahimy, Hoda H; Mahgoub, Abeer M A; El-Gebaly, Naglaa Saad M; Mousa, Wahid M A; Antably, Abeer S A E

    2012-09-01

    Fascioliasis is an important disease caused by Fasciola hepatica and Fasciola gigantica. The distributions of both species overlap in many areas of Asia and Africa including Egypt. Fifty adult Fasciola worms were collected from livers of cattle and sheep slaughtered in abattoirs, Cairo, Egypt. They were subjected to morphological and metric assessment of external features of fresh adults, morphological and metric assessment of internal anatomy of stained mounted worms, determination of electrophorezed bands of crude adult homogenates using SDS-PAGE, and molecular characterization of species-specific DNA segments using RFLP-PCR. It was found that the correlation between conventional morphology and its morphotype was statistically significant (P value = 0.00). Using SDS-PAGE, 13 bands were detected among both genotypes of Fasciola (35.7, 33.6, 32.4, 29.3, 27.5, 26, 24.4, 23, 21.45, 19, 16.75, 12.5, and 9.1 kDa).The most prevalent bands were that with a molecular weight of 29.3, 26, and 19 kDa. Bands detected were common for both species, but protein bands could not distinguish between F. hepatica and F. gigantica. The result of PCR for the amplification of the selected 28S rDNA fragment with the designed primer set yielded 618 bp long PCR products for F. hepatica and F. gigantica. Different band patterns generated after digestion of the 618 bp segment by the enzyme AvaII obtained with F. hepatica showed segments of the length 529, 62, 27 bp, while with F. gigantica 322, 269, 27 bp bands were obtained. Genotyping revealed no equivocal results. The conventional morphological parameters for species determination of Fasciola spp. endemic in Egypt were evaluated versus protein bands characterization and genotyping. It was concluded that conventional morphological and metric assessments were not useful for differentiation between F. gigantica and F. hepatica due to extensive overlap in the relative ranges. Similar conclusion was reached concerning protein band

  8. Characterization of molecular and atomic species adsorbed on ferroelectric and semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Bharath, Satyaveda Chavi

    In order to clarify the mechanisms behind the adsorption of atomic and molecular species adsorbed on ferroelectric surfaces, single crystalline lithium niobate (LiNbO3, LN), 'Z-cut' along the (0001) plane, has been prepared, characterized and subsequently exposed to molecular and atomic species. 4-n-octyl-4'-cyanobiphenyl (8CB) liquid crystal was chosen as a polar molecule for our model system for this study. Low-energy electron diffraction (LEED), atomic force microscopy (AFM), surface contact angles (CA), and X-ray photoelectron spectroscopy (XPS) were used to characterize the surface of LN as well as the nature of the liquid crystal films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. Also, for the purpose of gaining a fundamental understanding of low coverage interactions of metal atoms on ferroelectric surfaces, we choose to deposit gold onto the LN surface. These gold atomic layers were grown under UHV conditions and characterized. Understanding anchoring mechanisms and thin film organization for LC molecules and metal atoms on uniformly poled surfaces allows for a fuller appreciation of how molecular deposition of other polarizable molecules on patterned poled LN surfaces would occur as well as yielding greater insight on the atomic characteristics of metal on ferroelectric interfaces. Also, to reveal the mechanisms involved in the adsorption of organic aromatic molecules on high-index Si surfaces, thiophene (C4H 4S) and pyrrole (C4H5N) molecules were dosed on prepared Si(5 5 12)-2x1 surfaces as our experimental system. The Si(5 5 12) surface was prepared to produce a 2x1 reconstruction after which molecules were dosed at low exposure to observe the preferred adsorption sites on the surface. All surface preparation and experiments were performed in UHV and measurements of the surface before and after deposition were performed using scanning tunneling microscopy (STM). Fundamental

  9. 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.

  10. 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.

  11. Characterization, molecular docking, dynamics simulation and metadynamics of kisspeptin receptor with kisspeptin.

    PubMed

    Rather, Mohd Ashraf; Basha, Syed Hussain; Bhat, Irfan Ahmad; Sharma, Niti; Nandanpawar, Priyanka; Badhe, Mohan; P, Gireesh-Babu; Chaudhari, Aparna; Sundaray, Jitendra Kumar; Sharma, Rupam

    2017-03-20

    We report molecular characterization of the kisspeptin receptor (kiss1r), an essential gatekeeper for reproduction and onset of puberty in vertebrates. The full-length cDNA sequence of kiss1r is 1786bp which consist of 5' UTR (untranslated region) 261bp, 3' UTR of 424bp and open reading frame of 1101 encoding a putative protein of 366 amino acids. Basal tissue expression pattern of kiss1r mRNA revealed that it is mainly expressed in the brain and testis. We also report the structure of the kiss1r, along with plausible activation mechanism of this receptor by kisspeptin using computational modelling and dynamic simulation approach of multiple 100ns of timescale. A present modelling and simulations studies shed light on the molecular level of interaction, suggesting that direct hydrogen bonds between ASN4, SER5, GLY7, ARG9 and PHE10 of kisspeptin and TRP7, ASN8, GLU11, ILE17, ASN19 and TYR183 of kiss1r could be crucial role players in initial binding of receptor and the kisspeptin towards allosteric modulatory effects of kisspeptin on the receptor. To the best our knowledge, this is the first report on computational modelling and molecular dynamic simulations of kiss1r in animals shedding light on its possible mode of activation.

  12. Molecular characterization of the transition to mid-life in Caenorhabditis elegans.

    PubMed

    Eckley, D Mark; Rahimi, Salim; Mantilla, Sandra; Orlov, Nikita V; Coletta, Christopher E; Wilson, Mark A; Iser, Wendy B; Delaney, John D; Zhang, Yongqing; Wood, William; Becker, Kevin G; Wolkow, Catherine A; Goldberg, Ilya G

    2013-06-01

    We present an initial molecular characterization of a morphological transition between two early aging states. In previous work, an age score reflecting physiological age was developed using a machine classifier trained on images of worm populations at fixed chronological ages throughout their lifespan. The distribution of age scores identified three stable post-developmental states and transitions. The first transition occurs at day 5 post-hatching, where a significant percentage of the population exists in both state I and state II. The temperature dependence of the timing of this transition (Q 10 ~ 1.17) is too low to be explained by a stepwise process with an enzymatic or chemical rate-limiting step, potentially implicating a more complex mechanism. Individual animals at day 5 were sorted into state I and state II groups using the machine classifier and analyzed by microarray expression profiling. Despite being isogenic, grown for the same amount of time, and indistinguishable by eye, these two morphological states were confirmed to be molecularly distinct by hierarchical clustering and principal component analysis of the microarray results. These molecular differences suggest that pharynx morphology reflects the aging state of the whole organism. Our expression profiling yielded a gene set that showed significant overlap with those from three previous age-related studies and identified several genes not previously implicated in aging. A highly represented group of genes unique to this study is involved in targeted ubiquitin-mediated proteolysis, including Skp1-related (SKR), F-box-containing, and BTB motif adaptors.

  13. 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.

  14. 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.

  15. 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.

  16. 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).

  17. 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.

  18. 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.

  19. 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.

  20. Molecular characterization of the song control nucleus HVC in Bengalese finch brain.

    PubMed

    Kato, Masaki; Okanoya, Kazuo

    2010-11-11

    Songbirds have a specialized neural substrate for learned vocalization, called the song circuit, which consists of several song nuclei in the brain. The song control nucleus HVC (a letter-based name) is the intersection point of the song learning and vocal motor pathways. Knowledge of the types of genes expressed in the HVC is essential in understanding the molecular aspects of the HVC. Gene expression in the HVC under silent conditions shows the competence necessary for singing. To investigate this, we compared the HVC with its adjacent tissues in searching for the molecular specificities of the song nucleus HVC using an in-house cDNA microarray of the Bengalese finch (Lonchura striata var. domestica). Our microarray analysis revealed that 70 genes were differentially expressed in the HVC compared with the adjacent tissue. We investigated 27 of the microarray-selected genes that were enriched or repressed in the HVC by in situ hybridization. We found that multiple calcium-binding proteins (e.g., CAPS2, parvalbumin and ATH) were enriched in the HVC. Meanwhile, the adult HVC showed low expression levels of plasticity-related genes (e.g., CAMK2A and MAP2K1) compared with the juvenile HVC. The HVC plays an important role during song learning, but our results suggest that the plasticity of this nucleus may be suppressed during adulthood. Our findings provide new information about the molecular features that characterize the HVC.

  1. 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.

  2. Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

    PubMed

    Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

    2017-04-01

    The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses.

  3. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015.

    PubMed

    Al-Hatmi, Abdullah Ms; Hagen, Ferry; Menken, Steph Bj; Meis, Jacques F; de Hoog, G Sybren

    2016-12-07

    Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex).

  4. Global molecular epidemiology and genetic diversity of Fusarium, a significant emerging group of human opportunists from 1958 to 2015

    PubMed Central

    Al-Hatmi, Abdullah MS; Hagen, Ferry; Menken, Steph BJ; Meis, Jacques F; de Hoog, G Sybren

    2016-01-01

    Fusarium is a rapidly emerging, multidrug-resistant genus of fungal opportunists that was first identified in 1958 and is presently recognized in numerous cases of fusariosis each year. The authors examined trends in global Fusarium distribution, clinical presentation and prevalence since 1958 with the assumption that their distributions in each region had remained unaltered. The phylogeny and epidemiology of 127 geographically diverse isolates, representing 26 Fusarium species, were evaluated using partial sequences of the RPB2 and TEF1 genes, and compared with AFLP fingerprinting data. The molecular data of the Fusarium species were compared with archived data, which enabled the interpretation of hundreds of cases published in the literature. Our findings indicate that fusariosis is globally distributed with a focus in (sub)tropical areas. Considerable species diversity has been observed; genotypic features did not reveal any clustering with either the clinical data or environmental origins. This study suggests that infections with Fusarium species might be truly opportunistic. The three most common species are F. falciforme and F. keratoplasticum (members of F. solani species complex), followed by F. oxysporum (F. oxysporum species complex). PMID:27924809

  5. 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.

  6. Physiological and molecular characterization of drought responses and identification of candidate tolerance genes in cassava

    PubMed Central

    Turyagyenda, Laban F.; Kizito, Elizabeth B.; Ferguson, Morag; Baguma, Yona; Agaba, Morris; Harvey, Jagger J. W.; Osiru, David S. O.

    2013-01-01

    Cassava is an important root crop to resource-poor farmers in marginal areas, where its production faces drought stress constraints. Given the difficulties associated with cassava breeding, a molecular understanding of drought tolerance in cassava will help in the identification of markers for use in marker-assisted selection and genes for transgenic improvement of drought tolerance. This study was carried out to identify candidate drought-tolerance genes and expression-based markers of drought stress in cassava. One drought-tolerant (improved variety) and one drought-susceptible (farmer-preferred) cassava landrace were grown in the glasshouse under well-watered and water-stressed conditions. Their morphological, physiological and molecular responses to drought were characterized. Morphological and physiological measurements indicate that the tolerance of the improved variety is based on drought avoidance, through reduction of water loss via partial stomatal closure. Ten genes that have previously been biologically validated as conferring or being associated with drought tolerance in other plant species were confirmed as being drought responsive in cassava. Four genes (MeALDH, MeZFP, MeMSD and MeRD28) were identified as candidate cassava drought-tolerance genes, as they were exclusively up-regulated in the drought-tolerant genotype to comparable levels known to confer drought tolerance in other species. Based on these genes, we hypothesize that the basis of the tolerance at the cellular level is probably through mitigation of the oxidative burst and osmotic adjustment. This study provides an initial characterization of the molecular response of cassava to drought stress resembling field conditions. The drought-responsive genes can now be used as expression-based markers of drought stress tolerance in cassava, and the candidate tolerance genes tested in the context of breeding (as possible quantitative trait loci) and engineering drought tolerance in transgenics

  7. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

  8. Molecular characterization of multidrug-resistant avian pathogenic Escherichia coli isolated from septicemic broilers.

    PubMed

    Ahmed, Ashraf M; Shimamoto, Toshi; Shimamoto, Tadashi

    2013-12-01

    Avian pathogenic Escherichia coli (APEC) causes extensive mortality in poultry flocks, leading to extensive economic losses. To date, little information is available on the molecular basis of antimicrobial resistance in APEC in Africa. Therefore, the objective of this study was to characterize the virulence and antimicrobial resistance of multidrug-resistant APEC isolated from septicemic broilers in Egypt at the molecular level. Among 91 non-repetitive E. coli isolates, 73 (80.2%) carried three or more of the APEC virulence genes iroN, ompT, iss, iutA, and hlyF. All 73 APEC isolates showed multidrug resistance phenotypes, particularly against ampicillin, tetracycline, spectinomycin, streptomycin, kanamycin, and trimethoprim/sulfamethoxazole. PCR and DNA sequencing identified class 1 and class 2 integrons in 34 (46.6%) and seven (9.6%) isolates, respectively. The β-lactamase-encoding genes, bla(TEM-1), bla(TEM-104), bla(CMY-2), bla(OXA-30), bla(CTX-M-15), and bla(SHV-2); tetracycline resistance genes, tet(A), tet(B), tet(C), tet(D), and tet(E); the plasmid-mediated quinolone resistance genes, qnrA1, qnrB2, qnrS1, and aac(6')-Ib-cr, and florfenicol resistance gene, floR, were also identified in 69 (94.5%), 67 (91.8%), 47 (64.4%), and 13 (17.8%) isolates, respectively. To the best of our knowledge, this is the first report of molecular characterization of antimicrobial resistance in APEC strains from Africa.

  9. Molecular Characterization of Polio from Environmental Samples: ISSP, The Israeli Sewage Surveillance Protocol.

    PubMed

    Shulman, Lester M; Manor, Yossi; Hindiyeh, Musa; Sofer, Danit; Mendelson, Ella

    2016-01-01

    Polioviruses are enteric viruses that cause paralytic poliomyelitis in less than 0.5 % of infections and are asymptomatic in >90 % infections of naïve hosts. Environmental surveillance monitors polio in populations rather than in individuals. When this very low morbidity to infection ratio, drops drastically in highly vaccinated populations, environmental surveillance employing manual or automatic sampling coupled with molecular analysis carried out in well-equipped central laboratories becomes the surveillance method of choice since polioviruses are excreted by infected individuals regardless of whether or not the infection is symptomatic. This chapter describes a high throughput rapid turn-around time method for molecular characterization of polioviruses from sewage. It is presented in five modules: (1) Sewage collection and concentration of the viruses in the sewage; (2) Cell cultures for identification of virus in the concentrated sewage; (3) Nucleic acid extractions directly from sewage and from tissue cultures infected with aliquots of concentrated sewage; (4) Nucleic Acid Amplification for poliovirus serotype identification and intratypic differentiation (discriminating wild and vaccine derived polioviruses form vaccine strains); and (5) Molecular characterization of viral RNA by qRT-PCR, TR-PCR, and Sequence analysis. Monitoring silent or symptomatic transmission of vaccine-derived polioviruses or wild polioviruses is critical for the endgame of poliovirus eradication. We present methods for adapting standard kits and validating the changes for this purpose based on experience gained during the recent introduction and sustained transmission of a wild type 1 poliovirus in Israel in 2013 in a population with an initial IPV vaccine coverage >90 %.

  10. 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

  11. 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.

  12. Global land cover mapping and characterization: present situation and future research priorities

    USGS Publications Warehouse

    Giri, Chandra

    2005-01-01

    The availability and accessibility of global land cover data sets plays an important role in many global change studies. The importance of such science‐based information is also reflected in a number of international, regional, and national projects and programs. Recent developments in earth observing satellite technology, information technology, computer hardware and software, and infrastructure development have helped developed better quality land cover data sets. As a result, such data sets are increasingly becoming available, the user‐base is ever widening, application areas have been expanding, and the potential of many other applications are enormous. Yet, we are far from producing high quality global land cover data sets. This paper examines the progress in the development of digital global land cover data, their availability, and current applications. Problems and opportunities are also explained. The overview sets the stage for identifying future research priorities needed for operational land cover assessment and monitoring.

  13. 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...

  14. Global Modeling of Uranium Molecular Species Formation Using Laser-Ablated Plasmas

    NASA Astrophysics Data System (ADS)

    Curreli, Davide; Finko, Mikhail; Azer, Magdi; Armstrong, Mike; Crowhurst, Jonathan; Radousky, Harry; Rose, Timothy; Stavrou, Elissaios; Weisz, David; Zaug, Joseph

    2016-10-01

    Uranium is chemically fractionated from other refractory elements in post-detonation nuclear debris but the mechanism is poorly understood. Fractionation alters the chemistry of the nuclear debris so that it no longer reflects the chemistry of the source weapon. The conditions of a condensing fireball can be simulated by a low-temperature plasma formed by vaporizing a uranium sample via laser heating. We have developed a global plasma kinetic model in order to model the chemical evolution of U/UOx species within an ablated plasma plume. The model allows to track the time evolution of the density and energy of an uranium plasma plume moving through an oxygen atmosphere of given fugacity, as well as other relevant quantities such as average electron and gas temperature. Comparison of model predictions with absorption spectroscopy of uranium-ablated plasmas provide preliminary insights on the key chemical species and evolution pathways involved during the fractionation process. This project was sponsored by the DoD, Defense Threat Reduction Agency, Grant HDTRA1-16-1-0020. This work was performed in part under the auspices of the U.S. DoE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  15. In vivo characterization of a new abdominal aortic aneurysm mouse model with conventional and molecular MRI

    PubMed Central

    Klink, Ahmed; Heynens, Joeri; Herranz, Beatriz; Lobatto, Mark E.; Arias, Teresa; Sanders, Honorius M. H. F.; Strijkers, Gustav J.; Merkx, Maarten; Nicolay, Klaas; Fuster, Valentin; Tedgui, Alain; Mallat, Ziad; Mulder, Willem J.M.; Fayad, Zahi A.

    2014-01-01

    Objectives To use non-invasive conventional and molecular magnetic resonance imaging (MRI) to detect and characterize abdominal aortic aneurysms (AAAs) in vivo. Background Collagen is an essential constituent of aneurysms. Non-invasive MRI of collagen may represent an opportunity to help detect and better characterize AAA and initiate intervention. Methods We used an AAA C57BL/6 mouse model where a combination of angiotensin-II infusion and TGF-β neutralization results in AAA formation with incidence of aortic rupture. High-resolution multi-sequence MRI was performed to characterize the temporal progression of AAA. To allow molecular MRI of collagen, paramagnetic/fluorescent micellar nanoparticles functionalized with a collagen-binding protein (CNA-35) were intravenously administered. In vivo imaging results were corroborated with immunohistochemistry and confocal fluorescence microscopy. Results High-resolution multi-sequence MRI allowed the visualization of the primary fibrotic response in the aortic wall. As the aneurysm progressed, the formation of a secondary channel or dissection was detected. Further analysis revealed a dramatic increase of the aortic diameter. Injection of CNA-35 micelles resulted in a significant higher MR signal enhancement in the aneurysmal wall compared to non-specific micelles. Histological studies demonstrated the presence of collagen in regions of MR signal enhancement and confocal microscopy proved the precise colocalization of CNA-35 micelles with collagen-I. In addition, in a proof of concept experiment, we have shown the potential of CNA-35 micelles to discriminate between stable AAA lesions and aneurysms that were likely to rapidly progress/rupture. Conclusion Multi-sequence MRI allowed longitudinal monitoring of AAA progression while the presence of collagen was visualized by nanoparticle-enhanced MRI. PMID:22133853

  16. Molecular characterization of a collection of Neisseria meningitidis isolates from Croatia, June 2009 to January 2014.

    PubMed

    Bukovski, Suzana; Vacca, Paola; Anselmo, Anna; Knezovic, Ivica; Fazio, Cecilia; Neri, Arianna; Ciammaruconi, Andrea; Fortunato, Antonella; Palozzi, Anna Maria; Fillo, Silvia; Lista, Florigio; Stefanelli, Paola

    2016-09-01

    In the last decade, the incidence of invasive meningococcal disease (IMD) in Croatia remained stable at approximately 1 case per 100 000 inhabitants, affecting mainly children aged ≤5 years. We report the molecular characterization of meningococci causing IMD occurring from June 2009 to January 2014 in Croatia. Genomic DNA from 50 clinical isolates was analysed for serogroup, multilocus sequence typing and allele type of the two outer membrane protein genes, porA and the iron-regulated fetA. Furthermore, 22 of them were characterized by using whole-genome sequencing to define the meningococcal vaccine four-component meningococcal serogroup B (4CMenB) antigen genes factor H-binding protein (fHbp), Neisseria heparin-binding antigen (nhba) and Neisseria adhesin A (nadA) and the antimicrobial target resistance genes for penicillin (penicillin binding protein 2, penA), ciprofloxacin (DNA gyrase subunit A, gyrA) and rifampicin (β-subunit of RNA polymerase, rpoB). The Etest was used to phenotypically determine the antimicrobial susceptibility of isolated meningococci. The main serogroup/clonal complex combinations were MenB cc41/44, MenC/cc11, MenW/cc174 and MenY/cc23. PorA P1.7-2, FetA F5-5 and F1-5 were the most represented through the serogroups. Meningococci with decreased susceptibility to penicillin (38.9 %) and one strain resistant to ciprofloxacin were identified. Forty-two percent of MenB showed the presence of at least one of the 4CMenB vaccine antigens (fHbp, NHBA, NadA and PorA). Our findings highlight the genetic variability of meningococci causing IMD in Croatia, especially for the serogroup B. Molecular-based characterization of meningococci is crucial to enhance IMD surveillance and to better plan national immunization programmes.

  17. 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.

  18. Molecular Characterization of Clostridium botulinum Isolates from Foodborne Outbreaks in Thailand, 2010

    PubMed Central

    Wangroongsarb, Piyada; Kohda, Tomoko; Jittaprasartsin, Chutima; Suthivarakom, Karun; Kamthalang, Thanitchi; Umeda, Kaoru; Sawanpanyalert, Pathom; Kozaki, Shunji; Ikuta, Kazuyoshi

    2014-01-01

    Background Thailand has had several foodborne outbreaks of botulism, one of the biggest being in 2006 when laboratory investigations identified the etiologic agent as Clostridium botulinum type A. Identification of the etiologic agent from outbreak samples is laborious using conventional microbiological methods and the neurotoxin mouse bioassay. Advances in molecular techniques have added enormous information regarding the etiology of outbreaks and characterization of isolates. We applied these methods in three outbreaks of botulism in Thailand in 2010. Methodology/Principal Findings A total of 19 cases were involved (seven each in Lampang and Saraburi and five in Maehongson provinces). The first outbreak in Lampang province in April 2010 was associated with C. botulinum type F, which was detected by conventional methods. Outbreaks in Saraburi and Maehongson provinces occurred in May and December were due to C. botulinum type A1(B) and B that were identified by conventional methods and molecular techniques, respectively. The result of phylogenetic sequence analysis showed that C. botulinum type A1(B) strain Saraburi 2010 was close to strain Iwate 2007. Molecular analysis of the third outbreak in Maehongson province showed C. botulinum type B8, which was different from B1–B7 subtype. The nontoxic component genes of strain Maehongson 2010 revealed that ha33, ha17 and botR genes were close to strain Okra (B1) while ha70 and ntnh genes were close to strain 111 (B2). Conclusion/Significance This study demonstrates the utility of molecular genotyping of C. botulinum and how it contributes to our understanding the epidemiology and variation of boNT gene. Thus, the recent botulism outbreaks in Thailand were induced by various C. botulinum types. PMID:24475015

  19. 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

  20. Single particle characterization of biomass burning organic aerosol (BBOA): evidence for non-uniform mixing of high molecular weight organics and potassium

    NASA Astrophysics Data System (ADS)

    Lee, A. K. Y.; Willis, M. D.; Healy, R. M.; Wang, J. M.; Jeong, C.-H.; Wenger, J. C.; Evans, G. J.; Abbatt, J. P. D.

    2015-11-01

    Biomass burning is a major source of black carbon (BC) and primary organic aerosol globally. In particular, biomass burning organic aerosol (BBOA) is strongly associated with atmospheric brown carbon (BrC) that absorbs near ultraviolet and visible light, resulting in significant impacts on regional visibility degradation and radiative forcing. The mixing state of BBOA can play a critical role in the prediction of aerosol optical properties. In this work, single particle measurements from a soot-particle aerosol mass spectrometer coupled with a light scattering module (LS-SP-AMS) were performed to examine the mixing state of BBOA, refractory black carbon (rBC) and potassium (K+, a tracer for biomass burning aerosol) in an air mass influenced by aged biomass burning. Cluster analysis of single particle measurements identified five BBOA-related particle types. rBC accounted for 3-14 w.t. % of these particle types on average. Only one particle type exhibited a strong ion signal for K+, with mass spectra characterized by low molecular weight organic species. The remaining four particle types were classified based on the apparent molecular weight of the BBOA constituents. Two particle types were associated with low potassium content and significant amounts of high molecular weight (HMW) organic compounds. Our observations indicate non-uniform mixing of particles within a biomass burning plume in terms of molecular weight and illustrate that HMW BBOA can be a key contributor to low-volatility BrC observed in BBOA particles.

  1. 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

  2. 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.

  3. 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.

  4. 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

    2014-12-03

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

  5. Global view of the functional molecular organization of the avian cerebrum: mirror images and functional columns.

    PubMed

    Jarvis, Erich D; Yu, Jing; Rivas, Miriam V; Horita, Haruhito; Feenders, Gesa; Whitney, Osceola; Jarvis, Syrus C; Jarvis, Electra R; Kubikova, Lubica; Puck, Ana E P; Siang-Bakshi, Connie; Martin, Suzanne; McElroy, Michael; Hara, Erina; Howard, Jason; Pfenning, Andreas; Mouritsen, Henrik; Chen, Chun-Chun; Wada, Kazuhiro

    2013-11-01

    Based on quantitative cluster analyses of 52 constitutively expressed or behaviorally regulated genes in 23 brain regions, we present a global view of telencephalic organization of birds. The patterns of constitutively expressed genes revealed a partial mirror image organization of three major cell populations that wrap above, around, and below the ventricle and adjacent lamina through the mesopallium. The patterns of behaviorally regulated genes revealed functional columns of activation across boundaries of these cell populations, reminiscent of columns through layers of the mammalian cortex. The avian functionally regulated columns were of two types: those above the ventricle and associated mesopallial lamina, formed by our revised dorsal mesopallium, hyperpallium, and intercalated hyperpallium; and those below the ventricle, formed by our revised ventral mesopallium, nidopallium, and intercalated nidopallium. Based on these findings and known connectivity, we propose that the avian pallium has four major cell populations similar to those in mammalian cortex and some parts of the amygdala: 1) a primary sensory input population (intercalated pallium); 2) a secondary intrapallial population (nidopallium/hyperpallium); 3) a tertiary intrapallial population (mesopallium); and 4) a quaternary output population (the arcopallium). Each population contributes portions to columns that control different sensory or motor systems. We suggest that this organization of cell groups forms by expansion of contiguous developmental cell domains that wrap around the lateral ventricle and its extension through the middle of the mesopallium. We believe that the position of the lateral ventricle and its associated mesopallium lamina has resulted in a conceptual barrier to recognizing related cell groups across its border, thereby confounding our understanding of homologies with mammals.

  6. Molecular epidemiology of Aleutian mink disease virus (AMDV) in Estonia, and a global phylogeny of AMDV.

    PubMed

    Leimann, Aivi; Knuuttila, Anna; Maran, Tiit; Vapalahti, Olli; Saarma, Urmas

    2015-03-02

    Aleutian mink disease virus (AMDV) causes a severe disease called Aleutian disease (AD). AMDV infects primarily mustelids, but also other mammal species. Recent evidence suggests that AMDV may also affect humans. To examine AMDV in different wild animals and in farmed mink in Estonia, we collected 203 blood samples from eight mammal species in 2007-2010, of which 152 were from species living in the wild (American mink, European mink, pine marten, polecat, raccoon dog, badger, otter, and stone marten) and 51 were from farmed mink. AMDV was tested by PCR amplification of NS1 and VP2 gene fragments, and was only detected in 4 free-ranging (14.8%) and 11 farmed (21.6%) American mink. No other species was positive for AMDV. In addition, the VP2 gene fragment was sequenced for 14 farmed mink isolates from Finland for which NS1 sequences were already publicly available. None of the four Estonian AMDV isolates found in free-ranging mink had identical sequences with farmed mink. In fact, isolates from free-ranging and farmed mink belonged to different clades, suggesting that the analyzed virus isolates circulating in nature are not from escapees of current farms. Two global phylogenies were built: one based on NS1 (336 bp, 151 taxa from nine countries); the other based on a combined NS1-VP2 dataset (871 bp, 40 taxa from six countries). AMDV genotypes did not cluster according to their geographic origin, suggesting that transport of farm mink from multiple source farms has been intense. Nevertheless, one subclade in both phylogenies was comprised solely of isolates from farmed mink, while several subclades comprised isolates only from free-ranging mink, indicating that some isolates may circulate more in the wild and others among farm animals.

  7. Dependence of the star formation efficiency on global parameters of molecular clouds

    NASA Astrophysics Data System (ADS)

    Rosas-Guevara, Yetli; Vázquez-Semadeni, Enrique; Gómez, Gilberto C.; Jappsen, A.-Katharina

    2010-08-01

    We investigate the response of the star formation efficiency (SFE) to the main parameters of simulations of molecular cloud formation and evolution (growth and star formation) by the collision of warm diffuse medium [warm neutral medium (WNM)] cylindrical streams, and compare our results with theoretical predictions for this dependence. The parameters we vary are the Mach number of the inflow velocity of the streams, , the rms Mach number, , of the initial background turbulence in the WNM and the total mass contained in the colliding gas streams, Minf, which is eventually deposited in the forming clouds. Because the SFE is a function of time, we define two estimators for it, the `absolute' SFE, measured at t = 25Myr into the simulation's evolution (SFEabs,25), and the `relative' SFE, measured 5Myr after the onset of star formation in each simulation (SFErel,5). The latter is close to the `SFE per free-fall time' for gas at n = 100cm-3. Our simulations suggest that the dominant parameter controlling the SFE is Minf. The SFE in general decreases as this parameter is decreased, presumably because, with the other parameters being equal, smaller fragments are more weakly gravitationally bound. In terms of the initial virial parameter (α ≡ 2Ekin/|Egrav|) of the clouds, our results are qualitatively consistent with the theoretical prediction by Krumholz & McKee that the SFE decreases with increasing α. However, quantitatively, their prediction lies beyond the 1σ error of our observed trend. This may be due to the fact that the simulated clouds develop significant gravitational contraction motions, which overwhelm the initial turbulent motions, contrary to Krumholz & McKee's assumption of stationary turbulent support. We also observe that the SFE decreases (moderately) with increasing , although the SFR increases. The decrease of the SFE with is thus a consequence of the cloud mass accretion rate from the WNM increasing more steeply with this parameter than the SFR

  8. Identification and Characterization of Well-Preserved Impact Ejecta Deposits Using THEMIS Global Infrared Mosaics

    NASA Astrophysics Data System (ADS)

    Hill, J. R.; Christensen, P. R.

    2014-12-01

    The Thermal Emission Imaging System (THEMIS) onboard the 2001 Mars Odyssey spacecraft has been acquiring infrared observations of the Martian surface for nearly thirteen years. Daytime infrared images from the first twelve years of the mission have previously been used to generate a complete global mosaic, while nighttime infrared images have been used to generate a near-global mosaic between 60°N-60°S. A combined product has been generated by overlaying the daytime global mosaic with a colorized version of the nighttime global mosaic, resulting in a near-global map that can be used to more easily identify surface features with unique thermal characteristics.Well-preserved ejecta deposits associated with fresh impact craters are readily identifiable in the combined map by their characteristic nighttime temperature pattern, which is controlled by variations in the thermal inertia of the ejecta material. The pattern consists of relatively high thermal inertia material in and around the crater, an inner ejecta ring composed of intermediate thermal inertia material and an outer ejecta ring composed of low thermal inertia material.A near-global survey (60°N-60°S) of these well-preserved ejecta deposits has shown that the vast majority occur in a small region covering northern Terra Sirenum and eastern Daedalia Planum, with a smaller concentration present in Syria Planum. A comparison of THEMIS and Viking images has verified that the larger craters and ejecta deposits were present at the time of the Viking mission and are not the result of more recent impacts. The survey also identified similarly fresh impact craters across the planet that are lacking an outer ring of low thermal inertia ejecta material, possibly due to erosion of the original ejecta deposits. This suggests that local conditions in Terra Sirenum, Daedalia Planum and Syria Planum are favorable for the long-term preservation of the fine-grained component of fresh impact ejecta deposits.

  9. 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

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

    PubMed Central

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

    2011-01-01

    A cross sectional study was conducted on 906 apparently healthy camels slaughtered at Akaki and Metehara abattoirs to investigate the pathology of camel tuberculosis (TB) and characterize its causative agents using postmortem examination, mycobacteriological culturing, and multiplex polymerase chain reaction (PCR), region of difference-4 (RD4)-based PCR and spoligotyping. The prevalence of camel TB was 10.04% (91/906) on the basis of pathology and it was significantly higher in females (χ2 = 4.789; P = 0.029). The tropism of TB lesions was significantly different among the lymph nodes (χ2 = 22.697; P = 0.002) and lung lobes (χ2 = 17.901; P = 0.006). Mycobacterial growth was observed in 34% (31/91) of camels with grossly suspicious TB lesions. Upon further molecular characterization using multiplex PCR, 68% (21/31) of the colonies showed a positive signal for the genus Mycobacterium, of which two were confirmed Mycobacterium bovis (M. bovis) by RD4 deletion typing. Further characterization of the two M. bovis at strains level revealed that one of the strains was SB0133 while the other strain was new and had not been reported to the M. bovis database prior to this study. Hence, it has now been reported to the database, and designated as SB1953. In conclusion, the results of the present study have shown that the majority of camel TB lesions are caused by mycobacteria other than Mycobacterium tuberculosis complex. And hence further identification and characterization of these species would be useful towards the efforts made to control TB in camels. PMID:21283668

  11. 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

  12. Molecular clocks and the human condition: approaching their characterization in human physiology and disease.

    PubMed

    Fitzgerald, G A; Yang, G; Paschos, G K; Liang, X; Skarke, C

    2015-09-01

    Molecular clockworks knit together diverse biological networks and compelling evidence from model systems infers their importance in metabolism, immunological and cardiovascular function. Despite this and the diurnal variation in many aspects of human physiology and the phenotypic expression of disease, our understanding of the role and importance of clock function and dysfunction in humans is modest. There are tantalizing hints of connection across the translational divide and some correlative evidence of gene variation and human disease but most of what we know derives from forced desynchrony protocols in controlled environments. We now have the ability to monitor quantitatively ex vivo or in vivo the genome, metabolome, proteome and microbiome of humans in the wild. Combining this capability, with the power of mobile telephony and the evolution of remote sensing, affords a new opportunity for deep phenotyping, including the characterization of diurnal behaviour and the assessment of the impact of the clock on approved drug function.

  13. 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.

  14. Characterization of some yeasts isolated from foods by traditional and molecular tests.

    PubMed

    Senses-Ergul, Sule; Agoston, Réka; Belák, Agnes; Deák, Tibor

    2006-04-15

    In this study, 22 yeast strains isolated from foods were characterized by traditional and molecular techniques. With the help of traditional identification tests, yeast strains were grouped in 12 species belonging to 11 genera as follows: Candida parapsilosis, Rhodotorula mucilaginosa, Debaryomyces hansenii, Cryptococcus humicolus, Cryptococcus albidus, Aureobasidium spp., Hanseniaspora valbyensis, Metschnikowia pulcherrima, Lachancea thermotolerans, Pichia anomala, Geotrichum candidum and Yarrowia lipolytica. The patterns obtained by the digestion of ITS-18S rRNA gene with MspI and HaeIII restriction endonucleases were similar among strains belonging to the same species. With the help of randomly amplified polymorphic DNA (RAPD) analysis performed within the same species, discrimination of M. pulcherrima strains could be achieved.

  15. Synthesis and Characterization of Molecular Imprinting Polymer Microspheres of Piperine: Extraction of Piperine from Spiked Urine.

    PubMed

    Roland, Rachel Marcella; Bhawani, Showkat Ahmad

    2016-01-01

    Molecularly imprinted polymer (MIP) microspheres for Piperine were synthesized by precipitation polymerization with a noncovalent approach. In this research Piperine was used as a template, acrylic acid as a functional monomer, ethylene glycol dimethacrylate as a cross-linker, and 2,2'-azobisisobutyronitrile (AIBN) as an initiator and acetonitrile as a solvent. The imprinted and nonimprinted polymer particles were characterized by using Fourier transform infrared spectroscopy (FT-IR) and Scanning Electron Microscopy (SEM). The synthesized polymer particles were further evaluated for their rebinding efficiency by batch binding assay. The highly selected imprinted polymer for Piperine was MIP 3 with a composition (molar ratio) of 0.5 : 3 : 8, template : monomer : cross-linker, respectively. The MIP 3 exhibits highest binding capacity (84.94%) as compared to other imprinted and nonimprinted polymers. The extraction efficiency of highly selected imprinted polymer of Piperine from spiked urine was above 80%.

  16. Biochemical and Molecular Characterization of Obesumbacterium proteus, a Common Contaminant of Brewing Yeasts

    PubMed Central

    Prest, Andrew G.; Hammond, John R. M.; Stewart, Gordon S. A. B.

    1994-01-01

    We have evaluated the effectiveness of API 20E, Biolog testing, plasmid profiling, ribotyping, and enteric repetitive intergenic consensus (ERIC)-PCR to characterize, classify, and differentiate nine bacterial isolates of the common brewery contaminant Obesumbacterium proteus. Of the five typing techniques, Biolog testing, plasmid profiling, and ERIC-PCR provided the most differentiation, and API 20E testing and ribotyping were relatively indiscriminate. The molecular biology approach of ERIC-PCR offered the ideal combination of speed, simplicity, and discrimination in this study. Overall, the results are supportive of the view that O. proteus can be subdivided into two biogroups, biogroup 1, which has considerable biochemical and genetic homology to Hafnia alvei, and biogroup 2, which is relatively heterogeneous. Images PMID:16349260

  17. Molecular and functional characterization of cry1Ac transgenic pea lines.

    PubMed

    Teressa Negawo, Alemayehu; Baranek, Linda; Jacobsen, Hans-Jörg; Hassan, Fathi

    2016-10-01

    Transgenic pea lines transformed with the cry1Ac gene were characterized at molecular (PCR, RT-PCR, qRT-PCR and immunostrip assay) and functional levels (leaf paint and insect feeding bioassays). The results showed the presence, expression, inheritance and functionality of the introduced transgene at different progeny levels. Variation in the expression of the cry1Ac gene was observed among the different transgenic lines. In the insect bioassay studies using the larvae of Heliothis virescens, both larval survival and plant damage were highly affected on the different transgenic plants. Up to 100 % larval mortality was observed on the transgenic plants compared to 17.42 % on control plants. Most of the challenged transgenic plants showed very negligible to substantially reduced feeding damage indicating the insect resistance of the developed transgenic lines. Further analysis under field condition will be required to select promising lines for future uses.

  18. 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

  19. Preparation and characterization of novel molecularly imprinted polymers based on thiourea receptors for nitrocompounds recognition.

    PubMed

    Athikomrattanakul, Umporn; Katterle, Martin; Gajovic-Eichelmann, Nenad; Scheller, Frieder W

    2011-04-15

    Molecularly imprinted polymers (MIPs) for the recognition of nitro derivatives are prepared from three different (thio)urea-bearing functional monomers. The binding capability of the polymers is characterized by a batch binding experiment. The imprinting factors and affinity constants (K) of the imprinted polymers exhibit the same tendency as the binding constants (K(a)) of the functional monomers to the target substance in solution. Not only nitrofurantoin is efficiently bound by these MIPs but also a broad spectrum of other nitro compounds is bound with at the intermediate level, addressing that these (thio)urea-based monomers can be utilized to prepare a family of MIPs for various nitro compounds, which can be applied as recognition elements in separation and analytical application.

  20. 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.

  1. Synthesis and Characterization of Molecular Imprinting Polymer Microspheres of Piperine: Extraction of Piperine from Spiked Urine

    PubMed Central

    Roland, Rachel Marcella

    2016-01-01

    Molecularly imprinted polymer (MIP) microspheres for Piperine were synthesized by precipitation polymerization with a noncovalent approach. In this research Piperine was used as a template, acrylic acid as a functional monomer, ethylene glycol dimethacrylate as a cross-linker, and 2,2′-azobisisobutyronitrile (AIBN) as an initiator and acetonitrile as a solvent. The imprinted and nonimprinted polymer particles were characterized by using Fourier transform infrared spectroscopy (FT-IR) and Scanning Electron Microscopy (SEM). The synthesized polymer particles were further evaluated for their rebinding efficiency by batch binding assay. The highly selected imprinted polymer for Piperine was MIP 3 with a composition (molar ratio) of 0.5 : 3 : 8, template : monomer : cross-linker, respectively. The MIP 3 exhibits highest binding capacity (84.94%) as compared to other imprinted and nonimprinted polymers. The extraction efficiency of highly selected imprinted polymer of Piperine from spiked urine was above 80%. PMID:28018704

  2. Isolation and molecular characterization of Acanthamoeba and Balamuthia mandrillaris from combination shower units in Costa Rica.

    PubMed

    Retana-Moreira, Lissette; Abrahams-Sandí, Elizabeth; Cabello-Vílchez, Alfonso Martín; Reyes-Batlle, María; Valladares, Basilio; Martínez-Carretero, Enrique; Piñero, José E; Lorenzo-Morales, Jacob

    2014-11-01

    Free living amoebae (FLA) are ubiquitous protozoa, which may behave as parasites under certain conditions. Four genera are recognized as causal agents of infections in humans and animals: Naegleria, Sappinia, Acanthamoeba and Balamuthia. This work determines the presence of FLA in combination shower units and employs molecular biology for the characterization of isolates. The morphological analysis and partial sequencing of the 18S rDNA gene revealed the presence of Acanthamoeba genotype T4 in 30% of the units sampled. In addition to Acanthamoeba cysts, trophozoites with morphological characteristics similar to Balamuthia were identified. PCR assay using the mitochondrial 16S rRNA gene as a target confirmed the identification of the amoeba as Balamuthia mandrillaris. Up to date, this is the first report of the isolation of B. mandrillaris in Central America and the fifth report worldwide.

  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. 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.

  5. 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.

  6. Molecular characterization of a Korean bovine parainfluenza virus type 3 isolate.

    PubMed

    Oem, Jae-Ku; Lee, Eun-Yong; Lee, Kyoung-Ki; Kim, Seong-Hee; Lee, Myoung-Heon; Hyun, Bang-Hun

    2013-02-22

    Bovine parainfluenza virus type 3 (BPIV-3) was isolated from Korean native cattle that presented clinical signs of mild pneumonia. The complete genome of a representative isolate (12Q061) was sequenced. The newly identified strain, which was found to be distinct from the previously reported genotypes A (BPIV-3a) and B (BPIV-3b) and closely related to the Chinese strain SD0835, was tentatively classified as genotype C (BPIV-3c). Our results suggest a relationship between BPIV-3 genetic variation and the geographic location of its isolation. Identification of these new BPIV-3 genotypes may facilitate the development of improved diagnostic methods and vaccines. This is to our knowledge the first report of the identification and molecular characterization of BPIV-3 in Korea.

  7. 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.

  8. 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.

  9. 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

    2011-10-07

    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.

  10. 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.

  11. 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.

  12. Primary Intraosseous Smooth Muscle Tumor of Uncertain Malignant Potential: Original Report and Molecular Characterization

    PubMed Central

    Kropp, Lauren; Siegal, Gene P.; Frampton, Garrett M.; Rodriguez, Michael G.; McKee, Svetlana; Conry, Robert M.

    2016-01-01

    We report the first case of primary intraosseous smooth muscle tumor of uncertain malignant potential (STUMP) which is analogous to borderline malignant uterine smooth muscle tumors so designated. The tumor presented in the femur of an otherwise healthy 30-year-old woman. Over a 3-year period, the patient underwent 11 biopsies or resections and 2 cytologic procedures. Multiple pathologists reviewed the histologic material including musculoskeletal pathologists but could not reach a definitive diagnosis. However, metastases eventually developed and were rapidly progressive and responsive to gemcitabine and docetaxel. Molecular characterization and ultrastructural analysis was consistent with smooth muscle origin, and amplification of unmutated chromosome 12p and 12q segments appears to be the major genomic driver of this tumor. Primary intraosseous STUMP is thought to be genetically related to leiomyosarcoma of bone, but likely representing an earlier stage of carcinogenesis. Wide excision and aggressive follow-up is warranted for this potentially life-threatening neoplasm. PMID:27994831

  13. Molecular characterization of vanadyl and nickel non-porphyrin compounds in heavy crude petroleums and residua

    SciTech Connect

    Reynolds, J.G.; Biggs, W.R.; Fetzer, J.C.; Gallegos, E.J.; Fish, R.H.; Komlenic, J.J.; Wines, B.K.

    1984-01-01

    The molecular characterization of vanadium and nickel compounds in heavy crude petroleums has been the subject of current research. Arabian Heavy, Maya, Boscan, Cerro Negro, Prudhoe Bay, Wilmington Beta, Kern River, and Morichal crude petroleums have been examined. Fractions from D 2007 separations, porphyrin extractions, and solvent selective extraction with reversed phase column separations of these petroleums have been studied thoroughly by EPR. Important structural aspects are emerging from the presented data: (1) There are non-porphyrin metal complexes in the crude petroleums. (2) They appear to be smaller molecules with MW < 400 which are liberated when the tertiary structure of the large asphaltics is denatured. (3) The first coordination spheres of this class of compounds are possibly 4N, N O 2S, and 4S. 10 references, 3 figures, 1 table.

  14. Imported lassa fever in Germany: molecular characterization of a new lassa virus strain.</